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

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

De novo variants in CNOT9 cause a neurodevelopmental disorder with or without epilepsy.
Title: De novo variants in CNOT9 cause a neurodevelopmental disorder with or without epilepsy.
overexpression of miR-361-5p might act as a suppressor in triple-negative breast cancer by targeting RQCD1 to inhibit the EGFR/PI3K/Akt signaling pathway
Title: Overexpression of miR-361-5p in triple-negative breast cancer (TNBC) inhibits migration and invasion by targeting RQCD1 and inhibiting the EGFR/PI3K/Akt pathway.
Data suggest that the CCR4-NOT transcription complex subunit 1 (CNOT1)-CCR4-NOT transcription complex subunit 9 (CNOT9) components stimulate deadenylation by the nuclease module.
Title: The central region of CNOT1 and CNOT9 stimulates deadenylation by the Ccr4-Not nuclease module.
Authors show that a novel interaction between TTP and the CCR4-NOT subunit, CNOT9, is required for recruitment of the deadenylase complex. In addition to CNOT1, CNOT9 is now included in the identified CCR4-NOT subunits shown to interact with TTP.
Title: Tryptophan-Mediated Interactions between Tristetraprolin and the CNOT9 Subunit Are Required for CCR4-NOT Deadenylase Complex Recruitment.
Data indicate a recurrent somatic C > T change causing a P131L mutation in the RQCD1 (Required for Cell Differentiation1 Homolog) gene identified through whole exome sequencing of 20 metastatic melanomas.
Title: Whole exome sequencing identifies a recurrent RQCD1 P131L mutation in cutaneous melanoma.
Crystal structure of the DDX6, CNOT9 and CNOT1 complex.
Title: A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing.
Crystal structures of the DDX6, CNOT1 and CNOT9 complexes.
Title: Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression.
Our findings in this study imply the functional mechanism of RQCD1 in the Akt activity regulation as a mediator in the EGFR-signaling pathway
Title: Critical involvement of RQCD1 in the EGFR-Akt pathway in mammary carcinogenesis.
Report involvement of RQCD1 overexpression, a novel cancer-testis antigen, in the Akt pathway in breast cancer cells.
Title: Involvement of RQCD1 overexpression, a novel cancer-testis antigen, in the Akt pathway in breast cancer cells.
CCR4 plays a role in the regulation of certain endogenous RARalpha target genes and RCD1 and CCR4 might mediate their function through their interaction with NIF-1
Title: Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102962 (e-PCR)
- UniSTS:97296

RH93385 (e-PCR)
- UniSTS:87324

RH45666 (e-PCR)
- UniSTS:34636

D2S2903 (e-PCR)
- UniSTS:42203

RH69436 (e-PCR)
- UniSTS:42741

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables epidermal growth factor receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear receptor coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cytokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of intracellular estrogen receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA poly(A) tail shortening	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of epidermal growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of peptidyl-serine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in sex differentiation	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
part_of CCR4-NOT complex	IDA Inferred from Direct Assay more info	PubMed
part_of CCR4-NOT complex	NAS Non-traceable Author Statement more info	PubMed
part_of CCR4-NOT core complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

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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)

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
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
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

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

218568839..218597080

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047446272.1 → XP_047302228.1 CCR4-NOT transcription complex subunit 9 isoform X2
XM_047446271.1 → XP_047302227.1 CCR4-NOT transcription complex subunit 9 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

219055409..219083622

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054344476.1 → XP_054200451.1 CCR4-NOT transcription complex subunit 9 isoform X2
XM_054344475.1 → XP_054200450.1 CCR4-NOT transcription complex subunit 9 isoform X1