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C9orf116 Gene

protein-coding   GIFtS: 39
GCID: GC09M138387

Chromosome 9 Open Reading Frame 116

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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 9 Open Reading Frame 1161 2     RbEST472
P53-Induced Expression 1 In Rb−/− Cells1 2     Pierce 12
P53-Induced Expression In RB-Null Cells Protein 12 3     UPF0691 Protein C9orf1162
PIERCE12 5     Pierce13

External Ids:    HGNC: 284351   Entrez Gene: 1381622   Ensembl: ENSG000001603457   OMIM: 6145025   UniProtKB: Q5BN463   

Export aliases for C9orf116 gene to outside databases

Previous GC identifers: GC09M133827 GC09M135612 GC09M137526 GC09M107848


(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 C9orf116 Gene:
C9orf116 (chromosome 9 open reading frame 116) 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_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the C9orf116 gene promoter:
         AhR   FOXF2   NRSF form 1   CUTL1   NRSF form 2   Max   N-Myc   Zic3   En-1   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidC9orf116 promoter sequence
   Search Chromatin IP Primers for C9orf116

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf116


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

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.3   HGNC cytogenetic band: 9q34.3

C9orf116 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf116 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M138387:  view genomic region     (about GC identifiers)

Start:
138,387,026 bp from pter      End:
138,393,580 bp from pter
Size:
6,555 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: CI116_HUMAN, Q5BN46 (See protein sequence)
Recommended Name: UPF0691 protein C9orf116  
Size: 136 amino acids; 15260 Da
Developmental stage: May be up-regulated during progression from G1 to S phase of the cell cycle. Maximal
expression in S or G2 phase
Secondary accessions: Q5T897 Q8WU44
Alternative splicing: 2 isoforms:  Q5BN46-1   Q5BN46-2   

Explore the universe of human proteins at neXtProt for C9orf116: NX_Q5BN46

Explore proteomics data for C9orf116 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C9orf116 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001041730.1  NP_653255.1  

    ENSEMBL proteins: 
     ENSP00000395281   ENSP00000360854   ENSP00000360856   ENSP00000396392  

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    antibodies-online antibodies for C9orf116 (9 products) 

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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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    1 InterPro protein domain:
     IPR026507 UPF0691

    Graphical View of Domain Structure for InterPro Entry Q5BN46

    ProtoNet protein and cluster: Q5BN46

    UniProtKB/Swiss-Prot: CI116_HUMAN, Q5BN46
    Similarity: Belongs to the UPF0691 family


    Find genes that share domains with C9orf116           About GenesLikeMe


    (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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    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for C9orf116

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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
    nucleus2
    cytosol1

    (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 C9orf116
    Interactions:

        Search GeneGlobe Interaction Network for C9orf116

    (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 C9orf116 (CI116)



    (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 C9orf116 gene (2 alternative transcripts): 
    NM_001048265.1  NM_144654.2  

    Unigene Cluster for C9orf116:

    Chromosome 9 open reading frame 116
    Hs.414028  [show with all ESTs]
    Unigene Representative Sequence: AK024007
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000429260(uc004cft.1) ENST00000371789(uc004cfu.1) ENST00000371791(uc004cfs.1)
    ENST00000371786 ENST00000419770
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    Additional mRNA sequence: 

    AK024007.1 AY927868.1 BC021261.1 

    6 DOTS entries:

    DT.453183  DT.92037578  DT.91658234  DT.100759007  DT.95372492  DT.40131213 

    Selected AceView cDNA sequences (see all 68):

    NM_144654 AA363224 AI582146 CK904799 AI924352 BC021261 BU634102 AW136460 
    BF116143 BI769148 CK904800 AW418521 AI367252 BM455428 BI838039 U46429 
    BF317009 AA344961 AI028337 BI838181 AI367250 BG166524 CA503250 AK024007 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for C9orf116    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c
    SP1:                    -               
    SP2:                                    


    ECgene alternative splicing isoforms for C9orf116

    (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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    C9orf116 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGAAAGATGC
    C9orf116 Expression
    About this image


    C9orf116 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Epiblast (Early Embryonic Tissues)
             Epiblast Stem Cell line 5
     
     Testis (Reproductive System)
    C9orf116 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C9orf116 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.414028
        Custom PCR Arrays for C9orf116
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    In Situ
    Assay Products:
     

     
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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 chordates.

    Orthologs for C9orf116 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1700007K13Rik1 , 5 RIKEN cDNA 1700007K13 gene1, 5 79.37(n)1
    75.4(a)1
      2 (19.38 cM)5
    693271  NM_027040.11  NP_081316.11 
     284620015 
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ068288.12   -- 73.12(n)    BJ068288.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch211-248e11.21 si:ch211-248e11.2 52.22(n)
    45(a)
      557793  NM_001123243.1  NP_001116715.1 


    ENSEMBL Gene Tree for C9orf116 (if available)
    TreeFam Gene Tree for C9orf116 (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 C9orf116 (see all 112)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs48419901,2
    C,F,A,H--138386557(+) CATCAC/TCCCCT 2 -- int112Minor allele frequency- T:0.36NS EA NA WA CSA 786
    rs48419911,2
    C,F,A,H--138386597(+) TCTCTA/GCCCCT 2 -- int121Minor allele frequency- G:0.40NS EA NA WA CSA 2224
    rs1841678141,2
    --138386623(+) CCTTGA/CTGGAG 2 -- int10--------
    rs1501874321,2
    --138386628(+) CTGGAA/GCATGA 2 -- int10--------
    rs38278301,2
    C,F,A--138386745(+) GAGGCG/ATCTGC 2 -- int111Minor allele frequency- A:0.38NA WA CSA EA 373
    rs38278311,2
    C,F,H--138386867(+) TAGGAC/TGGGAG 2 -- int18Minor allele frequency- T:0.01NS EA NA 928
    rs1931941601,2
    --138386928(+) CGAGCA/GGAGTT 2 -- int10--------
    rs1387505171,2
    --138386943(+) ACCAGC/TGCTCC 2 -- int10--------
    rs1845814281,2
    --138387042(+) ACAACA/GTTTTT 2 -- ut310--------
    rs1138982251,2
    C--138387119(+) GCCCCA/GTTTGC 2 -- ut310--------

    HapMap Linkage Disequilibrium report for C9orf116 (138387026 - 138393580 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for C9orf116 (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2739138CNV Deletion23290073
    nsv894251CNV Loss21882294
    dgv8367n71CNV Loss21882294
    dgv8366n71CNV Loss21882294
    nsv894253CNV Loss21882294
    nsv894246CNV Loss21882294
    nsv469913CNV Loss18288195
    nsv825164CNV Gain20364138
    nsv894247CNV Gain21882294
    nsv466656CNV Gain19166990

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    (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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    OMIM gene information: 614502    OMIM disorders: --


    Find genes that share disorders with C9orf116           About GenesLikeMe


    Export disorders for C9orf116 gene to outside databases

    (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 C9orf116 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C9orf116)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    2. 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. (Genome Res. 2004)
    3. 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)
    4. Identification of a novel Rb-regulated gene associated with the cell cycle. (PubMed id 18182857)2 Sung Y.H.... Lee H.W. (Mol. Cells 2007)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 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: 138162 HGNC: 28435 AceView: C9orf116 Ensembl:ENSG00000160345 euGenes: HUgn138162
    ECgene: C9orf116 H-InvDB: C9orf116

    (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 C9orf116 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 C9orf116 gene:
    Search GeneIP for patents involving C9orf116

    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
    Advanced Cell Diagnostics, Animal models from genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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