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

    Gene ID: 23019, updated on 23-Nov-2023

    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 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CNOT1 in Genome Data Viewer
    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

    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: 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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ36492, FLJ90644, KIAA1007, DKFZp686O168, DKFZp686E0722

    Gene Ontology Provided by GOA

    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

    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)

    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_001265612.2NP_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, Q68DX7, Q7Z3K2, Q8IWB8, Q8TB53, Q9BVZ6, Q9UFR8, Q9UI27, Q9Y2L0
      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: 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)