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C15orf40 chromosome 15 open reading frame 40 [ Homo sapiens (human) ]

Gene ID: 123207, updated on 17-Jun-2024

Summary

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Official Symbol
C15orf40provided by HGNC
Official Full Name
chromosome 15 open reading frame 40provided by HGNC
Primary source
HGNC:HGNC:28443
See related
Ensembl:ENSG00000169609 AllianceGenome:HGNC:28443
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 active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in colon (RPKM 4.0), placenta (RPKM 3.8) and 25 other tissues See more
Orthologs
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Genomic context

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See C15orf40 in Genome Data Viewer
Location:
15q25.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (82988963..83011639, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (80853334..80875980, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (83657715..83680391, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6756 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:83501038-83502237 Neighboring gene WASP homolog associated with actin, golgi membranes and microtubules Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:83518553-83519328 Neighboring gene homer scaffold protein 2 Neighboring gene uncharacterized LOC105370928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:83620722-83621222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:83632148-83632648 Neighboring gene Sharpr-MPRA regulatory region 12194 Neighboring gene RNA guanine-7 methyltransferase activating subunit Neighboring gene uncharacterized LOC124903542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9968 Neighboring gene BTB domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6758 Neighboring gene fatty acid binding protein 5 pseudogene 8 Neighboring gene microRNA 4515

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. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Choy KW, et al. Physiol Genomics, 2006 Mar 13. PMID 16368877
  2. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776
  3. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article
  4. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Brandenberger R, et al. Nat Biotechnol, 2004 Jun. PMID 15146197
  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 (15) 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

  • FLJ33606, MGC29937

Gene Ontology Provided by GOA

Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
UPF0235 protein C15orf40

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_001160113.2 → NP_001153585.1  UPF0235 protein C15orf40 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform b which has a longer and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC022558, DC428269
    Conserved Domains (1) summary
    pfam02594
    Location:65 → 122
    DUF167; uncharacterized ACR, YggU family COG1872

  2. NM_001160114.2 → NP_001153586.1  UPF0235 protein C15orf40 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform c which has a distinct C-terminus with the same length compared to isoform a.
    Source sequence(s)
    AA905778, AL602775, AW105048, BE906569, DW416709
    UniProtKB/TrEMBL
    H3BMR1
    Related
    ENSP00000454502.1, ENST00000508990.2
    Conserved Domains (1) summary
    pfam02594
    Location:65 → 131
    DUF167; uncharacterized ACR, YggU family COG1872

  3. NM_001160115.2 → NP_001153587.1  UPF0235 protein C15orf40 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR and has multiple differences in the 3' coding region compared to variant 1. This results in a longer isoform (d) with a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC022558, AL602775, BY800475, CN347153, DW416709
    Consensus CDS
    CCDS53969.1
    UniProtKB/Swiss-Prot
    Q8WUR7
    Related
    ENSP00000403987.3, ENST00000451195.7
    Conserved Domains (1) summary
    pfam02594
    Location:65 → 122
    DUF167; uncharacterized ACR, YggU family COG1872

  4. NM_001160116.2 → NP_001153588.1  UPF0235 protein C15orf40 isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform e which has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL602775, BQ185982, DW416709
    Consensus CDS
    CCDS53968.1
    UniProtKB/Swiss-Prot
    Q8WUR7
    Related
    ENSP00000441077.2, ENST00000538348.6
    Conserved Domains (1) summary
    pfam02594
    Location:65 → 122
    DUF167; uncharacterized ACR, YggU family COG1872

  5. NM_144597.3 → NP_653198.2  UPF0235 protein C15orf40 isoform a

    See identical proteins and their annotated locations for NP_653198.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (a).
    Source sequence(s)
    AC022558, AL602775, AW105048, BC019820, BQ013375, DW416709
    Consensus CDS
    CCDS32312.2
    UniProtKB/Swiss-Prot
    A6NIC9, B2R5E7, F5GX92, F8WD31, G5EA00, Q8WUR7
    UniProtKB/TrEMBL
    A0A0S2Z6M2
    Related
    ENSP00000307071.6, ENST00000304177.10
    Conserved Domains (1) summary
    pfam02594
    Location:65 → 133
    DUF167; uncharacterized ACR, YggU family COG1872

RNA

  1. NR_027649.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC022558, AL602775
    Related
    ENST00000506912.6

  2. NR_027650.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC022558, AI239480, AJ705316, AL602775, AW105048, BQ013375

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    82988963..83011639 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    80853334..80875980 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WUR7.2 GenPept UniProtKB/Swiss-Prot:Q8WUR7

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