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    CNOT2 CCR4-NOT transcription complex subunit 2 [ Homo sapiens (human) ]

    Gene ID: 4848, updated on 3-Dec-2024

    Summary

    Official Symbol
    CNOT2provided by HGNC
    Official Full Name
    CCR4-NOT transcription complex subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:7878
    See related
    Ensembl:ENSG00000111596 MIM:604909; AllianceGenome:HGNC:7878
    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
    NOT2; CDC36; NOT2H; HSPC131; IDNADFS
    Summary
    This gene encodes a subunit of the multi-component CCR4-NOT complex. The CCR4-NOT complex regulates mRNA synthesis and degradation and is also thought to be involved in mRNA splicing, transport and localization. The encoded protein interacts with histone deacetylases and functions as a repressor of polymerase II transcription. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
    Expression
    Ubiquitous expression in bone marrow (RPKM 13.7), skin (RPKM 12.9) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CNOT2 in Genome Data Viewer
    Location:
    12q15
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (70243018..70354993)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (70222411..70334463)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (70636798..70748773)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene histone PARylation factor 1 pseudogene Neighboring gene MPRA-validated peak1797 silencer Neighboring gene MPRA-validated peak1798 silencer Neighboring gene long intergenic non-protein coding RNA 2821 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:70636499-70637698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6658 Neighboring gene progenitor renewal associated non-coding RNA Neighboring gene MPRA-validated peak1799 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:70650862-70651362 Neighboring gene NANOG hESC enhancer GRCh37_chr12:70652346-70652879 Neighboring gene MPRA-validated peak1802 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4656 Neighboring gene MPRA-validated peak1805 silencer Neighboring gene potassium calcium-activated channel subfamily M regulatory beta subunit 4 Neighboring gene MPRA-validated peak1806 silencer Neighboring gene RNA, U4 small nuclear 65, pseudogene

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2022-11-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2022-11-08)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ26456

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to poly(A)-specific ribonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables transcription corepressor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in membrane HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    CCR4-NOT transcription complex subunit 2
    Names
    CC chemokine receptor 4-negative regulator of transcription 2
    CCR4-associated factor 2
    negative regulator of transcription 2

    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_001199302.2NP_001186231.1  CCR4-NOT transcription complex subunit 2 isoform a

      See identical proteins and their annotated locations for NP_001186231.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 and 5 all encode the same isoform (a).
      Source sequence(s)
      AA234384, AC025569, AC092881, AK315715, BC002597
      Consensus CDS
      CCDS31857.1
      UniProtKB/Swiss-Prot
      Q9H3E0, Q9NSX5, Q9NWR6, Q9NZN8, Q9P028
      UniProtKB/TrEMBL
      B3KTL6
      Related
      ENSP00000412091.3, ENST00000418359.7
      Conserved Domains (1) summary
      pfam04153
      Location:396519
      NOT2_3_5; NOT2 / NOT3 / NOT5 family
    2. NM_001199303.2NP_001186232.1  CCR4-NOT transcription complex subunit 2 isoform a

      See identical proteins and their annotated locations for NP_001186232.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1-3 and 5 all encode the same isoform (a).
      Source sequence(s)
      AA234384, AC025569, AK095789, AK307479, BC002597
      Consensus CDS
      CCDS31857.1
      UniProtKB/Swiss-Prot
      Q9H3E0, Q9NSX5, Q9NWR6, Q9NZN8, Q9P028
      UniProtKB/TrEMBL
      B3KTL6
      Related
      ENSP00000449260.1, ENST00000551043.5
      Conserved Domains (1) summary
      pfam04153
      Location:396519
      NOT2_3_5; NOT2 / NOT3 / NOT5 family
    3. NM_001414651.1NP_001401580.1  CCR4-NOT transcription complex subunit 2 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/Swiss-Prot
      Q9H3E0, Q9NSX5, Q9NWR6, Q9NZN8, Q9P028
      UniProtKB/TrEMBL
      B3KTL6
    4. NM_001414652.1NP_001401581.1  CCR4-NOT transcription complex subunit 2 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6
    5. NM_001414653.1NP_001401582.1  CCR4-NOT transcription complex subunit 2 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VV52
      Related
      ENSP00000449659.1, ENST00000548159.5
    6. NM_001414654.1NP_001401583.1  CCR4-NOT transcription complex subunit 2 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VV52
    7. NM_001414655.1NP_001401584.1  CCR4-NOT transcription complex subunit 2 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VV52
    8. NM_001414656.1NP_001401585.1  CCR4-NOT transcription complex subunit 2 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6
    9. NM_001414657.1NP_001401586.1  CCR4-NOT transcription complex subunit 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VUB4
    10. NM_001414658.1NP_001401587.1  CCR4-NOT transcription complex subunit 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VUB4
    11. NM_001414659.1NP_001401588.1  CCR4-NOT transcription complex subunit 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VUB4
    12. NM_001414660.1NP_001401589.1  CCR4-NOT transcription complex subunit 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6, F8VUB4
      Related
      ENSP00000448024.2, ENST00000550641.6
    13. NM_001414661.1NP_001401590.1  CCR4-NOT transcription complex subunit 2 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B3KTL6
    14. NM_001414662.1NP_001401591.1  CCR4-NOT transcription complex subunit 2 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC025569, AC092881
      UniProtKB/TrEMBL
      B2RDX7, B3KTL6
    15. NM_014515.7NP_055330.1  CCR4-NOT transcription complex subunit 2 isoform a

