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

    Gene ID: 76246, updated on 5-Mar-2024

    Summary

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    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 AllianceGenome:MGI:1309480
    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; 2900005O08Rik; 6530416A09Rik
    Summary
    Predicted to enable RNA polymerase II C-terminal domain phosphoserine binding activity and single-stranded DNA binding activity. Involved in several processes, including endodermal cell fate commitment; histone H3-K4 trimethylation; and positive regulation of histone H3-K4 methylation. Acts upstream of or within blastocyst growth. Located in nucleolus. Part of Cdc73/Paf1 complex. Is expressed in several structures, including brain and retina nuclear layer. Orthologous to human RTF1 (RTF1 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 14.6), CNS E14 (RPKM 12.6) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rtf1 in Genome Data Viewer
    Location:
    2 E5; 2 59.97 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (119505549..119565888)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (119675068..119735407)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 Neighboring gene STARR-positive B cell enhancer ABC_E9201 Neighboring gene H3 histone, family 3C Neighboring gene STARR-positive B cell enhancer ABC_E7852 Neighboring gene STARR-seq mESC enhancer starr_05489 Neighboring gene predicted gene, 25857 Neighboring gene inositol 1,4,5-trisphosphate 3-kinase A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    Related articles in PubMed

    1. Structure and DNA binding of the human Rtf1 Plus3 domain. de Jong RN, et al. Structure, 2008 Jan. PMID 18184592
    2. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a. Strikoudis A, et al. Nat Cell Biol, 2016 Nov. PMID 27749823, Free PMC Article
    3. Capturing novel mouse genes encoding chromosomal and other nuclear proteins. Tate P, et al. J Cell Sci, 1998 Sep. PMID 9701556
    4. CTR9/PAF1c regulates molecular lineage identity, histone H3K36 trimethylation and genomic imprinting during preimplantation development. Zhang K, et al. Dev Biol, 2013 Nov 1. PMID 24036311, Free PMC Article
    5. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Ding L, et al. Cell Stem Cell, 2009 May 8. PMID 19345177

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2)  1 citation
    • Endonuclease-mediated (1) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

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

    General protein information

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    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)

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    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_030112.2 → NP_084388.2  RNA polymerase-associated protein RTF1 homolog

      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, Q08EC5
      Related
      ENSMUSP00000028767.9, ENSMUST00000028767.9
      Conserved Domains (2) summary
      COG5296
      Location:194 → 628
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:364 → 462
      Plus-3; Plus-3 domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      119505549..119565888
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036162668.1 → XP_036018561.1  RNA polymerase-associated protein RTF1 homolog isoform X3

      Conserved Domains (2) summary
      COG5296
      Location:148 → 413
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:149 → 249
      Plus-3; Plus-3 domain

    2. XM_036162666.1 → XP_036018559.1  RNA polymerase-associated protein RTF1 homolog isoform X1

      Conserved Domains (2) summary
      COG5296
      Location:154 → 588
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:324 → 424
      Plus-3; Plus-3 domain

    3. XM_036162667.1 → XP_036018560.1  RNA polymerase-associated protein RTF1 homolog isoform X2

      Conserved Domains (2) summary
      COG5296
      Location:3 → 437
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:173 → 273
      Plus-3; Plus-3 domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2AQ19.1 GenPept UniProtKB/Swiss-Prot:A2AQ19

    Gene LinkOut

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