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    Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component [ Rattus norvegicus (Norway rat) ]

    Gene ID: 293184, updated on 9-Dec-2024

    Summary

    Official Symbol
    Ctr9provided by RGD
    Official Full Name
    CTR9 homolog, Paf1/RNA polymerase II complex componentprovided by RGD
    Primary source
    RGD:1311097
    See related
    EnsemblRapid:ENSRNOG00000017195 AllianceGenome:RGD:1311097
    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
    Sh2bp1
    Summary
    Predicted to enable RNA polymerase II complex binding activity and SH2 domain binding activity. Predicted to be involved in several processes, including cell surface receptor signaling pathway; cellular response to lipopolysaccharide; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within blastocyst development and negative regulation of gene expression, epigenetic. Predicted to be located in euchromatin and nucleoplasm. Predicted to be part of Cdc73/Paf1 complex. Orthologous to human CTR9 (CTR9 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 172.0), Thymus (RPKM 158.9) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Ctr9 in Genome Data Viewer
    Location:
    1q33
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (174571952..174601974)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (165137277..165167303)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (175839140..175869167)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene lymphatic vessel endothelial hyaluronan receptor 1 Neighboring gene inositol 1,4,5-triphosphate receptor associated 1 Neighboring gene eukaryotic translation initiation factor 4, gamma 2 Neighboring gene small nucleolar RNA, C/D box 97 Neighboring gene zinc finger BED-type containing 5 like, pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding  
    enables SH2 domain binding  
    Process Evidence Code Pubs
    involved_in biological_process  
    acts_upstream_of_or_within blastocyst growth  
    acts_upstream_of_or_within blastocyst hatching  
    involved_in cell surface receptor signaling pathway via JAK-STAT  
    involved_in cellular response to lipopolysaccharide  
    involved_in chromatin organization  
    involved_in endodermal cell fate commitment  
    acts_upstream_of_or_within inner cell mass cell differentiation  
    involved_in interleukin-6-mediated signaling pathway  
    acts_upstream_of_or_within negative regulation of gene expression, epigenetic  
    involved_in negative regulation of myeloid cell differentiation  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in stem cell population maintenance  
    involved_in transcription elongation by RNA polymerase II  
    involved_in transcription elongation by RNA polymerase II  
    acts_upstream_of_or_within trophectodermal cell differentiation  
    Component Evidence Code Pubs
    part_of Cdc73/Paf1 complex  
    part_of Cdc73/Paf1 complex  
    located_in euchromatin  
    located_in nucleoplasm  
    located_in nucleus  

    General protein information

    Preferred Names
    RNA polymerase-associated protein CTR9 homolog
    Names
    Ctr9, Paf1/RNA polymerase II complex component, homolog
    SH2 domain binding protein 1 (tetratricopeptide repeat containing)

    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_001100661.1NP_001094131.1  RNA polymerase-associated protein CTR9 homolog

      See identical proteins and their annotated locations for NP_001094131.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A8I6A0W5, A6I832, G3V897
      Related
      ENSRNOP00000023741.5, ENSRNOT00000023741.9
      Conserved Domains (3) summary
      TIGR02917
      Location:110781
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:501525
      TPR; TPR repeat [structural motif]
      NF000535
      Location:9711173
      MSCRAMM_SdrC; MSCRAMM family adhesin SdrC

    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_086019.1 Reference GRCr8

      Range
      174571952..174601974
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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