7UND

Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	RNA polymerase subunits	8103068	3001823	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Plus3-like	8033751	3000248	SCOP2B (2022-06-29)
Y [auth Z]	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8039849	3000334	SCOP2B (2022-06-29)
DA [auth e]	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
Z [auth a]	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
EA [auth f]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
AA [auth b]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
FA [auth g]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
BA [auth c]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
CA [auth d]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
GA [auth h]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RPB6/omega subunit-like	8106082	3000189	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	RNA_pol_N	e7undJ1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
K	RNA_pol_L_2	e7undK1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
L	DNA_RNApol_7kD	e7undL1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
M	S1_1	e7undM7	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
M	HTH_44	e7undM1	A: alpha arrays	X: HTH	H: Tex N-terminal domain (From Topology)	T: Tex N-terminal domain	F: HTH_44	ECOD (1.6)
M	DLD	e7undM8	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DLD	ECOD (1.6)
M	HHH_7	e7undM6	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_7	ECOD (1.6)
M	F_UNCLASSIFIED	e7undM3	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Tex bundle domain-like (From Topology)	T: Tex bundle domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
M	Tex_N_3rd	e7undM5	A: alpha complex topology	X: Tex N-terminal region-like (From Topology)	H: Tex N-terminal region-like (From Topology)	T: Tex N-terminal region-like	F: Tex_N_3rd	ECOD (1.6)
M	SH2_2_C	e7undM2	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2_2_C	ECOD (1.6)
M	SH2_2_N	e7undM9	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2_2_N	ECOD (1.6)
M	Tex_YqgF	e7undM4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Tex_YqgF	ECOD (1.6)
O	TFIIS_M	e7undO2	A: alpha arrays	X: RuvA-C	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein (From Topology)	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: TFIIS_M	ECOD (1.6)
O	TFIIS_C	e7undO1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TFIIS_C	ECOD (1.6)
B	RNA_pol_Rpb2_6_3rd_2	e7undB4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
B	RNA_pol_Rpb2_6_2nd_1	e7undB6	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
B	RNA_pol_Rpb2_3	e7undB1	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
B	RNA_pol_Rpb2_1	e7undB3	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
B	RNA_pol_Rpb2_45_1	e7undB2	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
B	RNA_pol_Rpb2_7	e7undB5	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
B	RNA_pol_Rpb2_4	e7undB7	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
V [auth W]	ANAPC4_WD40_7	e7undW1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_7	ECOD (1.6)
X [auth Y]	Spt4	e7undY1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)
DA [auth e]	Histone	e7unde1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
Z [auth a]	Histone	e7unda1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
EA [auth f]	Histone_1	e7undf1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
AA [auth b]	Histone_1	e7undb1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
FA [auth g]	Histone_1	e7undg1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
BA [auth c]	Histone_1	e7undc1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
CA [auth d]	Histone	e7undd1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
GA [auth h]	Histone	e7undh1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
C	RNA_pol_L_1	e7undC1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_1	ECOD (1.6)
C	RNA_pol_A_bac_1	e7undC2	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
D	RNA_pol_Rpb4	e7undD1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
E	RNA_pol_Rpb5_C	e7undE1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
E	RNA_pol_Rpb5_N	e7undE2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Eukaryotic RPB5 N-terminal domain (From Topology)	T: Eukaryotic RPB5 N-terminal domain	F: RNA_pol_Rpb5_N	ECOD (1.6)
F	RNA_pol_Rpb6_1	e7undF1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
G	S1_1	e7undG1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
G	SHS2_Rpb7-N	e7undG2	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
H	RNA_pol_Rpb8	e7undH1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_Rpb8	ECOD (1.6)
I	RNA_POL_M_15KD	e7undI2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD	ECOD (1.6)
I	TFIIS_C	e7undI1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TFIIS_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
A	PF04990	RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)	RNA polymerase Rpb1, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].	Domain
A	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
A	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
A	PF04992	RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)	RNA polymerase Rpb1, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.	Domain
A	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
A	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
