CNOT1 CCR4-NOT transcription complex subunit 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CNOT1provided by HGNC
Official Full Name: CCR4-NOT transcription complex subunit 1provided by HGNC
Primary source: HGNC:HGNC:7877
See related: Ensembl:ENSG00000125107 MIM:604917; AllianceGenome:HGNC:7877
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NOT1; CDC39; HPE12; NOT1H; VIBOS; AD-005
Summary: Enables armadillo repeat domain binding activity; molecular adaptor activity; and nuclear receptor binding activity. Contributes to poly(A)-specific ribonuclease activity. Involved in several processes, including negative regulation of intracellular signal transduction; positive regulation of cytoplasmic mRNA processing body assembly; and regulation of gene expression. Located in P-body and cytosol. Part of CCR4-NOT complex. Implicated in Vissers-Bodmer syndrome and holoprosencephaly 12. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis (RPKM 56.3), esophagus (RPKM 28.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q21

Exon count:: 50

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (58519951..58629826, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (64315184..64422344, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (58553855..58663730, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Vissers-Bodmer syndrome caused by a novel de novo CNOT1 frameshift variant.
Title: Vissers-Bodmer syndrome caused by a novel de novo CNOT1 frameshift variant.
CCR4-NOT differentially controls host versus virus poly(a)-tail length and regulates HCMV infection.
Title: CCR4-NOT differentially controls host versus virus poly(a)-tail length and regulates HCMV infection.
Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements.
Title: Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements.
TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV.
Title: TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV.
Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization.
Title: Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization.
RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
Title: RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.
Title: Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.
ARE-binding protein ZFP36L1 interacts with CNOT1 to directly repress translation via a deadenylation-independent mechanism.
Title: ARE-binding protein ZFP36L1 interacts with CNOT1 to directly repress translation via a deadenylation-independent mechanism.
De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay.
Title: De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay.
A Quantitative Genetic Interaction Map of HIV Infection.
Title: A Quantitative Genetic Interaction Map of HIV Infection.

Submit: New GeneRIF Correction See all GeneRIFs (34)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Holoprosencephaly 12 with or without pancreatic agenesis MedGen: C5193131 OMIM: 618500 GeneReviews: Not available	Compare labs
Vissers-Bodmer syndrome MedGen: C5436647 OMIM: 619033 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2022-12-13) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2022-12-13) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A common variant in SLC8A1 is associated with the duration of the electrocardiographic QT interval. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at ten loci influence QT interval duration in the QTGEN Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at ten loci modulate the QT interval duration in the QTSCD Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. EBI GWAS Catalog EBI GWAS CatalogPubMed
Several common variants modulate heart rate, PR interval and QRS duration. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D16S2562E (e-PCR)
- UniSTS:27393

RH35951 (e-PCR)
- UniSTS:69380

RH70432 (e-PCR)
- UniSTS:74018

D16S3186 (e-PCR)
- UniSTS:17193

D16S2941 (e-PCR)
- UniSTS:7212

A002K05 (e-PCR)
- UniSTS:45133

RH69078 (e-PCR)
- UniSTS:18011

RH123148 (e-PCR)
- UniSTS:135529

SHGC-61172 (e-PCR)
- UniSTS:24175

RH41889 (e-PCR)
- UniSTS:47727

MARC_16903-16904:1022861972:1 (e-PCR)
- UniSTS:268150

A004F31 (e-PCR)
- UniSTS:16035

RH98939 (e-PCR)
- UniSTS:88814

Clone Names

FLJ36492, FLJ90644, KIAA1007, DKFZp686O168, DKFZp686E0722

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables armadillo repeat domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables molecular adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables molecular adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear estrogen receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear retinoic acid receptor binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to poly(A)-specific ribonuclease 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

Process	Evidence Code	Pubs
involved_in miRNA-mediated post-transcriptional gene silencing	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of intracellular estrogen receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of retinoic acid receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	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 cytoplasmic mRNA processing body assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in trophectodermal cell differentiation	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
located_in P-body	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in peroxisomal membrane	HDA more info	PubMed

General protein information

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Preferred Names: CCR4-NOT transcription complex subunit 1

Names: CCR4-associated factor 1; NOT1 (negative regulator of transcription 1, yeast) homolog; adrenal gland protein AD-005; negative regulator of transcription subunit 1 homolog

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_001265612.2 → NP_001252541.1 CCR4-NOT transcription complex subunit 1 isoform c

See identical proteins and their annotated locations for NP_001252541.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC009118, BC040523, BM023419, EF553522

Consensus CDS

CCDS58468.1

UniProtKB/Swiss-Prot

A5YKK6

Related

ENSP00000455635.1, ENST00000569240.5

Conserved Domains (2) summary

pfam16418
Location:500 → 650

CNOT1_HEAT; CCR4-NOT transcription complex subunit 1 HEAT repeat

cl26288
Location:835 → 2364

Not1; CCR4-Not complex component, Not1
NM_016284.5 → NP_057368.3 CCR4-NOT transcription complex subunit 1 isoform a

See identical proteins and their annotated locations for NP_057368.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC009118, AC010287, AL117492, AL833549, BM023419, BX537840

Consensus CDS

CCDS10799.1

UniProtKB/Swiss-Prot

A5YKK6, Q68DX7, Q7Z3K2, Q8IWB8, Q8TB53, Q9BVZ6, Q9UFR8, Q9UI27, Q9Y2L0

Related

ENSP00000320949.5, ENST00000317147.10

Conserved Domains (2) summary

pfam16418
Location:500 → 650

CNOT1_HEAT; CCR4-NOT transcription complex subunit 1 HEAT repeat

cl26288
Location:840 → 2369

Not1; CCR4-Not complex component, Not1
NM_206999.3 → NP_996882.1 CCR4-NOT transcription complex subunit 1 isoform b

See identical proteins and their annotated locations for NP_996882.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a.

Source sequence(s)

AC009118, AC010287, BC040523

Consensus CDS

CCDS45501.1

UniProtKB/Swiss-Prot

A5YKK6

Related

ENSP00000413113.2, ENST00000441024.6

Conserved Domains (4) summary

pfam12842
Location:1389 → 1480

DUF3819; Domain of unknown function (DUF3819)

pfam16415
Location:1088 → 1312

CNOT1_CAF1_bind; CCR4-NOT transcription complex subunit 1 CAF1-binding domain

pfam16417
Location:815 → 1004

CNOT1_TTP_bind; CCR4-NOT transcription complex subunit 1 TTP binding domain

pfam16418
Location:500 → 656

CNOT1_HEAT; CCR4-NOT transcription complex subunit 1 HEAT repeat

RNA

NR_049763.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice site and includes an alternate internal exon, 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)

AC009118, AC010287, AL833549, BM023419, BX537840, DB456343

Related

ENST00000567188.5