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C9orf135 Gene

protein-coding   GIFtS: 41
GCID: GC09P072435

Chromosome 9 Open Reading Frame 135

  Search for C9orf135
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 9 Open Reading Frame 1351 2
Uncharacterized Protein C9orf1352

External Ids:    HGNC: 314221   Entrez Gene: 1382552   Ensembl: ENSG000002047117   UniProtKB: Q5VTT23   
ORGUL members:         

Export aliases for C9orf135 gene to outside databases

Previous GC identifers: GC09P071625 GC09P042280


(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 C9orf135 Gene:
C9orf135 (chromosome 9 open reading frame 135) 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:
NC_000009.12  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C9orf135 gene promoter:
         Nkx3-1   Lmo2   HSF1 (long)   Nkx3-1 v1   HNF-1A   YY1   Nkx3-1 v2   HNF-1   Nkx3-1 v3   HSF1short   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C9orf135

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf135


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

Entrez Gene cytogenetic band: 9q21.12   Ensembl cytogenetic band:  9q21.12   HGNC cytogenetic band: 9q21.11

C9orf135 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf135 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P072435:  view genomic region     (about GC identifiers)

Start:
72,435,709 bp from pter      End:
72,521,148 bp from pter
Size:
85,440 bases      Orientation:
plus 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, 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: CI135_HUMAN, Q5VTT2 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf135  
Size: 229 amino acids; 26445 Da
Secondary accessions: B2RN61

Explore the universe of human proteins at neXtProt for C9orf135: NX_Q5VTT2

Explore proteomics data for C9orf135 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn75
  • Modification sites at PhosphoSitePlus

  • See C9orf135 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001010940.1  
    ENSEMBL proteins: 
     ENSP00000366402   ENSP00000431855   ENSP00000434032   ENSP00000436701   ENSP00000433973  
     ENSP00000433123  

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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:
     IPR027905 DUF4572

    Graphical View of Domain Structure for InterPro Entry Q5VTT2

    ProtoNet protein and cluster: Q5VTT2


    C9orf135 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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C9orf135
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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 UniProtKB/Swiss-Prot
    CI135_HUMAN, Q5VTT2: Membrane; Single-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    extracellular1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    C9orf135 for ontologies           About GeneDecksing


    (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 C9orf135
    Interactions:

        Search GeneGlobe Interaction Network for C9orf135

    (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 C9orf135 (CI135)



    (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 C9orf135 gene: 
    NM_001010940.1  

    Unigene Cluster for C9orf135:

    Chromosome 9 open reading frame 135
    Hs.444459  [show with all ESTs]
    Unigene Representative Sequence: NM_001010940
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000377197(uc004ahl.3 uc010moq.3 uc010mop.3) ENST00000527647
    ENST00000529446 ENST00000529131(uc011lrw.2) ENST00000466872(uc011lrx.2)
    ENST00000495399 ENST00000480564
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat C9orf135

    Additional mRNA sequence: 

    BC127686.1 BC127687.1 BC136709.1 BC144373.1 BC144374.1 BC144375.1 BC150564.1 

    4 DOTS entries:

    DT.99946013  DT.404735  DT.95301379  DT.92017153 

    22 AceView cDNA sequences:

    BE502978 AA948291 AI216761 AW014133 BI825449 AI768674 AA757101 CD684431 
    BX118754 CK126031 AA416815 AA416734 AA894567 BG193301 AA431486 BG192998 
    BF059207 BG182005 BG198579 BG213996 CA502919 BG218975 

    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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    C9orf135 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATGAGAGTGG
    C9orf135 Expression
    About this image


    C9orf135 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
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 8 entries
             Human embryonic stem cells (family)
             ESI-051   
     
     Testis (Reproductive System)
             Mature Sertoli Cells Seminiferous Tubules
    C9orf135 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C9orf135 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.444459
        Custom PCR Arrays for C9orf135
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf135

    (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 C9orf135 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1700028P14Rik1 , 5 RIKEN cDNA 1700028P14 gene1, 5 74.85(n)1
    63.6(a)1
      19 (18.44 cM)5
    674831  NM_026188.21  NP_080464.11 
     235587605 
    lizard
    (Anolis carolinensis)
    Reptilia C9orf1356
    chromosome 9 open reading frame 135
    45(a)
    1 ↔ 1
    2(49343176-49355994)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004856821 chromosome unknown open reading frame, human C9orf135 53.77(n)
    46.23(a)
      100485682  XM_002935587.2  XP_002935633.1 


    ENSEMBL Gene Tree for C9orf135 (if available)
    TreeFam Gene Tree for C9orf135 (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 C9orf135 (see all 1769)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs575675231,2
    C--42316509(+) AAAAA-/A/AA  
            
    CACAA
    1 -- int11NA 2
    rs1173178781,2
    C,F--72433739(+) ATATTG/AGTTTC 1 -- us2k11Minor allele frequency- A:0.05EA 120
    rs101142751,2
    C,F--72433773(+) CTAAAC/AGTAAG 1 -- us2k14Minor allele frequency- A:0.01NA 144
    rs1411603161,2
    --72433790(+) GAACAA/CATGAA 1 -- us2k10--------
    rs736472821,2
    C--72437692(+) TGGAAC/TGCTGT 1 -- int12Minor allele frequency- T:0.21WA 120
    rs1395796001,2
    --72437712(+) CAGCCA/GCTGCT 1 -- int10--------
    rs1450928581,2
    C--72437822(+) GCTACA/GTGTTG 1 -- int10--------
    rs111404651,2
    C,F,H--72437830(+) TTGGGG/TACATA 1 -- int19Minor allele frequency- T:0.10NS EA NA WA 664
    rs1885172651,2
    --72437849(+) GAAACA/CGATTC 1 -- int10--------
    rs1475638961,2
    --72437924(+) AGGGTA/GGCTGT 1 -- int10--------

    HapMap Linkage Disequilibrium report for C9orf135 (72435709 - 72521148 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for C9orf135:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv6552CNV Insertion18451855
    nsv524309CNV Loss19592680
    esv32574CNV Loss17666407
    nsv893439CNV Loss21882294
    nsv515734CNV Loss19592680
    nsv471310CNV Gain18288195
    nsv466416CNV Gain19166990
    nsv893438CNV Gain21882294
    nsv831612CNV Gain17160897
    nsv831611CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for C9orf135

    (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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    C9orf135 for disorders           About GeneDecksing

    Genetic Association Database (GAD): C9orf135
    Human Genome Epidemiology (HuGE) Navigator: C9orf135 (3 documents)

    Export disorders for C9orf135 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 C9orf135 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C9orf135)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A Bayesian approach to genetic association studies with family-based designs. (PubMed id 20818722)1, 4 Naylor M.G....Lange C. (Genet. Epidemiol. 2010)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)1, 2 Liu T.... Smith R.D. (J. Proteome Res. 2005)
    4. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    5. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. (PubMed id 17903297)4 Seshadri S....Wolf P.A. (BMC Med. Genet. 2007)
    6. Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. (PubMed id 17903294)4 Yang Q....O'Donnell C.J. (BMC Med. Genet. 2007)
    7. 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)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 138255 HGNC: 31422 AceView: LOC138255 Ensembl:ENSG00000204711 euGenes: HUgn138255
    ECgene: C9orf135 H-InvDB: C9orf135

    (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 C9orf135 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 C9orf135 gene:
    Search GeneIP for patents involving C9orf135

    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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