L	PF03604	DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)	DNA directed RNA polymerase, 7 kDa subunit	-	Domain
M	PF14639	Holliday-junction resolvase-like of SPT6 (YqgF)	Holliday-junction resolvase-like of SPT6	The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC [1] but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage [2]	Domain
M	PF17674	HHH domain (HHH_9)	HHH domain	-	Domain
M	PF14641	Helix-turn-helix DNA-binding domain of SPT6 (HTH_44)	Helix-turn-helix DNA-binding domain of SPT6	This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.	Domain
M	PF22706	Tex central region-like (Tex_central_region)	Tex central region-like	This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of ...	This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of a number of small helices that wrap around a long central helix.	Domain
M	PF14635	Helix-hairpin-helix motif (HHH_7)	Helix-hairpin-helix motif	-	Domain
O	PF01096	Transcription factor S-II (TFIIS) (TFIIS_C)	Transcription factor S-II (TFIIS)	-	Domain
O	PF07500	Transcription factor S-II (TFIIS), central domain (TFIIS_M)	Transcription factor S-II (TFIIS), central domain	Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is comp ...	Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and Pfam:PF01096 are required for transcription activity [1].	Domain
Q	PF13181	Tetratricopeptide repeat (TPR_8)	Tetratricopeptide repeat	-	Repeat
Q	PF13374	Tetratricopeptide repeat (TPR_10)	Tetratricopeptide repeat	-	Repeat
R	PF03126	Plus-3 domain (Plus-3)	Plus-3 domain	This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged ...	This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor [1].	Domain
B	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
B	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
B	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
B	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].	Domain
B	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
B	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
B	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
B	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
T [auth U]	PF04004	Leo1-like protein (Leo1)	Leo1-like protein	-	Family
U [auth V]	PF03985	Paf1 (Paf1)	Paf1	-	Family
V [auth W]	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
X [auth Y]	PF06093	Spt4/RpoE2 zinc finger (Spt4)	Spt4/RpoE2 zinc finger	This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via ...	This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles [1]. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in [3]. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.	Domain
Y [auth Z]	PF03439	Early transcription elongation factor of RNA pol II, NGN section (Spt5-NGN)	Early transcription elongation factor of RNA pol II, NGN section	-	Family
Y [auth Z]	PF00467	KOW motif (KOW)	KOW motif	-	Family
C	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
C	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
C	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
D	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family
E	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
E	PF03871	RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)	RNA polymerase Rpb5, N-terminal domain	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.	Domain
F	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
G	PF03876	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
G	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-directed RNA polymerase subunit	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding small molecule binding	-	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
J	RPB10	-	-	-
K	RPB11	-	-	-
L	RNA polymerase II subunit K	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase III complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex
M	Transcription elongation factor SPT6	protein binding binding histone binding RNA binding organic cyclic compound binding nucleic acid binding DNA binding protein-containing complex binding chromatin binding nucleosome binding	developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development RNA transport nitrogen compound transport developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport regulation of localization cellular localization regulation of cellular process nucleocytoplasmic transport regulation of mRNA export from nucleus cellular biosynthetic process nuclear transport mRNA export from nucleus establishment of localization in cell nuclear export ribonucleoprotein complex localization regulation of intracellular transport regulation of ribonucleoprotein complex localization regulation of biological process regulation of transport cellular metabolic process regulation of RNA export from nucleus regulation of nucleobase-containing compound transport biological regulation intracellular transport regulation of nucleocytoplasmic transport gene expression macromolecule biosynthetic process RNA export from nucleus biosynthetic process regulation of cellular localization cellular process metabolic process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA processing regulation of developmental process cellular developmental process regulation of cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation cell differentiation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process