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

Gene ID: 55071, updated on 17-Sep-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
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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: HPA RNA-seq normal tissues 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. 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)

Genotypes

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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