Mouse Gene Polr2j (ENSMUST00000041366.13) Description and Page Index
  Description: Mus musculus polymerase (RNA) II (DNA directed) polypeptide J (Polr2j), mRNA. (from RefSeq NM_011293)
Gencode Transcript: ENSMUST00000041366.13
Gencode Gene: ENSMUSG00000039771.13
Transcript (Including UTRs)
   Position: mm10 chr5:136,116,631-136,122,947 Size: 6,317 Total Exon Count: 4 Strand: +
Coding Region
   Position: mm10 chr5:136,116,753-136,122,777 Size: 6,025 Coding Exon Count: 4 

Page IndexSequence and LinksCTDRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:136,116,631-136,122,947)mRNA (may differ from genome)Protein (117 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.80122-0.343 Picture PostScript Text
3' UTR -51.70170-0.304 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009025 - DNA-dir_RNA_pol_RBP11-like
IPR008193 - RNA_pol_Rpb11_13-16kDa_CS

Pfam Domains:
PF01193 - RNA polymerase Rpb3/Rpb11 dimerisation domain
PF13656 - RNA polymerase Rpb3/Rpb11 dimerisation domain

SCOP Domains:
55257 - RBP11-like subunits of RNA polymerase

ModBase Predicted Comparative 3D Structure on Q6PI63
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details    Gene Details
Gene Sorter    Gene Sorter
GenBankRGDEnsemblEnsemblWormBaseSGD
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0030275 LRR domain binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005665 DNA-directed RNA polymerase II, core complex


-  Descriptions from all associated GenBank mRNAs
  AK158610 - Mus musculus visual cortex cDNA, RIKEN full-length enriched library, clone:K230026J18 product:polymerase (RNA) II (DNA directed) polypeptide J, full insert sequence.
AK158644 - Mus musculus visual cortex cDNA, RIKEN full-length enriched library, clone:K230037O17 product:polymerase (RNA) II (DNA directed) polypeptide J, full insert sequence.
BC042939 - Mus musculus polymerase (RNA) II (DNA directed) polypeptide J, mRNA (cDNA clone MGC:54637 IMAGE:6476299), complete cds.
D85818 - Mus musculus mRNA for RNA polymerase II subuunit RPB14, complete cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu00230 - Purine metabolism
mmu00240 - Pyrimidine metabolism
mmu01100 - Metabolic pathways
mmu03020 - RNA polymerase
mmu05016 - Huntington's disease

Reactome (by CSHL, EBI, and GO)

Protein Q6PI63 (Reactome details) participates in the following event(s):