regulation of DNA recombination response to stimulus regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response cell activation involved in immune response regulation of primary metabolic process leukocyte mediated immunity regulation of immune system process somatic diversification of immune receptors regulation of nucleobase-containing compound metabolic process somatic recombination of immunoglobulin genes involved in immune response system development immune response regulation of adaptive immune response DNA recombination regulation of cellular metabolic process DNA metabolic process regulation of B cell mediated immunity immune effector process somatic diversification of immunoglobulins regulation of gene expression regulation of leukocyte mediated immunity regulation of response to stimulus B cell mediated immunity regulation of immune response regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response regulation of metabolic process regulation of DNA metabolic process isotype switching immune system development immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination lymphocyte activation leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immunoglobulin mediated immune response leukocyte activation involved in immune response regulation of B cell activation regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process production of molecular mediator of immune response regulation of isotype switching B cell activation cell activation regulation of macromolecule metabolic process adaptive immune response immunoglobulin mediated immune response regulation of cellular biosynthetic process regulation of lymphocyte mediated immunity regulation of immunoglobulin production immune system process somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation RNA splicing transcription elongation by RNA polymerase II cellular component organization DNA-templated transcription transcription by RNA polymerase II chromatin organization chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling DNA-templated transcription elongation regulation of RNA metabolic process regulation of mRNA processing regulation of mRNA metabolic process protein-DNA complex organization protein-containing complex organization nucleosome organization positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process regulation of RNA biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
N	Non-template DNA	-	-	-
O	Transcription elongation factor A protein 1	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process transcription elongation by RNA polymerase II DNA-templated transcription elongation regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle RNA polymerase II transcription regulator complex RNA polymerase II, holoenzyme protein-containing complex nuclear protein-containing complex transcription regulator complex transferase complex nucleoplasm catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex transcription factor TFIID complex DNA-directed RNA polymerase complex intracellular protein-containing complex
P	RNA	-	-	-
Q	RNA polymerase-associated protein CTR9 homolog	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding SH2 domain binding protein domain specific binding	cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication cellular process signal transduction cell surface receptor signaling pathway via JAK-STAT interleukin-6-mediated signaling pathway response to interleukin-6 cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication cellular process signal transduction cell surface receptor signaling pathway via JAK-STAT interleukin-6-mediated signaling pathway response to interleukin-6 cellular response to interleukin-6 response to cytokine cytokine-mediated signaling pathway response to peptide response to chemical cellular response to cytokine stimulus developmental process multicellular organismal process maintenance of cell number stem cell population maintenance regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis chordate embryonic development embryo development inner cell mass cell differentiation in utero embryonic development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure formation involved in morphogenesis blastocyst development transcription elongation by RNA polymerase II cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process Wnt signaling pathway biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process formation of primary germ layer embryonic morphogenesis tissue development gastrulation cell fate commitment involved in formation of primary germ layer endoderm development endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation developmental growth growth blastocyst growth hatching blastocyst hatching organism emergence from protective structure positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process trophectodermal cell differentiation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen euchromatin intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nuclear protein-containing complex transferase complex catalytic complex Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
