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CNOT10 CCR4-NOT transcription complex subunit 10 [ Homo sapiens (human) ]

Gene ID: 25904, updated on 5-Mar-2024

Summary

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Official Symbol
CNOT10provided by HGNC
Official Full Name
CCR4-NOT transcription complex subunit 10provided by HGNC
Primary source
HGNC:HGNC:23817
See related
Ensembl:ENSG00000182973 MIM:620508; AllianceGenome:HGNC:23817
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
Summary
Predicted to be involved in mRNA catabolic process and negative regulation of translation. Located in membrane. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 18.8), thyroid (RPKM 7.6) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
3p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (32685188..32773875)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (32684705..32772074)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (32726680..32815367)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene IGBP1 pseudogene 3 Neighboring gene ribosomal protein L30 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14177 Neighboring gene uncharacterized LOC124905595 Neighboring gene CNOT10 antisense RNA 1 Neighboring gene SUGT1 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 10112 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:32821346-32822066 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32822067-32822788 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32822789-32823508 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:32828513-32828689 Neighboring gene ribosomal protein L23a pseudogene 43 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32841241-32842000 Neighboring gene Sharpr-MPRA regulatory region 2511 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:32859949-32860530 Neighboring gene MPRA-validated peak4592 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:32877349-32877906 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32878590-32879187 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32879188-32879784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32880383-32880978 Neighboring gene tripartite motif containing 71 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:32885158-32885753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32888797-32889377 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32895307-32895816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32897845-32898520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32902307-32902911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32905556-32906320 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32910977-32911780 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:32914193-32914996

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. Polymorphism of human immunoglobulin VH4 germ-line genes. Weng NP, et al. Eur J Immunol, 1992 Apr. PMID 1348029
  2. C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex. Mauxion F, et al. RNA Biol, 2013 Feb. PMID 23232451, Free PMC Article
  3. NOT10 and C2orf29/NOT11 form a conserved module of the CCR4-NOT complex that docks onto the NOT1 N-terminal domain. Bawankar P, et al. RNA Biol, 2013 Feb. PMID 23303381, Free PMC Article
  4. miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Fabian MR, et al. Nat Struct Mol Biol, 2011 Oct 7. PMID 21984185
  5. Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation. Raisch T, et al. Nat Commun, 2019 Jul 18. PMID 31320642, Free PMC Article

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Human CNOT10 and CNOT11 form a complex that interacts with the CNOT1 N-terminal domain.
    Title: NOT10 and C2orf29/NOT11 form a conserved module of the CCR4-NOT complex that docks onto the NOT1 N-terminal domain.
  2. CNOT11 interacts with the first amino acids of CNOT1 and with CNOT10 and is required for the association of CNOT10 with the CCR4-NOT complex.
    Title: C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex.
Submit: New GeneRIF Correction

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

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

  • FLJ12890, FLJ13165, DKFZp434K115

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of translation 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 regulatory ncRNA-mediated gene silencing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of CCR4-NOT complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
located_in cytosol TAS
Traceable Author Statement
more info
  
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 10

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)

  1. NM_001256741.2 → NP_001243670.1  CCR4-NOT transcription complex subunit 10 isoform 2

    See identical proteins and their annotated locations for NP_001243670.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC138972, AC139452
    Consensus CDS
    CCDS58821.1
    UniProtKB/TrEMBL
    E9PCN5
    Related
    ENSP00000329376.6, ENST00000331889.10
    Conserved Domains (2) summary
    COG0457
    Location:86 → 274
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:296 → 321
    TPR; TPR repeat [structural motif]

  2. NM_001256742.2 → NP_001243671.1  CCR4-NOT transcription complex subunit 10 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is longer and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC138972, AC139452
    Consensus CDS
    CCDS58822.1
    UniProtKB/Swiss-Prot
    Q9H9A5
    Related
    ENSP00000399862.2, ENST00000454516.7
    Conserved Domains (2) summary
    COG0457
    Location:146 → 334
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:356 → 381
    TPR; TPR repeat [structural motif]

  3. NM_001393366.1 → NP_001380295.1  CCR4-NOT transcription complex subunit 10 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC138972, AC139452
    Conserved Domains (2) summary
    COG0457
    Location:86 → 274
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:296 → 321
    TPR; TPR repeat [structural motif]

  4. NM_001393367.1 → NP_001380296.1  CCR4-NOT transcription complex subunit 10 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC138972, AC139452
    Conserved Domains (2) summary
    COG0457
    Location:86 → 274
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:296 → 321
    TPR; TPR repeat [structural motif]

