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    Rtf1 Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) [ Rattus norvegicus (Norway rat) ]

    Gene ID: 366169, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rtf1provided by RGD
    Official Full Name
    Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)provided by RGD
    Primary source
    RGD:1310654
    See related
    EnsemblRapid:ENSRNOG00000005183 AllianceGenome:RGD:1310654
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Gtl7
    Summary
    Predicted to enable RNA polymerase II C-terminal domain phosphoserine binding activity and single-stranded DNA binding activity. Predicted to be involved in several processes, including endodermal cell fate commitment; negative regulation of transcription by RNA polymerase II; and transcription elongation by RNA polymerase II. Predicted to act upstream of or within blastocyst growth. Predicted to be located in nucleolus. Predicted to be part of Cdc73/Paf1 complex. Orthologous to human RTF1 (RTF1 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 54.2), Adrenal (RPKM 53.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rtf1 in Genome Data Viewer
    Location:
    3q35
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (127113171..127172761)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (106659363..106718956)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (111478350..111537941)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene Opa interacting protein 5 Neighboring gene nucleolar and spindle associated protein 1 Neighboring gene 40S ribosomal protein S20 pseudogene Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 Neighboring gene inositol-trisphosphate 3-kinase A Neighboring gene leukocyte receptor tyrosine kinase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    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. The Paf1 complex: platform or player in RNA polymerase II transcription? Jaehning JA. Biochim Biophys Acta, 2010 May-Jun. PMID 20060942, Free PMC Article
    3. 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
    4. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Kim J, et al. Cell, 2010 Feb 19. PMID 20178742, Free PMC Article
    5. Capturing novel mouse genes encoding chromosomal and other nuclear proteins. Tate P, et al. J Cell Sci, 1998 Sep. PMID 9701556

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II C-terminal domain phosphoserine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within blastocyst growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endodermal cell fate commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    RNA polymerase-associated protein RTF1 homolog
    Names
    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_001401979.1 → NP_001388908.1  RNA polymerase-associated protein RTF1 homolog precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A8I6AGX2
      Related
      ENSRNOP00000094041.1, ENSRNOT00000105159.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      127113171..127172761
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063284277.1 → XP_063140347.1  RNA polymerase-associated protein RTF1 homolog isoform X1

      Related
      ENSRNOP00000053231.3, ENSRNOT00000056392.4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108958.1: Suppressed sequence

      Description
      NM_001108958.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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