R	RNA polymerase-associated protein RTF1 homolog	RNA binding binding organic cyclic compound binding nucleic acid binding DNA binding single-stranded DNA binding	developmental process multicellular organismal process maintenance of cell number stem cell population maintenance transcription elongation by RNA polymerase II cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process developmental process multicellular organismal process maintenance of cell number stem cell population maintenance transcription elongation by RNA polymerase II cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication signal transduction Wnt signaling pathway negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process formation of primary germ layer cellular developmental process embryonic morphogenesis embryo development tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure formation involved in morphogenesis anatomical structure development endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation developmental growth chordate embryonic development growth in utero embryonic development embryo development ending in birth or egg hatching blastocyst growth blastocyst development cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nuclear protein-containing complex transferase complex nucleoplasm catalytic complex Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
S [auth T]	Template DNA	-	-	-
B	DNA-directed RNA polymerase subunit beta	DNA binding binding organic cyclic compound binding nucleic acid binding ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity DNA binding binding organic cyclic compound binding nucleic acid binding ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding	-	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
T [auth U]	RNA polymerase-associated protein LEO1	phosphoprotein binding basal transcription machinery binding RNA polymerase binding binding RNA polymerase II C-terminal domain binding enzyme binding RNA polymerase II C-terminal domain phosphoserine binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding phosphoserine residue binding protein phosphorylated amino acid binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process developmental process multicellular organismal process maintenance of cell number stem cell population maintenance regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis transcription elongation by RNA polymerase II DNA-templated transcription DNA-templated transcription elongation transcription by RNA polymerase II cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction Wnt signaling pathway positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process formation of primary germ layer embryonic morphogenesis embryo development tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis endoderm development anatomical structure formation involved in morphogenesis endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation	intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center nuclear lumen RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nuclear protein-containing complex transferase complex nucleoplasm catalytic complex Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
U [auth V]	RNA polymerase II-associated factor 1 homolog	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding chromatin binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process developmental process multicellular organismal process maintenance of cell number stem cell population maintenance regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis regulation of cell cycle phase transition regulation of cell cycle process positive regulation of biological process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition positive regulation of cell cycle positive regulation of cell cycle G1/S phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process transcription elongation by RNA polymerase II DNA-templated transcription DNA-templated transcription elongation transcription by RNA polymerase II cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction Wnt signaling pathway biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process formation of primary germ layer embryonic morphogenesis embryo development tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis endoderm development anatomical structure formation involved in morphogenesis endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to nucleus	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center organelle intracellular non-membrane-bounded organelle membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nuclear protein-containing complex transferase complex nucleoplasm catalytic complex Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex cytoplasm
V [auth W]	WDR61	-	cellular component disassembly ribosome disassembly cellular biosynthetic process cellular metabolic process rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular component disassembly ribosome disassembly cellular biosynthetic process cellular metabolic process rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process protein metabolic process multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis transcription elongation by RNA polymerase II RNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction Wnt signaling pathway catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay negative regulation of cellular metabolic process macromolecule catabolic process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle organelle euchromatin intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle organelle euchromatin intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm catalytic complex intracellular membrane-bounded organelle Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen Ski complex
