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    C9orf40 chromosome 9 open reading frame 40 [ Homo sapiens (human) ]

    Gene ID: 55071, updated on 10-Dec-2024

    Summary

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    Official Symbol
    C9orf40provided by HGNC
    Official Full Name
    chromosome 9 open reading frame 40provided by HGNC
    Primary source
    HGNC:HGNC:23433
    See related
    Ensembl:ENSG00000135045 AllianceGenome:HGNC:23433
    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
    Expression
    Broad expression in testis (RPKM 6.6), small intestine (RPKM 6.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C9orf40 in Genome Data Viewer
    Location:
    9q21.13
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (74946583..74952912, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (87099484..87105814, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (77561499..77567828, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene transient receptor potential cation channel subfamily M member 6 Neighboring gene RNA, U6 small nuclear 445, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr9:77490497-77490998 Neighboring gene Sharpr-MPRA regulatory region 214 Neighboring gene required for meiotic nuclear division 1 homolog (S. cerevisiae) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19952 Neighboring gene CARNMT1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:77579717-77580289 Neighboring gene carnosine N-methyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19954 Neighboring gene nicotinamide riboside kinase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
    2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Olsen JV, et al. Cell, 2006 Nov 3. PMID 17081983
    3. Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4-Associated Factors, Cellular Functions, and Protein Substrates. Raisch J, et al. Mol Cell Proteomics, 2023 Oct. PMID 37689310, Free PMC Article
    4. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Maruyama K, et al. Gene, 1994 Jan 28. PMID 8125298
    5. Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Wheat A, et al. Proc Natl Acad Sci U S A, 2021 Aug 10. PMID 34349018, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10110, FLJ25795

    General protein information

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    Preferred Names
    uncharacterized protein C9orf40

    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_017998.3 → NP_060468.2  uncharacterized protein C9orf40

      See identical proteins and their annotated locations for NP_060468.2

      Status: VALIDATED

      Source sequence(s)
      AK000972, AL158825, BC039588, BM126413
      Consensus CDS
      CCDS6648.1
      UniProtKB/Swiss-Prot
      Q8IXQ3, Q9NWD3
      Related
      ENSP00000366050.5, ENST00000376854.6
      Conserved Domains (1) summary
      pfam15017
      Location:149 → 193
      WRNPLPNID; Putative WW-binding domain and destruction box

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      74946583..74952912 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      87099484..87105814 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IXQ3.1 GenPept UniProtKB/Swiss-Prot:Q8IXQ3

    Gene LinkOut

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

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