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Entry version 160 (02 Jun 2021)
Sequence version 1 (01 Nov 1998)
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Protein

DNA-directed RNA polymerase II subunit RPB9

Gene

rpb9

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template (By similarity).

Involved in the regulation of transcription elongation.

By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi7Zinc 1By similarity1
Metal bindingi10Zinc 1By similarity1
Metal bindingi29Zinc 1By similarity1
Metal bindingi32Zinc 1By similarity1
Metal bindingi75Zinc 2By similarity1
Metal bindingi78Zinc 2By similarity1
Metal bindingi103Zinc 2By similarity1
Metal bindingi106Zinc 2By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri7 – 32C4-typeSequence analysisAdd BLAST26
Zinc fingeri71 – 111TFIIS-typePROSITE-ProRule annotationAdd BLAST41

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processTranscription
LigandMetal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SPO-113418, Formation of the Early Elongation Complex
R-SPO-5578749, Transcriptional regulation by small RNAs
R-SPO-674695, RNA Polymerase II Pre-transcription Events
R-SPO-6781823, Formation of TC-NER Pre-Incision Complex
R-SPO-6782135, Dual incision in TC-NER
R-SPO-6782210, Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-6796648, TP53 Regulates Transcription of DNA Repair Genes
R-SPO-6807505, RNA polymerase II transcribes snRNA genes
R-SPO-72086, mRNA Capping
R-SPO-73776, RNA Polymerase II Promoter Escape
R-SPO-73779, RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SPO-75953, RNA Polymerase II Transcription Initiation
R-SPO-75955, RNA Polymerase II Transcription Elongation
R-SPO-76042, RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SPO-77075, RNA Pol II CTD phosphorylation and interaction with CE
R-SPO-9018519, Estrogen-dependent gene expression

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB9
Short name:
RNA polymerase II subunit B9
Alternative name(s):
DNA-directed RNA polymerase II 13.2 kDa polypeptide
DNA-directed RNA polymerase II subunit 9
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rpb9
ORF Names:SPAPYUG7.04c
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri284812 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002485 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome I

Organism-specific databases

Schizosaccharomyces pombe database

More...
PomBasei
SPAPYUG7.04c, rpb9

Eukaryotic Pathogen, Vector and Host Database Resources

More...
VEuPathDBi
FungiDB:SPAPYUG7.04c

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001214731 – 113DNA-directed RNA polymerase II subunit RPB9Add BLAST113

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
O74635

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
O74635

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
277972, 104 interactors

STRING: functional protein association networks

More...
STRINGi
4896.SPAPYUG7.04c.1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
O74635

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
O74635

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni54 – 74DisorderedSequence analysisAdd BLAST21

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri7 – 32C4-typeSequence analysisAdd BLAST26
Zinc fingeri71 – 111TFIIS-typePROSITE-ProRule annotationAdd BLAST41

Keywords - Domaini

Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2691, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_093932_0_1_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O74635

Identification of Orthologs from Complete Genome Data

More...
OMAi
TFRFCRD

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O74635

Family and domain databases

Conserved Domains Database

More...
CDDi
cd10508, Zn-ribbon_RPB9, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR019761, DNA-dir_RNA_pol-M_15_CS
IPR001529, DNA-dir_RNA_pol_M/15kDasu
IPR012164, Rpa12/Rpb9/Rpc10/TFS
IPR034012, Zn_ribbon_RPB9_C
IPR001222, Znf_TFIIS

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02150, RNA_POL_M_15KD, 1 hit
PF01096, TFIIS_C, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF005586, RNApol_RpoM, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00661, RPOL9, 1 hit
SM00440, ZnF_C2C2, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01030, RNA_POL_M_15KD, 1 hit
PS00466, ZF_TFIIS_1, 1 hit
PS51133, ZF_TFIIS_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

