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C9orf96 Gene

protein-coding   GIFtS: 38
GCID: GC09P136243

Chromosome 9 Open Reading Frame 96

  Search for C9orf96
at  

(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 961 2
Sugen Kinase 0712 3
SgK0712
Sk5212
Probable Inactive Protein Kinase-Like Protein SgK0712

External Ids:    HGNC: 286691   Entrez Gene: 1694362   Ensembl: ENSG000001988707   UniProtKB: Q8NE283   

Export aliases for C9orf96 gene to outside databases

Previous GC identifers: GC09P131520 GC09P133272 GC09P135233 GC09P105743


(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 C9orf96 Gene:
C9orf96 (chromosome 9 open reading frame 96) is a protein-coding gene. GO annotations related to this gene include protein kinase activity.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the C9orf96 gene promoter:
         HFH-3   Lmo2   STAT5A   Nkx2-5   HNF-3beta   C/EBPalpha   FOXL1   FOXI1   HOXA5   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C9orf96

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf96


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

Entrez Gene cytogenetic band: 9q34.2   Ensembl cytogenetic band:  9q34.2   HGNC cytogenetic band: 9q34.2

C9orf96 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf96 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P136243:  view genomic region     (about GC identifiers)

Start:
136,243,117 bp from pter      End:
136,271,220 bp from pter
Size:
28,104 bases      Orientation:
plus strand

1 alternative location:
Chr9+,NW_003315925 202,507-232,190     

(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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SGK71_HUMAN, Q8NE28 (See protein sequence)
Recommended Name: Probable inactive protein kinase-like protein SgK071  
Size: 680 amino acids; 75676 Da
Caution: Asn-157 is present instead of the conserved Asp which is expected to be an active site residue
Secondary accessions: Q5T8U8 Q6ZMP6 Q6ZMQ5
Alternative splicing: 3 isoforms:  Q8NE28-1   Q8NE28-2   Q8NE28-3   

Explore the universe of human proteins at neXtProt for C9orf96: NX_Q8NE28

Explore proteomics data for C9orf96 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C9orf96 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_714921.4  
    ENSEMBL proteins: 
     ENSP00000361025   ENSP00000398807   ENSP00000361023  

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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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    IUPHAR Guide to PHARMACOLOGY protein family classification: chromosome 9 open reading frame 96
    Other-unique family

    3 InterPro protein domains:
     IPR011009 Kinase-like_dom
     IPR000719 Prot_kinase_dom
     IPR016024 ARM-type_fold

    Graphical View of Domain Structure for InterPro Entry Q8NE28

    ProtoNet protein and cluster: Q8NE28

    UniProtKB/Swiss-Prot: SGK71_HUMAN, Q8NE28
    Domain: The protein kinase domain is predicted to be catalytically inactive
    Similarity: Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. STKL subfamily
    Similarity: Contains 1 protein kinase domain


    C9orf96 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004672protein kinase activity IEA--
    GO:0004713protein tyrosine kinase activity ----
    GO:0005488binding ----
    GO:0005524ATP binding IEA--
    GO:0016301kinase activity ----
         
    C9orf96 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for C9orf96:
     Decreased substrate adherent c  Decreased viability with RAF26 

    Animal Models:
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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
    peroxisome1
    plasma membrane1

    (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 C9orf96
    Interactions:

        Search GeneGlobe Interaction Network for C9orf96

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006468protein phosphorylation ----

    C9orf96 for ontologies           About GeneDecksing



    (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 C9orf96 (SGK71)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for C9orf96 gene: 
    NM_153710.4  

    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000371957(uc004cdk.3) ENST00000468046 ENST00000475232 ENST00000462310
    ENST00000477284 ENST00000426926 ENST00000371955(uc004cdl.3)
    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate C9orf96:
    hsa-miR-3690 hsa-miR-4254
    SwitchGear 3'UTR luciferase reporter plasmidC9orf96 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat C9orf96
      QuantiFast Probe-based Assays in human, mouse, rat C9orf96

    Selected AceView cDNA sequences (see all 30):

    BX114483 BC036504 AL044935 BQ944986 AI936591 NM_153710 AV763896 BQ184985 
    BM015576 AK131533 Z39384 BX454132 AI554166 Z43309 AI658791 AK131545 
    AW183662 BF983763 BI913727 AA418660 CD630108 AI799141 CB050444 BI458908 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for C9orf96    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
    SP1:                                                  -                       -           -                                 
    SP2:                                                                                                                        
    SP3:                                            -     -     -     -           -                                             
    SP4:                                                                                                                        