W [auth X]	Parafibromin	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding	cellular biosynthetic process positive regulation of biological process RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing cellular biosynthetic process positive regulation of biological process RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing regulation of mRNA processing regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process mRNA 3'-end processing biological regulation regulation of mRNA 3'-end processing positive regulation of mRNA metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process biosynthetic process positive regulation of mRNA processing metabolic process cellular process macromolecule metabolic process positive regulation of mRNA 3'-end processing regulation of mRNA metabolic process regulation of metabolic process protein destabilization regulation of protein stability regulation of biological quality regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to stimulus response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling developmental process multicellular organismal process maintenance of cell number stem cell population maintenance negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle process regulation of mitotic cell cycle phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis fibroblast proliferation regulation of fibroblast proliferation negative regulation of fibroblast proliferation positive regulation of cell cycle positive regulation of cell cycle G1/S phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle process transcription elongation by RNA polymerase II DNA-templated transcription DNA-templated transcription elongation transcription by RNA polymerase II positive regulation of macromolecule biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process formation of primary germ layer embryonic morphogenesis embryo development tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis endoderm development anatomical structure formation involved in morphogenesis endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle
X [auth Y]	Transcription elongation factor SPT4	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding protein heterodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding protein heterodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process transcription elongation by RNA polymerase II cellular component organization transcription by RNA polymerase II chromatin organization chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of DNA-templated transcription, elongation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of transcription elongation by RNA polymerase II regulation of transcription elongation by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
Y [auth Z]	Transcription elongation factor SPT5	chromatin binding binding protein heterodimerization activity protein binding protein dimerization activity RNA binding organic cyclic compound binding nucleic acid binding mRNA binding enzyme binding	regulation of cellular process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation regulation of cellular process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of DNA-templated transcription, elongation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process transcription elongation by RNA polymerase II transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II catabolic process macroautophagy autophagy regulation of autophagy cellular catabolic process positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process positive regulation of cellular catabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
DA [auth e], Z [auth a]	Histone H3.2	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
AA [auth b], EA [auth f]	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
BA [auth c], FA [auth g]	Histone H2A	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
CA [auth d], GA [auth h]	Histone H2B 1.1	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	DNA-directed RNA polymerase II subunit RPB3	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding protein dimerization activity	-	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
D	RPOL4c domain-containing protein	protein binding binding translation initiation factor binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process transcription initiation at RNA polymerase II promoter	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen RNA polymerase II, holoenzyme protein-containing complex nuclear protein-containing complex transferase complex RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
E	DNA-directed RNA polymerase II subunit E	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase I activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase I activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA polymerase II activity RNA polymerase III activity	-	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen fibrillar center RNA polymerase III complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex
