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

C9orf171 Gene

protein-coding   GIFtS: 37
GCID: GC09P135285          (predicted)

chromosome 9 open reading frame 171
  Search for C9orf171
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C9orf171    

Aliases
for C9orf171 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 9 Open Reading Frame 1711 2
FLJ460821
Uncharacterized Protein C9orf1712

External Ids:    HGNC: 337761   Entrez Gene: 3897992   Ensembl: ENSG000001885237   UniProtKB: Q6ZQR23   

Export aliases for C9orf171 gene to outside databases

Previous GC identifers: GC09P134277 GC09P104778


Summaries
for C9orf171 gene

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

Genomic Views
for C9orf171 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.1  NT_035014.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C9orf171 gene promoter:
         LHX3b/Lhx3b   RP58   HNF-3beta   FOXJ2 (long isoform)   Cart-1   LHX3a/Lhx3a   FOXJ2   TGIF   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C9orf171

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C9orf171


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

Entrez Gene cytogenetic band: 9q34.13   Ensembl cytogenetic band:  9q34.13   HGNC cytogenetic band: 9q34.13

C9orf171 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf171 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P135285:  view genomic region     (about GC identifiers)

Start:
 135,285,430 bp from pter      End:
 135,448,704 bp from pter
Size:
 163,275 bases      Orientation:
 plus strand

Proteins
for C9orf171 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: CI171_HUMAN, Q6ZQR2 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf171  
Size: 320 amino acids; 36499 Da
Secondary accessions: Q147X1
Alternative splicing: 2 isoforms:  Q6ZQR2-1   Q6ZQR2-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C9orf171: NX_Q6ZQR2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6ZQR2

    • C9orf171 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_997300.1  
    ENSEMBL proteins: 
     ENSP00000376908   ENSP00000343290   ENSP00000376909  

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    Protein Domains /
    Families
    for C9orf171 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q6ZQR2


    Function
    for C9orf171 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
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    Pathways & Interactions
    for C9orf171 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C9orf171

    Drugs & Compounds
    for C9orf171 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
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    Browse Tocris compounds for C9orf171
    Search CenterWatch for drugs/clinical trials and news about C9orf171 / CI171 

    Transcripts
    for C9orf171 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
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    About This Section
    REFSEQ mRNAs for C9orf171 gene: 
    NM_207417.1  

    Unigene Cluster for C9orf171:

    Chromosome 9 open reading frame 171
    Hs.201709  [show with all ESTs]
    Unigene Representative Sequence: AK128819
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000393215 ENST00000343036(uc004cbn.3 uc004cbo.3) ENST00000393216


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    hsa-miR-544 hsa-miR-330-3p
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    Additional cDNA sequence: 

    AK128819.1 BC118593.1 BC124555.1 

    3 DOTS entries:

    DT.100723291  DT.100761911  DT.40126507 

    8 AceView cDNA sequences:

    AI697241 BX395046 AK128819 NM_207417 BX395047 BX119796 AA912895 BX115412 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for C9orf171    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7
    SP1:                                                
    SP2:              -                                 


    ECgene alternative splicing isoforms for C9orf171

    Expression
    for C9orf171 gene

    (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

    C9orf171 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AGTTTTAATT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    C9orf171 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    N2/LSB induced-cells (Generation of midbra...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See C9orf171 Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.201709
        SABiosciences Custom PCR Arrays for C9orf171
    Primer
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    In Situ
    Assay Products:     
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    Orthologs
    for C9orf171 gene

    (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 chordates.

    Orthologs for C9orf171 gene from 3/13 species (see all 13)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia 1700101E01Rik1 , 5 RIKEN cDNA 1700101E01 gene1, 5 84.84(n)1
    88.11(a)1    		   2 (19.38 cM)5
    3293751  NM_001166705.11  NP_001160177.11 
     289553735 
    chicken
    (Gallus gallus)    		 Aves C17H9orf1711 chromosome 17 open reading frame, human C9orf171 61.95(n)
    52.79(a)    		   417168  XM_415451.3  XP_415451.2 
    zebrafish
    (Danio rerio)    		 Actinopterygii si:ch211-215c18.41 si:ch211-215c18.4 49.79(n)
    40.51(a)    		   558957  NM_001144790.1  NP_001138262.1 


    ENSEMBL Gene Tree for C9orf171 (if available)
    TreeFam Gene Tree for C9orf171 (if available) 

    Paralogs
    for C9orf171 gene

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

    Genomic Variants
    for C9orf171 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/35 NCBI SNPs in C9orf171 are shown (see all 35)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 9 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs106437171,2
    		C--135293278(+) CCCCCCT/-TTCTG 1 -- int1 trp32Minor allele frequency- -:0.00NA CSA 4
    rs605958271,2
    		C--135297014(+) GTTCT-/CATGCTCTGGTTTCTCTTCAAATCGTATAAATCTTTC
    GCCTTTTACTAAAGATTTCTGTGGAGAATCCTGGGTTCT    TCTCC     		1 -- int11Minor allele frequency- CATGCTCTGGTTTCTCTTCAAATCGTATAAATCTTTCGCCTTTTACTAAAGATTTCTGTGGAGAATCCTGGGTTCT:0.00NA 2
    rs1501943981,2
    		C,--135297069(+) GATTT-/CTGTG 
                GAGAA     		1 -- int10--------
    rs1114737341,2
    		C--135297073(+) TCTGTG/TGAGAA 1 -- int10--------
    rs1444772671,2
    		C,--135304199(+) GAAGA-/CCCCCC 1 -- int10--------
    rs355851481,2
    		C,--135344178(+) ACACG-/CACACAC 1 -- int10--------
    rs5313181,2
    		C,F,A,H,--135353137(+) TGTCTG/AGGGGG 1 -- int111Minor allele frequency- A:0.41NA WA CSA EA 375
    rs2017553021,2
    		--135353137(+) TGTCT-/AGGGGG 1 -- int10--------
    rs1426731321,2
    		--135357346(+) ATGGT-/TGGGG 
                GGGGG     		1 -- int10--------
    rs585425821,2
    		C,--135399845(+) AAATAC/TAAAAA 1 -- int15Minor allele frequency- T:0.37NA CSA WA EA 362

    HapMap Linkage Disequilibrium report for C9orf171 (135285430 - 135448704 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 6 variations for C9orf171
         2 CNVs: 6721 52733
         4 Indels: 13204 41290 41842 62952

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    Disorders / Diseases
    for C9orf171 gene

    (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.)
    About This Section
    C9orf171 for disorders           About MalaCards

    C9orf171 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: C9orf171 (4 documents)

    Export disorders for C9orf171 gene to outside databases

    Publications
    for C9orf171 gene

    (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 C9orf171 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C9orf171)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    2. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (2010)
    3. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
    4. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    5. 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. (2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    7. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (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. (2002)

    External Searches for C9orf171 gene

    (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)

    Genome Databases showing C9orf171 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 389799 HGNC: 33776 AceView: FLJ46082 Ensembl:ENSG00000188523 euGenes: HUgn389799
    ECgene: C9orf171 H-InvDB: C9orf171

    Other Databases showing C9orf171 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C9orf171 gene

    (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 C9orf171 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C9orf171 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for C9orf171 gene:
    Search GeneIP for patents involving C9orf171

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



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    for C9orf171 gene

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    About This Section

     
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