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    CTR9 CTR9 homolog, Paf1/RNA polymerase II complex component [ Homo sapiens (human) ]

    Gene ID: 9646, updated on 5-May-2024

    Summary

    Official Symbol
    CTR9provided by HGNC
    Official Full Name
    CTR9 homolog, Paf1/RNA polymerase II complex componentprovided by HGNC
    Primary source
    HGNC:HGNC:16850
    See related
    Ensembl:ENSG00000198730 MIM:609366; AllianceGenome:HGNC:16850
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TSBP; p150; SH2BP1; p150TSP
    Summary
    The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones. [provided by RefSeq, Oct 2016]
    Expression
    Ubiquitous expression in testis (RPKM 19.1), thyroid (RPKM 14.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    11p15.4
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (10751246..10779746)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (10836160..10864657)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (10772793..10801293)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene IRAG1 antisense RNA 1 Neighboring gene lymphatic vessel endothelial hyaluronan receptor 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:10615146-10616345 Neighboring gene inositol 1,4,5-triphosphate receptor associated 1 Neighboring gene Sharpr-MPRA regulatory regions 8950 and 14430 Neighboring gene MPRA-validated peak1195 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4441 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:10678394-10679593 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:10680716-10681915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10696121-10696708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10697483-10697984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4444 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10772162-10772662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4447 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:10785333-10786532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:10813405-10813954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:10813955-10814504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4450 Neighboring gene uncharacterized LOC101928053 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10830951-10831557 Neighboring gene eukaryotic translation initiation factor 4 gamma 2 Neighboring gene small nucleolar RNA, C/D box 97

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0155

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables SH2 domain binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in blastocyst growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell surface receptor signaling pathway via JAK-STAT ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in endodermal cell fate commitment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner cell mass cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in interleukin-6-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of gene expression, epigenetic IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of myeloid cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in stem cell population maintenance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transcription elongation by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in transcription elongation by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in trophectodermal cell differentiation IEA
    Inferred from Electronic Annotation
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of euchromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     

    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)
    TPR-containing, SH2-binding phosphoprotein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_051671.1 RefSeqGene

      Range
      5260..33760
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001346279.2NP_001333208.1  RNA polymerase-associated protein CTR9 homolog isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC116535
      UniProtKB/TrEMBL
      A8K6X9
    2. NM_014633.5NP_055448.1  RNA polymerase-associated protein CTR9 homolog isoform 1

      See identical proteins and their annotated locations for NP_055448.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BP223102, BP250198, D63875
      Consensus CDS
      CCDS7805.1
      UniProtKB/Swiss-Prot
      D3DQV8, Q15015, Q6PD62
      UniProtKB/TrEMBL
      A8K6X9
      Related
      ENSP00000355013.2, ENST00000361367.7
      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]
      NF033609
      Location:10291173
      MSCRAMM_ClfA; MSCRAMM family adhesin clumping factor ClfA

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      10751246..10779746
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      10836160..10864657
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)