  5. NM_001393368.1 → NP_001380297.1  CCR4-NOT transcription complex subunit 10 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC138972, AC139452
    Conserved Domains (2) summary
    COG0457
    Location:86 → 274
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:296 → 321
    TPR; TPR repeat [structural motif]

  6. NM_001393369.1 → NP_001380298.1  CCR4-NOT transcription complex subunit 10 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC138972, AC139452
    UniProtKB/TrEMBL
    E9PCN5
    Conserved Domains (2) summary
    COG0457
    Location:86 → 274
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:296 → 321
    TPR; TPR repeat [structural motif]

  7. NM_015442.3 → NP_056257.1  CCR4-NOT transcription complex subunit 10 isoform 1

    See identical proteins and their annotated locations for NP_056257.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AC138972, AC139452
    Consensus CDS
    CCDS2655.1
    UniProtKB/Swiss-Prot
    B7Z7L1, F8WAF2, Q9BU30, Q9H5J7, Q9H8X1, Q9H9A5, Q9H9W0, Q9HAH3, Q9UFJ2
    Related
    ENSP00000330060.5, ENST00000328834.10
    Conserved Domains (2) summary
    COG0457
    Location:86 → 274
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:296 → 321
    TPR; TPR repeat [structural motif]

RNA

  1. NR_046352.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks three exons and includes an alternate 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)
    AC138972, AC139452
    Related
    ENST00000435630.5

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    32685188..32773875
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713085.4 → XP_006713148.1  CCR4-NOT transcription complex subunit 10 isoform X2

    Conserved Domains (2) summary
    COG0457
    Location:146 → 334
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:356 → 381
    TPR; TPR repeat [structural motif]

  2. XM_006713084.4 → XP_006713147.1  CCR4-NOT transcription complex subunit 10 isoform X1

    Conserved Domains (2) summary
    COG0457
    Location:146 → 334
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:356 → 381
    TPR; TPR repeat [structural motif]

  3. XM_047447927.1 → XP_047303883.1  CCR4-NOT transcription complex subunit 10 isoform X3

  4. XM_011533566.3 → XP_011531868.1  CCR4-NOT transcription complex subunit 10 isoform X4

    Conserved Domains (2) summary
    COG0457
    Location:146 → 334
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:356 → 381
    TPR; TPR repeat [structural motif]

  5. XM_047447928.1 → XP_047303884.1  CCR4-NOT transcription complex subunit 10 isoform X5

  6. XM_011533567.3 → XP_011531869.1  CCR4-NOT transcription complex subunit 10 isoform X6

    Conserved Domains (1) summary
    sd00006
    Location:68 → 93
    TPR; TPR repeat [structural motif]

RNA

  1. XR_007095661.1 RNA Sequence

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791770.1 Reference GRCh38.p14 PATCHES

    Range
    53414..142101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333004.1 → XP_054188979.1  CCR4-NOT transcription complex subunit 10 isoform X2

  2. XM_054333003.1 → XP_054188978.1  CCR4-NOT transcription complex subunit 10 isoform X1

  3. XM_054333005.1 → XP_054188980.1  CCR4-NOT transcription complex subunit 10 isoform X3

  4. XM_054333006.1 → XP_054188981.1  CCR4-NOT transcription complex subunit 10 isoform X4

  5. XM_054333007.1 → XP_054188982.1  CCR4-NOT transcription complex subunit 10 isoform X5

  6. XM_054333008.1 → XP_054188983.1  CCR4-NOT transcription complex subunit 10 isoform X6

RNA

  1. XR_008485815.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    32684705..32772074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346086.1 → XP_054202061.1  CCR4-NOT transcription complex subunit 10 isoform X2

  2. XM_054346085.1 → XP_054202060.1  CCR4-NOT transcription complex subunit 10 isoform X1

  3. XM_054346087.1 → XP_054202062.1  CCR4-NOT transcription complex subunit 10 isoform X3

  4. XM_054346088.1 → XP_054202063.1  CCR4-NOT transcription complex subunit 10 isoform X4

  5. XM_054346089.1 → XP_054202064.1  CCR4-NOT transcription complex subunit 10 isoform X5

  6. XM_054346090.1 → XP_054202065.1  CCR4-NOT transcription complex subunit 10 isoform X6

RNA

  1. XR_008486698.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H9A5.1 GenPept UniProtKB/Swiss-Prot:Q9H9A5

Gene LinkOut

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