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C10orf40 Gene

protein-coding   GIFtS: 29
GCID: GC10M061717

Chromosome 10 Open Reading Frame 40

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chromosome 10 Open Reading Frame 401 2

External Ids:    HGNC: 235241   Entrez Gene: 2830252   Ensembl: ENSG000002359317   UniProtKB: A4QN013   

Export aliases for C10orf40 gene to outside databases

Previous GC identifers: GC10M061062 GC10M061387 GC10U900730 GC10M055705


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for C10orf40 Gene:
C10orf40 (chromosome 10 open reading frame 40) is a protein-coding gene.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000010.10  NC_018921.2  NT_030059.14  
Regulatory elements:
   Regulatory transcription factor binding sites in the C10orf40 gene promoter:
         STAT5B   IRF-2   S8   LHX3b/Lhx3b   FOXC1   Chx10   LHX3a/Lhx3a   Pax-4a   Arnt   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C10orf40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C10orf40


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10q21.2   Ensembl cytogenetic band:  10q21.2   HGNC cytogenetic band: 10q21.3

C10orf40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C10orf40 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M061717:  view genomic region     (about GC identifiers)

Start:
61,715,188 bp from pter      End:
61,720,671 bp from pter
Size:
5,484 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CJ040_HUMAN, A4QN01 (See protein sequence)
Recommended Name: Putative uncharacterized protein C10orf40  
Size: 128 amino acids; 15288 Da
Secondary accessions: A6NCD0

Explore the universe of human proteins at neXtProt for C10orf40: NX_A4QN01

Explore proteomics data for C10orf40 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C10orf40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


    ENSEMBL proteins: 
     ENSP00000430990   ENSP00000391066   ENSP00000394188  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    ProtoNet protein and cluster: A4QN01


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Phenotypes:
         1 GenomeRNAi human phenotype for C10orf40:
     Decreased POU5F1-GFP protein e 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for C10orf40

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol1
    mitochondrion1
    nucleus1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for C10orf40
    Interactions:

        Search GeneGlobe Interaction Network for C10orf40

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for C10orf40 (CJ040)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for C10orf40 gene: 
    NM_001017982.1  

    Unigene Cluster for C10orf40:

    Chromosome 10 open reading frame 40
    Hs.522955  [show with all ESTs]
    Unigene Representative Sequence: CR933684
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000521074(uc021prf.1) ENST00000444900(uc001jku.3) ENST00000430888

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    Additional mRNA sequence: 

    BC038741.1 BC048976.2 BC119749.2 BC119750.2 BC126326.1 BC130402.1 CR933684.1 NR_024340.1 

    2 DOTS entries:

    DT.204440  DT.101957393 

    10 AceView cDNA sequences:

    BX105262 AI252778 BX642984 BG723969 AA776736 BC048976 BI463999 BC038741 
    BG724062 AA436670 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: GCCTAATTCC

    C10orf40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C10orf40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.522955
        Custom PCR Arrays for C10orf40
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of human and chimp.

    Orthologs for C10orf40 gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia C10orf406
    chromosome 10 open reading frame 40
    98(a)
    1 ↔ 1
    10(58310720-58311106)


    ENSEMBL Gene Tree for C10orf40 (if available)
    TreeFam Gene Tree for C10orf40 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for C10orf40 (see all 102)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1913033921,2
    --61717707(+) CTATTC/TAAAGT 1 -- ds50010--------
    rs1812107061,2
    C--61717833(+) CCCATC/TCCCAA 1 -- ds50010--------
    rs1853856791,2
    --61718003(+) AATAAA/CATGTC 1 -- nc-transcript-variant0--------
    rs1441079441,2
    --61718047(+) ATTAGG/TCCATG 1 -- nc-transcript-variant0--------
    rs1897475981,2
    --61718204(+) TCCCAA/GTTCCT 1 -- nc-transcript-variant0--------
    rs71006871,2
    C,A--61718274(+) GTAAGG/AGGACA 1 -- nc-transcript-variant1Minor allele frequency- A:0.00EU 591
    rs1409688841,2
    --61718327(+) CCTTAA/TAAAAA 1 -- nc-transcript-variant0--------
    rs1833923971,2
    --61718356(+) GCTGAG/TGAACT 1 -- nc-transcript-variant0--------
    rs71008391,2
    C,F,A,H--61718369(+) AAACCG/ATCTAA 1 -- nc-transcript-variant9Minor allele frequency- A:0.00NS EA NA EU 1481
    rs1474925031,2
    --61718390(+) TCTTTA/CTTTTT 1 -- nc-transcript-variant0--------

    HapMap Linkage Disequilibrium report for C10orf40 (61715188 - 61720671 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for C10orf40: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing C10orf40
    DNA2.0 Custom Variant and Variant Library Synthesis for C10orf40

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for C10orf40 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C10orf40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    2. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)2 Deloukas P.... Rogers J. (Nature 2004)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 283025 HGNC: 23524 AceView: C10orf40 Ensembl:ENSG00000235931 euGenes: HUgn283025
    ECgene: C10orf40 H-InvDB: C10orf40

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for C10orf40 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for C10orf40 gene:
    Search GeneIP for patents involving C10orf40

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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