      See identical proteins and their annotated locations for NP_055330.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-3 and 5 all encode the same isoform (a).
      Source sequence(s)
      AC025569, AC092881
      Consensus CDS
      CCDS31857.1
      UniProtKB/Swiss-Prot
      Q9H3E0, Q9NSX5, Q9NWR6, Q9NZN8, Q9P028
      UniProtKB/TrEMBL
      B3KTL6
      Related
      ENSP00000229195.3, ENST00000229195.8
      Conserved Domains (1) summary
      pfam04153
      Location:396519
      NOT2_3_5; NOT2 / NOT3 / NOT5 family

    RNA

    1. NR_037615.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an alternate internal exon compared to variant 1. This variant is represented as non-coding because 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)
      AA234384, AC025569, AK307479, BC002597

    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

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      70243018..70354993
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428882.1XP_047284838.1  CCR4-NOT transcription complex subunit 2 isoform X2

      UniProtKB/TrEMBL
      B3KTL6, F8VUB4
    2. XM_017019348.2XP_016874837.1  CCR4-NOT transcription complex subunit 2 isoform X1

      UniProtKB/TrEMBL
      B3KTL6, F8VV52
      Conserved Domains (1) summary
      pfam04153
      Location:387510
      NOT2_3_5; NOT2 / NOT3 / NOT5 family
    3. XM_024448986.2XP_024304754.1  CCR4-NOT transcription complex subunit 2 isoform X5

      Conserved Domains (1) summary
      pfam04153
      Location:250373
      NOT2_3_5; NOT2 / NOT3 / NOT5 family
    4. XM_006719433.5XP_006719496.1  CCR4-NOT transcription complex subunit 2 isoform X4

      See identical proteins and their annotated locations for XP_006719496.1

      Conserved Domains (1) summary
      pfam04153
      Location:259382
      NOT2_3_5; NOT2 / NOT3 / NOT5 family
    5. XM_047428885.1XP_047284841.1  CCR4-NOT transcription complex subunit 2 isoform X3

    6. XM_024448988.2XP_024304756.1  CCR4-NOT transcription complex subunit 2 isoform X6

    7. XM_047428886.1XP_047284842.1  CCR4-NOT transcription complex subunit 2 isoform X4

    8. XM_047428884.1XP_047284840.1  CCR4-NOT transcription complex subunit 2 isoform X2

      UniProtKB/TrEMBL
      B3KTL6, F8VUB4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      70222411..70334463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372116.1XP_054228091.1  CCR4-NOT transcription complex subunit 2 isoform X2

      UniProtKB/TrEMBL
      B3KTL6, F8VUB4
    2. XM_054372115.1XP_054228090.1  CCR4-NOT transcription complex subunit 2 isoform X1

      UniProtKB/TrEMBL
      B3KTL6, F8VV52
    3. XM_054372121.1XP_054228096.1  CCR4-NOT transcription complex subunit 2 isoform X8

    4. XM_054372119.1XP_054228094.1  CCR4-NOT transcription complex subunit 2 isoform X7

    5. XM_054372118.1XP_054228093.1  CCR4-NOT transcription complex subunit 2 isoform X3

    6. XM_054372122.1XP_054228097.1  CCR4-NOT transcription complex subunit 2 isoform X6

    7. XM_054372120.1XP_054228095.1  CCR4-NOT transcription complex subunit 2 isoform X7

    8. XM_054372117.1XP_054228092.1  CCR4-NOT transcription complex subunit 2 isoform X2

      UniProtKB/TrEMBL
      B3KTL6, F8VUB4