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

Gene ID: 23019, updated on 3-May-2020

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
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; AD-005
Expression
Ubiquitous expression in testis (RPKM 56.3), esophagus (RPKM 28.6) and 25 other tissues See more
Orthologs

Genomic context

See CNOT1 in Genome Data Viewer
Location:
16q21
Exon count:
50
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (58519951..58629826, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58553850..58663790, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2137 Neighboring gene Sharpr-MPRA regulatory region 12894 Neighboring gene NDRG family member 4 Neighboring gene RNA, U6 small nuclear 103, pseudogene 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 pseudogene Neighboring gene solute carrier family 38 member 7 Neighboring gene glutamic-oxaloacetic transaminase 2 Neighboring gene RNY5 pseudogene 9

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?

Phenotypes

Associated conditions

Description Tests
HOLOPROSENCEPHALY 12 WITH OR WITHOUT PANCREATIC AGENESIS
MedGen: CN261026 OMIM: 618500 GeneReviews: Not available
not available

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ36492, FLJ90644, KIAA1007, DKFZp686O168, DKFZp686E0722

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
armadillo repeat domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
estrogen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
molecular adaptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
molecular adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to poly(A)-specific ribonuclease activity IDA
Inferred from Direct Assay
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 
retinoic acid receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest TAS
Traceable Author Statement
more info
 
RNA phosphodiester bond hydrolysis, exonucleolytic IEA
Inferred from Electronic Annotation
more info
 
gene silencing by miRNA IDA
Inferred from Direct Assay
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of intracellular estrogen receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of retinoic acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA poly(A) tail shortening TAS
Traceable Author Statement
more info
 
positive regulation of cytoplasmic mRNA processing body assembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of nuclear-transcribed mRNA poly(A) tail shortening IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of nuclear-transcribed mRNA poly(A) tail shortening IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of stem cell population maintenance IMP
Inferred from Mutant Phenotype
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 IDA
Inferred from Direct Assay
more info
PubMed 
P-body ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
membrane HDA PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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_001265612.2NP_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:500650
    CNOT1_HEAT; CCR4-NOT transcription complex subunit 1 HEAT repeat
    cl26288
    Location:8352364
    Not1; CCR4-Not complex component, Not1
  2. NM_016284.5NP_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
    Related
    ENSP00000320949.5, ENST00000317147.10
    Conserved Domains (2) summary
    pfam16418
    Location:500650
    CNOT1_HEAT; CCR4-NOT transcription complex subunit 1 HEAT repeat
    cl26288
    Location:8402369
    Not1; CCR4-Not complex component, Not1
  3. NM_206999.3NP_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:13891480
    DUF3819; Domain of unknown function (DUF3819)
    pfam16415
    Location:10881312
    CNOT1_CAF1_bind; CCR4-NOT transcription complex subunit 1 CAF1-binding domain
    pfam16417
    Location:8151004
    CNOT1_TTP_bind; CCR4-NOT transcription complex subunit 1 TTP binding domain
    pfam16418
    Location:500656
    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: 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_000016.10 Reference GRCh38.p13 Primary Assembly

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