R-MMU-5578742 AGO1,2:small RNA complexes interact with chromatin
R-MMU-6810238 RNA polymerase II binds initiation factors at promoter of snRNA gene (U1, U2, U4, U4atac, U5, U11, U12)
R-MMU-113429 Elongating transcript encounters a lesion in the template
R-MMU-109638 Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex
R-MMU-73946 Abortive initiation
R-MMU-75856 Abortive Initiation Before Second Transition
R-MMU-75891 Abortive Initiation After Second Transition
R-MMU-112395 Abortive termination of elongation after arrest
R-MMU-6781840 ERCC6 binds stalled RNA Pol II
R-MMU-113407 DSIF complex binds to RNA Pol II (hypophosphorylated)
R-MMU-112383 Hypophosphorylation of RNA Pol II CTD by FCP1P protein
R-MMU-9012315 ESR1:ESTG:P-TEFb recruited to paused RNA polymerase II on MYB gene
R-MMU-9012319 p-TEFb phosphorylates serine 2 in RNA polymerase II CTD
R-MMU-6782211 DNA polymerases delta, epsilon or kappa bind the TC-NER site
R-MMU-6782204 5' incision of damaged DNA strand by ERCC1:ERCC4 in TC-NER
R-MMU-6782208 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER
R-MMU-6782224 3' incision by ERCC5 (XPG) in TC-NER
R-MMU-6782227 Ligation of newly synthesized repair patch to incised DNA in TC-NER
R-MMU-6810235 RPAP2 binds RNA polymerase II phosphorylated at serine-7 residues of heptad repeats in the C-terminal domain
R-MMU-6810233 CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter
R-MMU-77095 Recognition and binding of the mRNA cap by the cap-binding complex
R-MMU-77090 Methylation of GMP-cap by RNA Methyltransferase
R-MMU-156661 Formation of Exon Junction Complex
R-MMU-72143 Lariat Formation and 5'-Splice Site Cleavage
R-MMU-77068 Activation of GT
R-MMU-77073 SPT5 subunit of Pol II binds the RNA triphosphatase (RTP)
R-MMU-77069 RNA Polymerase II CTD (phosphorylated) binds to CE
R-MMU-77071 Phosphorylation (Ser5) of RNA pol II CTD
R-MMU-77077 Capping complex formation
R-MMU-75080 Formation of AT-AC A complex
R-MMU-72095 Internal Methylation of mRNA
R-MMU-75864 Newly Formed Phosphodiester Bond Stabilized and PPi Released
R-MMU-75095 Binding of TFIIE to the growing preinitiation complex
R-MMU-75861 NTP Binds Active Site of RNA Polymerase II
R-MMU-75862 Fall Back to Closed Pre-initiation Complex
R-MMU-75949 RNA Polymerase II Promoter Opening: First Transition
R-MMU-75866 Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP
R-MMU-75873 Addition of Nucleotides 5 through 9 on the growing Transcript
R-MMU-76576 Addition of nucleotides 10 and 11 on the growing transcript: Third Transition
R-MMU-111264 Addition of nucleotides between position +11 and +30
R-MMU-113430 Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex
R-MMU-6803523 PTB and hnRNPA1 bind FGFR2 pre-mRNA to repress IIIb splicing and promote formation of FGFR2c mRNA
R-MMU-6803527 ESRP1 and 2 bind FGFR2 pre-mRNA to promote FGFR2b maturation and expression
R-MMU-112379 Recruitment of elongation factors to form elongation complex
R-MMU-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-MMU-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing
R-MMU-113412 Pol II elongation complex moves on the template as transcript elongates
R-MMU-113413 TFIIS-mediated recovery of elongation from arrest
R-MMU-112385 Addition of nucleotides leads to transcript elongation
R-MMU-112392 Resumption of elongation after recovery from pausing
R-MMU-112396 Separation of elongating transcript from template
R-MMU-6781833 ERCC8 (CSA) binds stalled RNA Pol II
R-MMU-113402 Formation of DSIF:NELF:early elongation complex
R-MMU-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA
R-MMU-77078 Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme
R-MMU-77081 Formation of the CE:GMP intermediate complex
R-MMU-77085 Dissociation of transcript with 5'-GMP from GT
R-MMU-77083 Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA
R-MMU-72127 Formation of the Spliceosomal B Complex
R-MMU-72139 Formation of the active Spliceosomal C (B*) complex
R-MMU-75081 Formation of AT-AC B Complex
R-MMU-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-MMU-109639 Formation of the closed pre-initiation complex
R-MMU-6797616 CCNK:CDK12 binds RNA Pol II at DNA repair genes
R-MMU-6781867 ERCC8:DDB1:CUL4:RBX1 ubiquitinates ERCC6 and RNA Pol II
R-MMU-113409 Abortive termination of early transcription elongation by DSIF:NELF
R-MMU-6782004 Assembly of the pre-incision complex in TC-NER
R-MMU-6797606 CDK12 phosphorylates RNA Pol II CTD at DNA repair genes
R-MMU-6782069 UVSSA:USP7 deubiquitinates ERCC6
R-MMU-6782131 RNA Pol II backtracking in TC-NER
R-MMU-6782138 ERCC5 and RPA bind TC-NER site
R-MMU-6782141 Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in TC-NER
R-MMU-5578749 Transcriptional regulation by small RNAs
R-MMU-6781823 Formation of TC-NER Pre-Incision Complex
R-MMU-6807505 RNA polymerase II transcribes snRNA genes
R-MMU-674695 RNA Polymerase II Pre-transcription Events
R-MMU-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-MMU-211000 Gene Silencing by RNA
R-MMU-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-MMU-73857 RNA Polymerase II Transcription
R-MMU-113418 Formation of the Early Elongation Complex
R-MMU-9018519 Estrogen-dependent gene expression
R-MMU-6782135 Dual incision in TC-NER
R-MMU-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-MMU-72086 mRNA Capping
R-MMU-72163 mRNA Splicing - Major Pathway
R-MMU-77075 RNA Pol II CTD phosphorylation and interaction with CE
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-75953 RNA Polymerase II Transcription Initiation
R-MMU-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-MMU-6803529 FGFR2 alternative splicing
R-MMU-74160 Gene expression (Transcription)
R-MMU-5696398 Nucleotide Excision Repair
R-MMU-112382 Formation of RNA Pol II elongation complex
R-MMU-75955 RNA Polymerase II Transcription Elongation
R-MMU-8939211 ESR-mediated signaling
R-MMU-8953854 Metabolism of RNA
R-MMU-72172 mRNA Splicing
R-MMU-5654738 Signaling by FGFR2
R-MMU-73894 DNA Repair
R-MMU-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-MMU-9006931 Signaling by Nuclear Receptors
R-MMU-190236 Signaling by FGFR
R-MMU-3700989 Transcriptional Regulation by TP53
R-MMU-162582 Signal Transduction
R-MMU-9006934 Signaling by Receptor Tyrosine Kinases
R-MMU-212436 Generic Transcription Pathway

-  Other Names for This Gene
  Alternate Gene Symbols: mCG_1879, NM_011293, Q6PI63, Q6PI63_MOUSE, uc008zzw.1, uc008zzw.2, uc008zzw.3
UCSC ID: uc008zzw.3
RefSeq Accession: NM_011293
Protein: Q6PI63 CCDS: CCDS19751.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.