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C9orf50 chromosome 9 open reading frame 50 [ Homo sapiens (human) ]

Gene ID: 375759, updated on 27-Nov-2024

Summary

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Official Symbol
C9orf50provided by HGNC
Official Full Name
chromosome 9 open reading frame 50provided by HGNC
Primary source
HGNC:HGNC:23677
See related
Ensembl:ENSG00000179058 AllianceGenome:HGNC:23677
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
Biased expression in testis (RPKM 1.6), brain (RPKM 0.2) and 1 other tissue See more
Orthologs
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Genomic context

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See C9orf50 in Genome Data Viewer
Location:
9q34.11
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129612225..129621924, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141816825..141826511, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (132374504..132383380, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132252097-132252756 Neighboring gene extensin-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132252757-132253416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132253417-132254075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132256099-132256899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132256900-132257699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132257700-132258500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132258501-132259299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132259614-132260182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132260183-132260750 Neighboring gene long intergenic non-protein coding RNA 963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132287329-132287829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132310394-132310894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132317282-132317929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132318577-132319224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132319225-132319870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132320519-132321164 Neighboring gene HNF1 motif-containing MPRA enhancer 89 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332093-132332956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332957-132333820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132333821-132334682 Neighboring gene uncharacterized LOC105376292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132346053-132346610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132349961-132350644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132362549-132363048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132366575-132367074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132369161-132369798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373341-132373842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373843-132374342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132382842-132383492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29118 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132388415-132388953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132393630-132394420 Neighboring gene N-terminal Xaa-Pro-Lys N-methyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132402376-132402933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132402934-132403490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132409664-132410412 Neighboring gene ankyrin repeat and SOCS box containing 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132431437-132431938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132431939-132432438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132439411-132440254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132441550-132442050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132442051-132442551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132448034-132448578 Neighboring gene paired related homeobox 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132474701-132475516 Neighboring gene PRRX2 antisense RNA 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
  • 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. Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. Clark SL, et al. Psychol Med, 2012 Jun. PMID 22041458, Free PMC Article
  2. Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. Yu B, et al. Genet Epidemiol, 2013 Dec. PMID 23934736, Free PMC Article
  3. Identification of the human testis protein phosphatase 1 interactome. Fardilha M, et al. Biochem Pharmacol, 2011 Nov 15. PMID 21382349
  4. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073
  5. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Aregger M, et al. Nat Metab, 2020 Jun. PMID 32694731, Free PMC Article

See all (8) 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

EBI GWAS Catalog

Description
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
EBI GWAS Catalog
Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D.
EBI GWAS Catalog

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

  • FLJ35803

General protein information

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Preferred Names
uncharacterized protein C9orf50

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_199350.4 → NP_955382.3  uncharacterized protein C9orf50

    See identical proteins and their annotated locations for NP_955382.3

    Status: VALIDATED

    Source sequence(s)
    AL391056, AL590369
    Consensus CDS
    CCDS35159.1
    UniProtKB/Swiss-Prot
    Q2M1I2, Q5SZB4, Q8NA65
    Related
    ENSP00000361556.4, ENST00000372478.5
    Conserved Domains (1) summary
    pfam15737
    Location:193 → 301
    DUF4685; Domain of unknown function (DUF4685)

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
    129612225..129621924 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518656.2 → XP_011516958.1  uncharacterized protein C9orf50 isoform X1

    See identical proteins and their annotated locations for XP_011516958.1

    UniProtKB/Swiss-Prot
    Q2M1I2, Q5SZB4, Q8NA65
    Conserved Domains (1) summary
    pfam15737
    Location:193 → 301
    DUF4685; Domain of unknown function (DUF4685)

  2. XM_011518655.2 → XP_011516957.1  uncharacterized protein C9orf50 isoform X1

    See identical proteins and their annotated locations for XP_011516957.1

    UniProtKB/Swiss-Prot
    Q2M1I2, Q5SZB4, Q8NA65
    Conserved Domains (1) summary
    pfam15737
    Location:193 → 301
    DUF4685; Domain of unknown function (DUF4685)

  3. XM_011518658.3 → XP_011516960.2  uncharacterized protein C9orf50 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141816825..141826511 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362940.1 → XP_054218915.1  uncharacterized protein C9orf50 isoform X1

    UniProtKB/Swiss-Prot
    Q2M1I2, Q5SZB4, Q8NA65

  2. XM_054362941.1 → XP_054218916.1  uncharacterized protein C9orf50 isoform X1

    UniProtKB/Swiss-Prot
    Q2M1I2, Q5SZB4, Q8NA65

  3. XM_054362942.1 → XP_054218917.1  uncharacterized protein C9orf50 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SZB4.1 GenPept UniProtKB/Swiss-Prot:Q5SZB4

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