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

Gene ID: 23019, updated on 7-Apr-2024

Summary

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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 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 holoprosencephaly. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 56.3), esophagus (RPKM 28.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q21
Exon count:
50
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (58519951..58629826, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (64315184..64422344, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58553855..58663730, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7551 Neighboring gene long intergenic non-protein coding RNA 2137 Neighboring gene Sharpr-MPRA regulatory region 11516 Neighboring gene Sharpr-MPRA regulatory region 12894 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:58521475-58521826 Neighboring gene Sharpr-MPRA regulatory region 13659 Neighboring gene NDRG family member 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58529535-58530090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:58530091-58530646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58533905-58534721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58534722-58535539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58535540-58536356 Neighboring gene RNA, U6 small nuclear 103, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10930 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43903 Neighboring gene SET domain containing 6, protein lysine methyltransferase Neighboring gene small nucleolar RNA, H/ACA box 46 Neighboring gene small nucleolar RNA, H/ACA box 50A Neighboring gene transmembrane protein 254-like Neighboring gene uncharacterized LOC124903804 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58662807-58663483 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58663484-58664159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10933 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58718046-58718890 Neighboring gene solute carrier family 38 member 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:58732240-58732406 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:58733934-58734162 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:58751959-58753158 Neighboring gene Sharpr-MPRA regulatory region 2773 Neighboring gene glutamic-oxaloacetic transaminase 2 Neighboring gene RNY5 pseudogene 9

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements. Zhang Q, et al. Protein Sci, 2022 Mar. PMID 34923703, Free PMC Article
  2. Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization. Gillen SL, et al. Genome Biol, 2021 Oct 6. PMID 34615539, Free PMC Article
  3. Exome analysis of HIV patients submitted to dendritic cells therapeutic vaccine reveals an association of CNOT1 gene with response to the treatment. Moura R, et al. J Int AIDS Soc, 2014. PMID 24433985, Free PMC Article
  4. TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV. Matkovic R, et al. Nat Commun, 2022 Jan 10. PMID 35013187, Free PMC Article
  5. ARE-binding protein ZFP36L1 interacts with CNOT1 to directly repress translation via a deadenylation-independent mechanism. Otsuka H, et al. Biochimie, 2020 Jul. PMID 32311426

See all (188) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Common variants at ten loci influence QT interval duration in the QTGEN Study.
EBI GWAS Catalog
Common variants at ten loci modulate the QT interval duration in the QTSCD Study.
EBI GWAS Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
EBI GWAS Catalog
Several common variants modulate heart rate, PR interval and QRS duration.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ36492, FLJ90644, KIAA1007, DKFZp686O168, DKFZp686E0722

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA 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 PubMed 
located_in membrane HDA PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

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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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_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

  2. 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

  3. 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

  1. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    58519951..58629826 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    64315184..64422344 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A5YKK6.2 GenPept UniProtKB/Swiss-Prot:A5YKK6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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