Annotations: 8XMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	RNA polymerase subunit RPB10	8106328	3001213	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RNA polymerase subunits	8106336	3001823	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RPB6/omega subunit-like	8106334	3000189	SCOP2B (2022-06-29)

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	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
J	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit	-	Domain
K	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	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. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
L	PF03604	DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)	DNA directed RNA polymerase, 7 kDa subunit	-	Domain
M	PF05183	RNA dependent RNA polymerase (RdRP)	RNA dependent RNA polymerase	-	Family
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	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
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	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	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
H	PF03870	RNA polymerase Rpb8 (RNA_pol_Rpb8)	RNA polymerase Rpb8	-	Family
I	PF02150	RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD)	RNA polymerases M/15 Kd subunit	-	Domain
I	PF01096	Transcription factor S-II (TFIIS) (TFIIS_C)	Transcription factor S-II (TFIIS)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-directed RNA polymerase IV subunit 1	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 cation binding 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 cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process RNA processing primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule 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 positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process post-transcriptional gene silencing nucleic acid catabolic process catabolic process positive regulation of biological process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process RNA destabilization siRNA-mediated gene silencing by mRNA destabilization siRNA-mediated post-transcriptional gene silencing siRNA-mediated long-distance post-transcriptional gene silencing regulation of catabolic process mRNA metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process DNA-templated transcription	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex RNA polymerase IV complex DNA-directed RNA polymerase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
J	DNA-directed RNA polymerases II, IV and V subunit 10	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 biosynthetic process metabolic 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex organelle lumen nuclear lumen
K	DNA-directed RNA polymerases II, IV and V subunit 11	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	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 catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex organelle lumen nuclear lumen
L	DNA-directed RNA polymerases II, IV and V subunit 12	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 biosynthetic process metabolic 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex RNA polymerase IV complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex organelle lumen nuclear lumen
M	RNA-dependent RNA polymerase 2	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding cation binding ion binding metal ion binding small molecule binding DNA/RNA hybrid binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule 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 positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process post-transcriptional gene silencing nucleic acid catabolic process catabolic process positive regulation of biological process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process RNA destabilization siRNA-mediated gene silencing by mRNA destabilization siRNA-mediated post-transcriptional gene silencing siRNA-mediated long-distance post-transcriptional gene silencing regulation of catabolic process mRNA metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process siRNA transcription RNA-templated transcription biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to fungus defense response to other organism response to stress response to external biotic stimulus response to fungus	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 nucleoplasm
N	Nontemplate_DNA	-	-	-
O	RNA	-	-	-
P [auth Q]	Template_DNA	-	-	-
B	DNA-directed RNA polymerases IV and V subunit 2	ribonucleoside binding binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA 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 ribonucleoside binding binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA 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 cation binding ion binding metal ion binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process post-transcriptional regulation of gene expression regulatory ncRNA-mediated post-transcriptional gene silencing post-transcriptional gene silencing cellular component organization siRNA-mediated heterochromatin formation chromatin organization DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic gene silencing by siRNA-directed DNA methylation response to stimulus regulation of response to stimulus immune response immune system process regulation of immune response regulation of immune system process DNA-templated transcription biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus response to biotic stimulus defense response to fungus defense response to other organism response to stress response to external biotic stimulus response to fungus retrotransposon silencing retrotransposon silencing by heterochromatin formation retrotransposition siRNA-mediated retrotransposon silencing by heterochromatin formation transposition	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex intracellular non-membrane-bounded organelle chromatin chromosome heterochromatin non-membrane-bounded organelle
C	DNA-directed RNA polymerases II, IV and V subunit 3	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 protein binding 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 protein binding protein dimerization activity	developmental process multicellular organism development multicellular organismal process stomatal complex patterning anatomical structure development pattern specification process regionalization stomatal complex development plant epidermis development post-embryonic development tissue development cellular biosynthetic process cellular metabolic process RNA metabolic process developmental process multicellular organism development multicellular organismal process stomatal complex patterning anatomical structure development pattern specification process regionalization stomatal complex development plant epidermis development post-embryonic development tissue development 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 biosynthetic process metabolic process cellular process macromolecule metabolic 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 protein-containing complex catalytic complex nuclear protein-containing complex transferase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase V complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex cytoplasm
D	DNA-directed RNA polymerases IV and V subunit 4	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 DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process post-transcriptional regulation of gene expression negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing 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 post-transcriptional gene silencing regulation of macromolecule biosynthetic process regulation of metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex
E	DNA-directed RNA polymerases II and IV subunit 5A	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 biosynthetic process metabolic 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex RNA polymerase IV complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex organelle lumen nuclear lumen
F	DNA-directed RNA polymerases II, IV and V subunit 6A	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 biosynthetic process metabolic 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex organelle lumen nuclear lumen
G	DNA-directed RNA polymerase IV subunit 7	-	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex RNA polymerase IV complex DNA-directed RNA polymerase complex intracellular protein-containing complex
H	DNA-directed RNA polymerases II, IV and V subunit 8B	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 biosynthetic process metabolic 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex organelle lumen nuclear lumen
I	DNA-directed RNA polymerases II, IV and V subunit 9A	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 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 biosynthetic process metabolic 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 biosynthetic process metabolic process cellular process macromolecule metabolic 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 protein-containing complex catalytic complex nuclear protein-containing complex transferase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase V complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
A	IPR040402	DNA-directed RNA polymerase IV/V subunit 1, C-terminal	Domain
A	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A	IPR040403	DNA-directed RNA polymerase IV/V subunit 1, N-terminal	Domain
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
J	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
J	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
J	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
K	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
K	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
K	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
K	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
K	IPR037685	RNA polymerase RBP11	Family
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	IPR007855	RNA-dependent RNA polymerase, eukaryotic-type	Family
B	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B	IPR007646	RNA polymerase Rpb2, domain 4	Domain
B	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
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	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
B	IPR007641	RNA polymerase Rpb2, domain 7	Domain
C	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
C	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
C	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
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	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
E	IPR036710	RNA polymerase Rpb5, N-terminal domain 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	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
G	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G	IPR045113	RNA polymerase subunit Rpb7-like	Family
G	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
H	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
H	IPR005570	DNA-directed RNA polymerases I, II, and III subunit RPABC3	Family
I	IPR012164	DNA-directed RNA polymerase subunit/transcription factor S	Family
I	IPR001222	Zinc finger, TFIIS-type	Domain
I	IPR034012	Pol II subunit B9, C-terminal zinc ribbon	Domain
I	IPR019761	DNA-directed RNA polymerase M, 15kDa subunit, conserved site	Conserved Site
I	IPR001529	DNA-directed RNA polymerase, M/15kDa subunit	Domain