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Protein

DNA-directed RNA polymerase II subunit RPB9

Gene

Polr2i

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi17 – 171Zinc 1By similarity
Metal bindingi20 – 201Zinc 1By similarity
Metal bindingi39 – 391Zinc 1By similarity
Metal bindingi42 – 421Zinc 1By similarity
Metal bindingi86 – 861Zinc 2By similarity
Metal bindingi89 – 891Zinc 2By similarity
Metal bindingi114 – 1141Zinc 2By similarity
Metal bindingi119 – 1191Zinc 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri17 – 4226C4-typeSequence analysisAdd
BLAST
Zinc fingeri82 – 12443TFIIS-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-112382. Formation of RNA Pol II elongation complex.
R-MMU-113418. Formation of the Early Elongation Complex.
R-MMU-5578749. Transcriptional regulation by small RNAs.
R-MMU-5601884. PIWI-interacting RNA (piRNA) biogenesis.
R-MMU-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-MMU-674695. RNA Polymerase II Pre-transcription Events.
R-MMU-6781823. Formation of TC-NER Pre-Incision Complex.
R-MMU-6782135. Dual incision in TC-NER.
R-MMU-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-MMU-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-MMU-6803529. FGFR2 alternative splicing.
R-MMU-6807505. RNA polymerase II transcribes snRNA genes.
R-MMU-72086. mRNA Capping.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72165. mRNA Splicing - Minor Pathway.
R-MMU-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-MMU-73776. RNA Polymerase II Promoter Escape.
R-MMU-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-MMU-75953. RNA Polymerase II Transcription Initiation.
R-MMU-75955. RNA Polymerase II Transcription Elongation.
R-MMU-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-MMU-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

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 subunit I
RNA polymerase II 14.5 kDa subunit
Short name:
RPB14.5
Gene namesi
Name:Polr2i
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 7

Organism-specific databases

MGIiMGI:1917170. Polr2i.

Subcellular locationi

  • Nucleusnucleolus By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 125125DNA-directed RNA polymerase II subunit RPB9PRO_0000121468Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP60898.
MaxQBiP60898.
PaxDbiP60898.
PRIDEiP60898.

PTM databases

PhosphoSiteiP60898.

Miscellaneous databases

PMAP-CutDBP60898.

Expressioni

Gene expression databases

BgeeiP60898.
CleanExiMM_POLR2I.
ExpressionAtlasiP60898. baseline and differential.
GenevisibleiP60898. MM.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi213757. 9 interactions.
IntActiP60898. 2 interactions.
MINTiMINT-4428023.
STRINGi10090.ENSMUSP00000019882.

Structurei

3D structure databases

ProteinModelPortaliP60898.
SMRiP60898. Positions 15-125.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Contains 1 TFIIS-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri17 – 4226C4-typeSequence analysisAdd
BLAST
Zinc fingeri82 – 12443TFIIS-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG2691. Eukaryota.
COG1594. LUCA.
GeneTreeiENSGT00550000075063.
HOGENOMiHOG000228134.
HOVERGENiHBG009981.
InParanoidiP60898.
KOiK03017.
OMAiQLADSNC.
OrthoDBiEOG7BW0M6.
PhylomeDBiP60898.
TreeFamiTF103032.

Family and domain databases

InterProiIPR019761. DNA-dir_RNA_pol-M_15_CS.
IPR001529. DNA-dir_RNA_pol_M/15kDasu.
IPR012164. Rpa12/Rpb9/Rpc10/TFS.
IPR001222. Znf_TFIIS.
[Graphical view]
PfamiPF02150. RNA_POL_M_15KD. 1 hit.
PF01096. TFIIS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF005586. RNApol_RpoM. 1 hit.
SMARTiSM00661. RPOL9. 1 hit.
SM00440. ZnF_C2C2. 1 hit.
[Graphical view]
PROSITEiPS01030. RNA_POL_M_15KD. 1 hit.
PS00466. ZF_TFIIS_1. 1 hit.
PS51133. ZF_TFIIS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P60898-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN
60 70 80 90 100
SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKCG HKEAVFFQSH
110 120
SARAEDAMRL YYVCTAPHCG HRWTE
Length:125
Mass (Da):14,523
Last modified:April 13, 2004 - v1
Checksum:i6520687BB57EE018
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC062812 mRNA. Translation: AAH62812.1.
CCDSiCCDS21084.1.
RefSeqiNP_081535.1. NM_027259.1.
UniGeneiMm.440028.