G	DNA-directed RNA polymerase II subunit RPB7	protein binding binding translation initiation factor binding RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding DNA binding single-stranded DNA binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of translational initiation regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process translation regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process positive regulation of translational initiation regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process positive regulation of nuclear-transcribed mRNA poly(A) tail shortening regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process nuclear-transcribed mRNA poly(A) tail shortening negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process regulation of nuclear-transcribed mRNA poly(A) tail shortening negative regulation of macromolecule metabolic process nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular non-membrane-bounded organelle cytoplasm supramolecular complex P-body non-membrane-bounded organelle
H	RPB8	-	-	-
I	RPB9	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A	IPR007073	RNA polymerase Rpb1, domain 7	Domain
A	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
A	IPR007075	RNA polymerase Rpb1, domain 6	Domain
A	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
A	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
A	IPR000722	RNA polymerase, alpha subunit	Domain
A	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A	IPR006592	RNA polymerase, N-terminal	Domain
A	IPR007080	RNA polymerase Rpb1, domain 1	Domain
L	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
L	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
L	IPR039747	DNA-directed RNA polymerases I, II, and III subunit RPABC4	Family
M	IPR042066	Spt6, Death-like domain	Homologous Superfamily
M	IPR028231	Transcription elongation factor Spt6, YqgF domain	Domain
M	IPR037027	YqgF/RNase H-like domain superfamily	Homologous Superfamily
M	IPR036860	SH2 domain superfamily	Homologous Superfamily
M	IPR000980	SH2 domain	Domain
M	IPR006641	YqgF/RNase H-like domain	Domain
M	IPR041692	HHH domain 9	Domain
M	IPR010994	RuvA domain 2-like	Homologous Superfamily
M	IPR023319	Tex-like protein, HTH domain superfamily	Homologous Superfamily
M	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
M	IPR017072	Transcription elongation factor Spt6	Family
M	IPR035420	Spt6, SH2 domain	Domain
M	IPR032706	Transcription elongation factor Spt6, helix-hairpin-helix motif	Domain
M	IPR003029	S1 domain	Domain
M	IPR023323	Tex-like domain superfamily	Homologous Superfamily
M	IPR028088	Helix-turn-helix DNA-binding domain of Spt6	Domain
M	IPR035019	Spt6, SH2 domain, N terminus	Domain
M	IPR035018	Spt6, SH2 domain, C terminus	Domain
M	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
M	IPR028083	Spt6 acidic, N-terminal domain	Domain
O	IPR006289	Transcription elongation factor, TFIIS	Family
O	IPR001222	Zinc finger, TFIIS-type	Domain
O	IPR003618	Transcription elongation factor S-II, central domain	Domain
O	IPR035441	TFIIS/LEDGF domain superfamily	Homologous Superfamily
O	IPR036575	Transcription elongation factor S-II, central domain superfamily	Homologous Superfamily
O	IPR035100	Transcription elongation factor, IIS-type	Family
O	IPR017923	Transcription factor IIS, N-terminal	Domain
O	IPR003617	Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type	Domain
Q	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
Q	IPR031101	RNA polymerase-associated protein Ctr9	Family
Q	IPR019734	Tetratricopeptide repeat	Repeat
R	IPR036128	Plus3-like superfamily	Homologous Superfamily
R	IPR004343	Plus-3 domain	Domain
B	IPR007642	RNA polymerase Rpb2, domain 2	Domain
B	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
B	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
B	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
B	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B	IPR007646	RNA polymerase Rpb2, domain 4	Domain
B	IPR007647	RNA polymerase Rpb2, domain 5	Domain
B	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
B	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
B	IPR007641	RNA polymerase Rpb2, domain 7	Domain
T [auth U]	IPR007149	Leo1-like protein	Family
U [auth V]	IPR007133	RNA polymerase II associated factor Paf1	Family
V [auth W]	IPR019775	WD40 repeat, conserved site	Conserved Site
V [auth W]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
V [auth W]	IPR051510	Superkiller complex protein 8	Family
V [auth W]	IPR001680	WD40 repeat	Repeat
V [auth W]	IPR020472	G-protein beta WD-40 repeat	Repeat
V [auth W]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
W [auth X]	IPR038103	Cell division control protein 73, C-terminal domain superfamily	Homologous Superfamily
W [auth X]	IPR031336	Cell division control protein 73, C-terminal	Domain
W [auth X]	IPR007852	Cdc73/Parafibromin	Family
W [auth X]	IPR032041	Paf1 complex subunit Cdc73, N-terminal domain	Domain
X [auth Y]	IPR038510	Spt4 superfamily	Homologous Superfamily
X [auth Y]	IPR009287	Transcription initiation Spt4	Family
X [auth Y]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
X [auth Y]	IPR022800	Spt4/RpoE2 zinc finger	Domain
Y [auth Z]	IPR041980	Spt5, KOW domain repeat 6	Domain
Y [auth Z]	IPR041976	Spt5, KOW domain repeat 3	Domain
Y [auth Z]	IPR039385	NGN domain, eukaryotic	Domain
Y [auth Z]	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
