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

Gene ID: 123207, updated on 4-May-2020

Summary

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
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
Ubiquitous expression in colon (RPKM 4.0), placenta (RPKM 3.8) and 25 other tissues See more
Orthologs

Genomic context

See C15orf40 in Genome Data Viewer
Location:
15q25.2
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (82988297..83012298, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (83657715..83681050, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene WASP homolog associated with actin, golgi membranes and microtubules Neighboring gene homer scaffold protein 2 Neighboring gene uncharacterized LOC105370928 Neighboring gene RNA guanine-7 methyltransferase activating subunit Neighboring gene BTB domain containing 1 Neighboring gene fatty acid binding protein 5 pseudogene 8 Neighboring gene microRNA 4515

Genomic regions, transcripts, and products

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33606, MGC29937

Gene Ontology Provided by GOA

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

NCBI Reference Sequences (RefSeq)

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_001160113.2NP_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:65122
    DUF167; uncharacterized ACR, YggU family COG1872
  2. NM_001160114.2NP_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
    Related
    ENSP00000454502.1, ENST00000508990.2
    Conserved Domains (1) summary
    pfam02594
    Location:65131
    DUF167; uncharacterized ACR, YggU family COG1872
  3. NM_001160115.2NP_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:65122
    DUF167; uncharacterized ACR, YggU family COG1872
  4. NM_001160116.2NP_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:65122
    DUF167; uncharacterized ACR, YggU family COG1872
  5. NM_144597.3NP_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
    Q8WUR7
    Related
    ENSP00000307071.6, ENST00000304177.10
    Conserved Domains (1) summary
    pfam02594
    Location:65133
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    82988297..83012298 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521213.2XP_011519515.1  UPF0235 protein C15orf40 isoform X2

    Conserved Domains (1) summary
    pfam02594
    Location:65125
    DUF167; uncharacterized ACR, YggU family COG1872
  2. XM_006720385.2XP_006720448.1  UPF0235 protein C15orf40 isoform X3

    Conserved Domains (1) summary
    pfam02594
    Location:65122
    DUF167; uncharacterized ACR, YggU family COG1872
  3. XM_011521212.2XP_011519514.1  UPF0235 protein C15orf40 isoform X1

    Conserved Domains (1) summary
    pfam02594
    Location:65122
    DUF167; uncharacterized ACR, YggU family COG1872
  4. XM_011521214.2XP_011519516.1  UPF0235 protein C15orf40 isoform X4

    Conserved Domains (1) summary
    pfam02594
    Location:65122
    DUF167; uncharacterized ACR, YggU family COG1872
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