Genome annotation databases

EnsembliENSMUST00000019882; ENSMUSP00000019882; ENSMUSG00000019738.
GeneIDi69920.
KEGGimmu:69920.
UCSCiuc009gdt.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC062812 mRNA. Translation: AAH62812.1.
CCDSiCCDS21084.1.
RefSeqiNP_081535.1. NM_027259.1.
UniGeneiMm.440028.

3D structure databases

ProteinModelPortaliP60898.
SMRiP60898. Positions 15-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi213757. 9 interactions.
IntActiP60898. 2 interactions.
MINTiMINT-4428023.
STRINGi10090.ENSMUSP00000019882.

PTM databases

PhosphoSiteiP60898.

Proteomic databases

EPDiP60898.
MaxQBiP60898.
PaxDbiP60898.
PRIDEiP60898.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000019882; ENSMUSP00000019882; ENSMUSG00000019738.
GeneIDi69920.
KEGGimmu:69920.
UCSCiuc009gdt.1. mouse.

Organism-specific databases

CTDi5438.
MGIiMGI:1917170. Polr2i.

Phylogenomic databases

eggNOGiKOG2691. Eukaryota.
COG1594. LUCA.
GeneTreeiENSGT00550000075063.
HOGENOMiHOG000228134.
HOVERGENiHBG009981.
InParanoidiP60898.
KOiK03017.
OMAiQLADSNC.
OrthoDBiEOG7BW0M6.
PhylomeDBiP60898.
TreeFamiTF103032.

Enzyme and pathway databases

ReactomeiR-MMU-112382. Formation of RNA Pol II elongation complex.
R-MMU-113418. Formation of the Early Elongation Complex.
R-MMU-5578749. Transcriptional regulation by small RNAs.
R-MMU-5601884. PIWI-interacting RNA (piRNA) biogenesis.
R-MMU-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-MMU-674695. RNA Polymerase II Pre-transcription Events.
R-MMU-6781823. Formation of TC-NER Pre-Incision Complex.
R-MMU-6782135. Dual incision in TC-NER.
R-MMU-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-MMU-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-MMU-6803529. FGFR2 alternative splicing.
R-MMU-6807505. RNA polymerase II transcribes snRNA genes.
R-MMU-72086. mRNA Capping.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72165. mRNA Splicing - Minor Pathway.
R-MMU-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-MMU-73776. RNA Polymerase II Promoter Escape.
R-MMU-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-MMU-75953. RNA Polymerase II Transcription Initiation.
R-MMU-75955. RNA Polymerase II Transcription Elongation.
R-MMU-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-MMU-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

PMAP-CutDBP60898.
PROiP60898.
SOURCEiSearch...

Gene expression databases

BgeeiP60898.
CleanExiMM_POLR2I.
ExpressionAtlasiP60898. baseline and differential.
GenevisibleiP60898. MM.

Family and domain databases

InterProiIPR019761. DNA-dir_RNA_pol-M_15_CS.
IPR001529. DNA-dir_RNA_pol_M/15kDasu.
IPR012164. Rpa12/Rpb9/Rpc10/TFS.
IPR001222. Znf_TFIIS.
[Graphical view]
PfamiPF02150. RNA_POL_M_15KD. 1 hit.
PF01096. TFIIS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF005586. RNApol_RpoM. 1 hit.
SMARTiSM00661. RPOL9. 1 hit.
SM00440. ZnF_C2C2. 1 hit.
[Graphical view]
PROSITEiPS01030. RNA_POL_M_15KD. 1 hit.
PS00466. ZF_TFIIS_1. 1 hit.
PS51133. ZF_TFIIS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Mammary gland.
  2. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Kidney and Testis.

Entry informationi

Entry nameiRPB9_MOUSE
AccessioniPrimary (citable) accession number: P60898
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: April 13, 2004
Last modified: June 8, 2016
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.