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

Gene ID: 9125, updated on 7-Jun-2020

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
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

Genomic context

See CNOT9 in Genome Data Viewer
Location:
2q35
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (218568578..218597080)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219433303..219461158)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene villin 1 Neighboring gene ubiquitin specific peptidase 37 Neighboring gene RN7SK pseudogene 38 Neighboring gene RNA, U6 small nuclear 136, pseudogene Neighboring gene tRNA-Gln (anticodon CTG) 16-1 Neighboring gene phospholipase C delta 4 Neighboring gene zinc finger protein 142

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
epidermal growth factor receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
CCR4-NOT complex IDA
Inferred from Direct Assay
more info
PubMed 
CCR4-NOT core complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
P-body ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
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)

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_001271634.2NP_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/Swiss-Prot
    Q92600
    Related
    ENSP00000486540.1, ENST00000627282.2
    Conserved Domains (1) summary
    pfam04078
    Location:33315
    Rcd1; Cell differentiation family, Rcd1-like
  2. NM_001271635.1NP_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, DC299874
    Consensus CDS
    CCDS63123.1
    UniProtKB/Swiss-Prot
    Q92600
    Related
    ENSP00000295701.5, ENST00000295701.9
    Conserved Domains (1) summary
    pfam04078
    Location:25244
    Rcd1; Cell differentiation family, Rcd1-like
  3. NM_005444.3NP_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
    Q92600
    UniProtKB/TrEMBL
    D5MQE1
    Related
    ENSP00000273064.6, ENST00000273064.10
    Conserved Domains (1) summary
    pfam04078
    Location:25283
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    218568578..218597080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005249.2XP_016860738.1  CCR4-NOT transcription complex subunit 9 isoform X3

  2. XM_011512138.3XP_011510440.1  CCR4-NOT transcription complex subunit 9 isoform X1

    Conserved Domains (1) summary
    pfam04078
    Location:16230
    Rcd1; Cell differentiation family, Rcd1-like
  3. XM_017005248.1XP_016860737.1  CCR4-NOT transcription complex subunit 9 isoform X2

    Conserved Domains (1) summary
    pfam04078
    Location:1229
    Rcd1; Cell differentiation family, Rcd1-like
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