Y [auth Z]	IPR022581	Spt5 transcription elongation factor, N-terminal	Domain
Y [auth Z]	IPR024945	Spt5 C-terminal domain	Domain
Y [auth Z]	IPR006645	NusG-like, N-terminal	Domain
Y [auth Z]	IPR041975	Spt5, KOW domain repeat 2	Domain
Y [auth Z]	IPR039659	Transcription elongation factor SPT5	Family
Y [auth Z]	IPR036735	NusG, N-terminal domain superfamily	Homologous Superfamily
Y [auth Z]	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
Y [auth Z]	IPR041973	Spt5, KOW domain repeat 1	Domain
Y [auth Z]	IPR005100	NGN domain	Domain
Y [auth Z]	IPR041977	Spt5, KOW domain repeat 4	Domain
Y [auth Z]	IPR017071	Transcription elongation factor Spt5, eukaryote	Family
Y [auth Z]	IPR005824	KOW	Domain
Y [auth Z]	IPR041978	Spt5, KOW domain repeat 5	Domain
DA [auth e], Z [auth a]	IPR009072	Histone-fold	Homologous Superfamily
DA [auth e], Z [auth a]	IPR007125	Histone H2A/H2B/H3	Domain
DA [auth e], Z [auth a]	IPR000164	Histone H3/CENP-A	Family
AA [auth b], EA [auth f]	IPR009072	Histone-fold	Homologous Superfamily
AA [auth b], EA [auth f]	IPR001951	Histone H4	Family
AA [auth b], EA [auth f]	IPR035425	CENP-T/Histone H4, histone fold	Domain
AA [auth b], EA [auth f]	IPR019809	Histone H4, conserved site	Conserved Site
AA [auth b], EA [auth f]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
BA [auth c], FA [auth g]	IPR009072	Histone-fold	Homologous Superfamily
BA [auth c], FA [auth g]	IPR007125	Histone H2A/H2B/H3	Domain
BA [auth c], FA [auth g]	IPR002119	Histone H2A	Family
BA [auth c], FA [auth g]	IPR032454	Histone H2A, C-terminal domain	Domain
BA [auth c], FA [auth g]	IPR032458	Histone H2A conserved site	Conserved Site
CA [auth d], GA [auth h]	IPR009072	Histone-fold	Homologous Superfamily
CA [auth d], GA [auth h]	IPR007125	Histone H2A/H2B/H3	Domain
CA [auth d], GA [auth h]	IPR000558	Histone H2B	Family
C	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
C	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
C	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
C	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
C	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
D	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
D	IPR010997	HRDC-like superfamily	Homologous Superfamily
D	IPR006590	RNA polymerase Rpb4/RPC9, core	Domain
D	IPR038324	Rpb4/RPC9 superfamily	Homologous Superfamily
D	IPR045222	DNA-directed RNA polymerase II subunit Rpb4-like	Family
E	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
E	IPR036710	RNA polymerase Rpb5, N-terminal domain superfamily	Homologous Superfamily
E	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
E	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
E	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
E	IPR005571	RNA polymerase, Rpb5, N-terminal	Domain
F	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
F	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F	IPR028363	DNA-directed RNA polymerase, subunit RPB6	Family
F	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
G	IPR003029	S1 domain	Domain
G	IPR045113	RNA polymerase subunit Rpb7-like	Family
G	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
G	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
G	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
M	Pharos: Q7KZ85	astrocytic tumor large cell medulloblastoma atypical teratoid rhabdoid tumor osteosarcoma glioblastoma
O	Pharos: P23193	lymphoplasmacytic lymphoma ovarian cancer plasma cell myeloma
Q	Pharos: Q6PD62	heart disease plasma cell myeloma lymphoplasmacytic lymphoma ovarian cancer
R	Pharos: Q92541	allergic rhinitis ovarian cancer metabolic syndrome X osteosarcoma
T [auth U]	Pharos: Q8WVC0	lung carcinoma pancreatic intraductal papillary-mucinous carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pancreatic ductal adenocarcinoma
U [auth V]	Pharos: Q8N7H5	cancer osteosarcoma ovarian cancer
V [auth W]	Pharos: Q9GZS3	acute myeloid leukemia ovarian cancer glioblastoma plasma cell myeloma lymphoplasmacytic lymphoma
W [auth X]	Pharos: Q6P1J9	parathyroid gland carcinoma hyperparathyroidism 1 hyperparathyroidism 2 with jaw tumors parathyroid gland adenoma Parathyroid Gland Adenocarcinoma atypical teratoid rhabdoid tumor familial isolated hyperparathyroidism head and neck carcinoma lung cancer ossifying fibroma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer familial parathyroid adenoma head and neck neoplasm malignant ependymoma parathyroid gland carcinoma hyperparathyroidism 1 hyperparathyroidism 2 with jaw tumors parathyroid gland adenoma Parathyroid Gland Adenocarcinoma atypical teratoid rhabdoid tumor familial isolated hyperparathyroidism head and neck carcinoma lung cancer ossifying fibroma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer familial parathyroid adenoma head and neck neoplasm malignant ependymoma osteosarcoma cancer head and neck cancer hyperparathyroidism myopathy pancreatic intraductal papillary-mucinous neoplasm
X [auth Y]	Pharos: P63272	Alzheimer disease lung cancer pancreatic ductal adenocarcinoma prostate carcinoma breast cancer osteosarcoma pituitary cancer psoriasis hypertensive disorder ovarian cancer plasma cell myeloma
Y [auth Z]	Pharos: O00267	diabetes mellitus ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047
Y [auth Z]	TPO	Parent Component: THR RESID: AA0037 , AA0038 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047 , O-phospho-L-threonine MOD:00047