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

    Gene ID: 123207, updated on 10-Dec-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
    Located in mitochondrion. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in colon (RPKM 4.0), placenta (RPKM 3.8) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (82988963..83011639, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (80853334..80875980, complement)
    RS_2024_09 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: 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. 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 (16) 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

    • FLJ33606, MGC29937

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    UPF0235 protein C15orf40

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_2024_08

    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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