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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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    See CNOT10 in Genome Data Viewer
    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

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

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