Format

Send to:

Choose Destination
    • Showing Current items.

    Rtf1 RTF1, Paf1/RNA polymerase II complex component [ Mus musculus (house mouse) ]

    Gene ID: 76246, updated on 31-Jan-2019

    Summary

    Official Symbol
    Rtf1provided by MGI
    Official Full Name
    RTF1, Paf1/RNA polymerase II complex componentprovided by MGI
    Primary source
    MGI:MGI:1309480
    See related
    Ensembl:ENSMUSG00000027304
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Gtl7; cbp82; AI853581; AU043144; AW553985; 2900005O08Rik; 6530416A09Rik
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 14.6), CNS E14 (RPKM 12.6) and 28 other tissues See more
    Orthologs

    Genomic context

    See Rtf1 in Genome Data Viewer
    Location:
    2; 2 E5
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (119675068..119735407)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (119500804..119561143)

    Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 Neighboring gene H3 histone, family 3C Neighboring gene inositol 1,4,5-trisphosphate 3-kinase A Neighboring gene leukocyte tyrosine kinase

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (1) 

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II C-terminal domain phosphoserine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    contributes_to protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    blastocyst growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endodermal cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone H3-K4 trimethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone modification IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of histone H3-K4 methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription elongation from RNA polymerase II promoter ISO
    Inferred from Sequence Orthology
    more info
     
    stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
     
    transcription elongation from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Cdc73/Paf1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Cdc73/Paf1 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Cdc73/Paf1 complex ISO
    Inferred from Sequence Orthology
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    RNA polymerase-associated protein RTF1 homolog
    Names
    Rtf1, Paf1/RNA polymerase II complex component, homolog
    gene trap locus 7

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_030112.2NP_084388.2  RNA polymerase-associated protein RTF1 homolog precursor

      See identical proteins and their annotated locations for NP_084388.2

      Status: VALIDATED

      Source sequence(s)
      AK019305, AL844536, AW491091, BC117849, BY270385, CN532066, CN839001
      Consensus CDS
      CCDS50673.1
      UniProtKB/Swiss-Prot
      A2AQ19
      UniProtKB/TrEMBL
      Q9CTY6
      Related
      ENSMUSP00000028767.8, ENSMUST00000028767.8
      Conserved Domains (2) summary
      COG5296
      Location:194628
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:364462
      Plus-3; Plus-3 domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      119675068..119735407
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319319.1XP_017174808.1  RNA polymerase-associated protein RTF1 homolog isoform X1

      Conserved Domains (2) summary
      COG5296
      Location:3437
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:173271
      Plus-3; Plus-3 domain
    Support Center