    ECgene alternative splicing isoforms for C9orf96

    (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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    C9orf96 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGTAACTGCT
    C9orf96 Expression
    About this image

    C9orf96 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C9orf96 Protein Expression
        Custom PCR Arrays for C9orf96
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    In Situ
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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 C9orf96 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Gm7111 , 5 predicted gene 7111, 5 72.94(n)1
    62.34(a)1
      2 (19.12 cM)5
    2790291  NM_198628.21  NP_941030.21 
     269340475 
    chicken
    (Gallus gallus)
    Aves C17H9ORF961 chromosome 17 open reading frame, human C9orf96 51.97(n)
    38.93(a)
      417154  XM_004945935.1  XP_004945992.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    31(a)
    29(a)
    1 ↔ many
    1 ↔ many
    AAWZ02040132(99-7103)
    GL344658.1(17803-27321)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004919151 chromosome unknown open reading frame, human C9orf96 49.08(n)
    33.39(a)
      100491915  XM_002942276.2  XP_002942322.2 


    ENSEMBL Gene Tree for C9orf96 (if available)
    TreeFam Gene Tree for C9orf96 (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 C9orf96 (see all 774)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1475046731,2
    --136245095(+) AAGGCC/TGGATT 1 -- int10--------
    rs1159982341,2
    C,F--136245228(+) ATCCCC/TGGCCC 1 -- int11Minor allele frequency- T:0.10WA 118
    rs1402420811,2
    --136245229(+) TCCCCA/GGCCCA 1 -- int10--------
    rs1391805211,2
    C--136245285(+) GGTGG-/CCA   
       TCTCT
    CCAGA
    1 -- int10--------
    rs1429707761,2
    --136245416(+) CCCCAA/GTGTAA 1 -- int10--------
    rs1122719151,2
    C--136245686(+) AGAAG-/AGCTCC 1 -- int11Minor allele frequency- A:0.50CSA 2
    rs1852743011,2
    --136245758(+) GGGCCA/CTTTCC 1 -- int10--------
    rs78528031,2
    C,F,A,H--136245903(+) TGCTGA/GTAGGT 1 -- int122Minor allele frequency- G:0.11NA EA NS CSA WA EU 3790
    rs563601061,2
    C--136245912(+) GTTTTA/GTACCA 2 L syn10--------
    rs1469009351,2
    C,F--136245917(+) GTACCA/GGCTGA 2 Q R mis11Minor allele frequency- G:0.00NA 4552

    HapMap Linkage Disequilibrium report for C9orf96 (136243117 - 136271220 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for C9orf96:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2657001CNV Deletion23128226
    esv2739138CNV Deletion23290073
    nsv512995CNV Insertion21212237
    nsv512996CNV Insertion21212237
    nsv894081CNV Loss21882294
    nsv894076CNV Loss21882294
    dgv8325n71CNV Loss21882294
    nsv894080CNV Loss21882294
    nsv433408CNV Gain18776910

    Site Specific Mutation Identification with PCR Assays
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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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    C9orf96 for disorders           About GeneDecksing

    Genetic Association Database (GAD): C9orf96

    Export disorders for C9orf96 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 C9orf96 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C9orf96)
        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. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    4. The protein kinase complement of the human genome. (PubMed id 12471243)1, 2 Manning G.... Sudarsanam S. (Science 2002)
    5. 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)
    6. Linkage analysis identifies a locus for plasma von Willebrand factor undetected by genome-wide association. (PubMed id 23267103)1 Desch K.C....Ginsburg D. (Proc. Natl. Acad. Sci. U.S.A. 2013)
    7. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. (PubMed id 19729612)4 Paterson A.D....Bull S.B. (Arterioscler. Thromb. Vasc. Biol. 2009)
    8. Patterns of somatic mutation in human cancer genomes. (PubMed id 17344846)2 Greenman C.... Stratton M.R. (Nature 2007)

    (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: 169436 HGNC: 28669 AceView: C9orf96 Ensembl:ENSG00000198870 euGenes: HUgn169436
    ECgene: C9orf96 H-InvDB: C9orf96

    (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 C9orf96 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 C9orf96 gene:
    Search GeneIP for patents involving C9orf96

    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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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 inGenious Targeting Laboratory, genOway)
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