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

Gene ID: 9646, updated on 10-Dec-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
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Genomic context

See CTR9 in Genome Data Viewer
Location:
11p15.4
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (10751246..10779746)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (10836160..10864657)
RS_2024_09 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

General gene information

Clone Names

  • KIAA0155

Gene Ontology Provided by GOA

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

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)

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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.

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_2024_08

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)
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