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    CNOT9 CCR4-NOT transcription complex subunit 9 [ Homo sapiens (human) ]

    Gene ID: 9125, updated on 10-Dec-2024

    Summary

    Official Symbol
    CNOT9provided by HGNC
    Official Full Name
    CCR4-NOT transcription complex subunit 9provided by HGNC
    Primary source
    HGNC:HGNC:10445
    See related
    Ensembl:ENSG00000144580 MIM:612054; AllianceGenome:HGNC:10445
    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
    RCD1; CAF40; CT129; RCD-1; RQCD1
    Summary
    This gene encodes a member of the highly conserved RCD1 protein family. The encoded protein is a transcriptional cofactor and a core protein of the CCR4-NOT complex. It may be involved in signal transduction as well as retinoic acid-regulated cell differentiation and development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2012]
    Expression
    Ubiquitous expression in testis (RPKM 10.4), lymph node (RPKM 9.1) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CNOT9 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218568839..218597080)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (219055409..219083622)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219433562..219461803)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219289129-219289629 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:219290512-219290729 Neighboring gene villin 1 Neighboring gene Sharpr-MPRA regulatory region 3568 Neighboring gene ubiquitin specific peptidase 37 Neighboring gene NANOG hESC enhancer GRCh37_chr2:219366267-219366838 Neighboring gene RN7SK pseudogene 38 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219432917-219433544 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219433545-219434172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:219442335-219442835 Neighboring gene RNA, U6 small nuclear 136, pseudogene Neighboring gene uncharacterized LOC124906133 Neighboring gene phospholipase C delta 4 Neighboring gene tRNA-Gln (anticodon CTG) 16-1

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of CCR4-NOT complex PubMed 
    part_of CCR4-NOT complex PubMed 
    part_of CCR4-NOT core complex  
    is_active_in P-body  
    located_in P-body  
    located_in cytosol  
    located_in membrane PubMed 
    located_in nucleus  
    part_of protein-containing complex PubMed 

    General protein information

    Preferred Names
    CCR4-NOT transcription complex subunit 9
    Names
    RCD1 required for cell differentiation1 homolog
    cancer/testis antigen 129
    cell differentiation protein RCD1 homolog
    cell differentiation protein RQCD1 homolog
    protein involved in sexual development

    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.

    mRNA and Protein(s)

    1. NM_001271634.2 → NP_001258563.1  CCR4-NOT transcription complex subunit 9 isoform 1

      See identical proteins and their annotated locations for NP_001258563.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC012510, AK293281
      Consensus CDS
      CCDS63122.1
      UniProtKB/TrEMBL
      B2RE59
      Related
      ENSP00000486540.1, ENST00000627282.2
      Conserved Domains (1) summary
      pfam04078
      Location:33 → 315
      Rcd1; Cell differentiation family, Rcd1-like
    2. NM_001271635.2 → NP_001258564.1  CCR4-NOT transcription complex subunit 9 isoform 3

      See identical proteins and their annotated locations for NP_001258564.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the coding region and includes an alternate terminal exon, compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AA806815, AC012510, BC007102
      Consensus CDS
      CCDS63123.1
      UniProtKB/TrEMBL
      B2RE59
      Related
      ENSP00000295701.5, ENST00000295701.9
      Conserved Domains (1) summary
      pfam04078
      Location:25 → 244
      Rcd1; Cell differentiation family, Rcd1-like
    3. NM_005444.3 → NP_005435.1  CCR4-NOT transcription complex subunit 9 isoform 2

      See identical proteins and their annotated locations for NP_005435.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1.
      Source sequence(s)
      AC012510, BC137455, DC299874
      Consensus CDS
      CCDS33379.1
      UniProtKB/Swiss-Prot
      B2RPI0, B5MDQ4, B7Z1E5, Q92600, Q96IX4
      UniProtKB/TrEMBL
      B2RE59, D5MQE1
      Related
      ENSP00000273064.6, ENST00000273064.11
      Conserved Domains (1) summary
      pfam04078
      Location:25 → 283
      Rcd1; Cell differentiation family, Rcd1-like

    RNA

    1. NR_073390.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate internal exon in the coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC012510

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      218568839..218597080
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446272.1 → XP_047302228.1  CCR4-NOT transcription complex subunit 9 isoform X2

    2. XM_047446271.1 → XP_047302227.1  CCR4-NOT transcription complex subunit 9 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      219055409..219083622
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344476.1 → XP_054200451.1  CCR4-NOT transcription complex subunit 9 isoform X2

    2. XM_054344475.1 → XP_054200450.1  CCR4-NOT transcription complex subunit 9 isoform X1

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