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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C9orf40 Gene

protein-coding   GIFtS: 41
GCID: GC09M077561

Chromosome 9 Open Reading Frame 40

  Search for C9orf40
at  

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

Aliases
Chromosome 9 Open Reading Frame 401 2
Uncharacterized Protein C9orf402

External Ids:    HGNC: 234331   Entrez Gene: 550712   Ensembl: ENSG000001350457   UniProtKB: Q8IXQ33   

Export aliases for C9orf40 gene to outside databases

Previous GC identifers: GC09M073018 GC09M074791 GC09M076751 GC09M047383


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for C9orf40 Gene: 
C9orf40 (chromosome 9 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.2  NT_008470.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C9orf40 gene promoter:
         GR   AML1a   POU3F1   GCNF   POU2F1   GCNF-1   POU2F1a   PPAR-gamma2   GR-alpha   GCNF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C9orf40

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C9orf40


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

Entrez Gene cytogenetic band: 9q21.13   Ensembl cytogenetic band:  9q21.13   HGNC cytogenetic band: 9q21.31

C9orf40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf40 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M077561:  view genomic region     (about GC identifiers)

Start:
77,561,497 bp from pter      End:
77,567,802 bp from pter
Size:
6,306 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CI040_HUMAN, Q8IXQ3 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf40  
Size: 194 amino acids; 21063 Da
Secondary accessions: Q9NWD3

Explore the universe of human proteins at neXtProt for C9orf40: NX_Q8IXQ3

Explore proteomics data for C9orf40 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8IXQ3

  • C9orf40 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    C9orf40 Protein Expression
    REFSEQ proteins: NP_060468.2  
    ENSEMBL proteins: 
     ENSP00000366050  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR020521 Uncharacterised_C9orf40

    Graphical View of Domain Structure for InterPro Entry Q8IXQ3

    ProtoNet protein and cluster: Q8IXQ3


    C9orf40 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidC9orf40 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C9orf40

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for C9orf40 (ENSP000003660504) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for C9orf40 (CI040)

    Search CenterWatch for drugs/clinical trials and news about C9orf40 / CI040

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for C9orf40 gene: 
    NM_017998.2  

    Unigene Cluster for C9orf40:

    Chromosome 9 open reading frame 40
    Hs.532296  [show with all ESTs]
    Unigene Representative Sequence: NM_017998
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000376854(uc004ajo.4)
    miRNA
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    hsa-miR-548j hsa-let-7d hsa-miR-106a hsa-miR-199a-3p hsa-let-7g hsa-let-7a hsa-miR-93 hsa-miR-548a-5p
    SwitchGear 3'UTR luciferase reporter plasmidC9orf40 3' UTR sequence
    Inhib. RNA
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    Primer
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    Additional mRNA sequence: 

    AK000972.1 AK225349.1 BC039588.1 

    2 DOTS entries:

    DT.313669  DT.95135879 

    24/84 AceView cDNA sequences (see all 84):

    CK819008 AW612715 BM126413 AW297437 BM126911 BC039588 AA251796 BU631993 
    AI625799 AI080231 CR596886 AI423542 BM785372 CD743157 AW276200 CR599227 
    AA766518 AA968731 AI681247 AA480970 NM_017998 AW383614 BE786144 BG260673 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    C9orf40 expression in normal human tissues (normalized intensities)      C9orf40 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGTCCTGAT
    C9orf40 Expression
    About this image


    C9orf40 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Gut Tube (Gastrointestinal Tract)
             Definitive endoderm-like cells ( A scalable, suspension protocol for derivation of...

    See C9orf40 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C9orf40

    SOURCE GeneReport for Unigene cluster: Hs.532296
        SABiosciences Custom PCR Arrays for C9orf40
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf40

    (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)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for C9orf40 gene from 1/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia D030056L22Rik1 , 5 RIKEN cDNA D030056L22 gene1, 5 75.1(n)1
    62.35(a)1
      19 (13.20 cM)5
    2259951  NM_177640.41  NP_808308.11 
     187132365 


    ENSEMBL Gene Tree for C9orf40 (if available)
    TreeFam Gene Tree for C9orf40 (if available)

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

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/145 SNPs in C9orf40 are shown (see all 145)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1833106341,2
    --77561000(+) TTTTCA/GTAAGT 1 -- ds50010--------
    rs111441661,2
    C,F,H--77561136(+) TAAACA/CACTTT 1 -- ds50017Minor allele frequency- C:0.11EA NS NA 630
    rs1874040181,2
    --77561215(+) GACAGA/GATTTT 1 -- ds50010--------
    rs1472920681,2
    C--77561302(+) ATCGT-/AAGTTG
            
    AAAAT
    1 -- ds50010--------
    rs1922501961,2
    --77561635(+) ATGCAA/GTACAG 1 -- ut310--------
    rs759250451,2
    F--77561704(+) ACACAA/CAAAAA 1 -- ut311Minor allele frequency- C:0.01NA 120
    rs1132597221,2
    C,F--77561715(+) ATCAAG/CTTTTT 1 -- ut311Minor allele frequency- C:0.50NA 2
    rs1154365481,2
    C,F--77561716(+) TCAAGT/GTTTTC 1 -- ut311Minor allele frequency- G:0.01WA 118
    rs1831349551,2
    --77561835(+) CTGGAC/TGCAGT 1 -- ut310--------
    rs1878566791,2
    --77561862(+) TTAATC/GACTGA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for C9orf40 (77561497 - 77567802 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for C9orf40:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv507518CNV Insertion20534489
    nsv518305CNV Loss19592680

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

    (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)
    About This Section

    PubMed articles for C9orf40 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with C9orf40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (2004)
    4. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    5. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    6. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    7. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (2009)
    8. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    9. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (PubMed id 18691976)2 Daub H.... Mann M. (2008)
    10. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 55071 HGNC: 23433 AceView: C9orf40 Ensembl:ENSG00000135045 euGenes: HUgn55071
    ECgene: C9orf40 H-InvDB: C9orf40

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for C9orf40 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for C9orf40 gene:
    Search GeneIP for patents involving C9orf40

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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