O74635-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSNFQYCIEC NNMLYPREDK VDRVLRLACR NCDYSEIAAT SKVYRHELQS
60 70 80 90 100
SNVENTTVSH DASTDPTLPR SDKECPRCHQ HEAVFYQTHS RRGDTMMTLI
110
YVCVHCGFAF EEQ
Length:113
Mass (Da):13,175
Last modified:November 1, 1998 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i55A1ABAF5832671A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AB007988 Genomic DNA Translation: BAA33021.1
AF237418 Genomic DNA Translation: AAL55660.1
CU329670 Genomic DNA Translation: CAB66313.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T43279

NCBI Reference Sequences

More...
RefSeqi
NP_594705.1, NM_001020132.2

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
SPAPYUG7.04c.1; SPAPYUG7.04c.1:pep; SPAPYUG7.04c

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
2541470

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
spo:SPAPYUG7.04c

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007988 Genomic DNA Translation: BAA33021.1
AF237418 Genomic DNA Translation: AAL55660.1
CU329670 Genomic DNA Translation: CAB66313.1
PIRiT43279
RefSeqiNP_594705.1, NM_001020132.2

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65I/U1-113[»]
5U0Selectron microscopy7.80i1-113[»]
SMRiO74635
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi277972, 104 interactors
STRINGi4896.SPAPYUG7.04c.1

Proteomic databases

MaxQBiO74635
PaxDbiO74635

Genome annotation databases

EnsemblFungiiSPAPYUG7.04c.1; SPAPYUG7.04c.1:pep; SPAPYUG7.04c
GeneIDi2541470
KEGGispo:SPAPYUG7.04c

Organism-specific databases

PomBaseiSPAPYUG7.04c, rpb9
VEuPathDBiFungiDB:SPAPYUG7.04c

Phylogenomic databases

eggNOGiKOG2691, Eukaryota
HOGENOMiCLU_093932_0_1_1
InParanoidiO74635
OMAiTFRFCRD
PhylomeDBiO74635

Enzyme and pathway databases

ReactomeiR-SPO-113418, Formation of the Early Elongation Complex
R-SPO-5578749, Transcriptional regulation by small RNAs
R-SPO-674695, RNA Polymerase II Pre-transcription Events
R-SPO-6781823, Formation of TC-NER Pre-Incision Complex
R-SPO-6782135, Dual incision in TC-NER
R-SPO-6782210, Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-6796648, TP53 Regulates Transcription of DNA Repair Genes
R-SPO-6807505, RNA polymerase II transcribes snRNA genes
R-SPO-72086, mRNA Capping
R-SPO-73776, RNA Polymerase II Promoter Escape
R-SPO-73779, RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SPO-75953, RNA Polymerase II Transcription Initiation
R-SPO-75955, RNA Polymerase II Transcription Elongation
R-SPO-76042, RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SPO-77075, RNA Pol II CTD phosphorylation and interaction with CE
R-SPO-9018519, Estrogen-dependent gene expression

Miscellaneous databases

EvolutionaryTraceiO74635

Protein Ontology

More...
PROi
PR:O74635

Family and domain databases

CDDicd10508, Zn-ribbon_RPB9, 1 hit
InterProiView protein in InterPro
IPR019761, DNA-dir_RNA_pol-M_15_CS
IPR001529, DNA-dir_RNA_pol_M/15kDasu
IPR012164, Rpa12/Rpb9/Rpc10/TFS
IPR034012, Zn_ribbon_RPB9_C
IPR001222, Znf_TFIIS
PfamiView protein in Pfam
PF02150, RNA_POL_M_15KD, 1 hit
PF01096, TFIIS_C, 1 hit
PIRSFiPIRSF005586, RNApol_RpoM, 1 hit
SMARTiView protein in SMART
SM00661, RPOL9, 1 hit
SM00440, ZnF_C2C2, 1 hit
PROSITEiView protein in PROSITE
PS01030, RNA_POL_M_15KD, 1 hit
PS00466, ZF_TFIIS_1, 1 hit
PS51133, ZF_TFIIS_2, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRPB9_SCHPO
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O74635
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 14, 2001
Last sequence update: November 1, 1998
Last modified: June 2, 2021
This is version 160 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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