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C9orf106 Gene

RNA gene   GIFtS: 28
GCID: GC09P132083

Chromosome 9 Open Reading Frame 106

  Search for C9orf106
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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Subcategory (RNA class): processed_transcript

Quality score for this RNA gene is 3

Aliases
Chromosome 9 Open Reading Frame 1061 2
bA65J3.52
Putative Uncharacterized Protein C9orf1062

External Ids:    HGNC: 313701   Entrez Gene: 4143182   Ensembl: ENSG000001790827   UniProtKB: Q8NAJ23   

Export aliases for C9orf106 gene to outside databases

Previous GC identifers: GC09U900597 GC09P129163 GC09P131123 GC09P101689


(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 C9orf106 Gene:
C9orf106 (chromosome 9 open reading frame 106) is an RNA gene, and is affiliated with the processed_transcript RNA class.


(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  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the C9orf106 gene promoter:
         HOXA9   HOXA9B   AML1a   POU3F2 (N-Oct-5a)   POU3F2   Meis-1b   RORalpha2   SEF-1 (1)   Pax-4a   Meis-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf106


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

Entrez Gene cytogenetic band: 9q34.11   Ensembl cytogenetic band:  9q34.11   HGNC cytogenetic band: 9q34.11

C9orf106 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf106 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P132083:  view genomic region     (about GC identifiers)

Start:
132,083,295 bp from pter      End:
132,087,184 bp from pter
Size:
3,890 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CI106_HUMAN, Q8NAJ2 (See protein sequence)
Recommended Name: Putative uncharacterized protein C9orf106  
Size: 232 amino acids; 25113 Da

Explore the universe of human proteins at neXtProt for C9orf106: NX_Q8NAJ2

REFSEQ proteins: NP_001012733.2  

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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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ProtoNet protein and cluster: Q8NAJ2


(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:
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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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(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 C9orf106
Interactions:

    Search GeneGlobe Interaction Network for C9orf106

(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 C9orf106 (CI106)



(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,
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 C9orf106 gene: 
NM_001012715.3  

Unigene Cluster for C9orf106:

Chromosome 9 open reading frame 106
Hs.449434  [show with all ESTs]
Unigene Representative Sequence: AK092588
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000316786(processed_transcript)
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Additional mRNA sequence: 

AK092588.1 BC132699.1 BC132701.1 

1 DOTS entry:

DT.91984149 

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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Expression evidence for C9orf106:none

C9orf106 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTCCCAGGCC
C9orf106 Expression
About this image

C9orf106 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.449434
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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 human and chimp.

Orthologs for C9orf106 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia C9H9orf1061 chromosome 9 open reading frame, human C9orf106 98.85(n)
96.98(a)
  100615955  XM_003312310.1  XP_003312358.1 


ENSEMBL Gene Tree for C9orf106 (if available)
TreeFam Gene Tree for C9orf106 (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 C9orf106 (see all 108)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1843621061,2
--132081307(+) AGGTGA/GGGTTC 1 -- us2k10--------
rs174829351,2
C,F--132081331(+) CCCCCC/TGTCGC 1 -- us2k11Minor allele frequency- T:0.17EA 120
rs762670681,2
C,F--132081347(+) CCCTGG/ACCCTG 1 -- us2k12Minor allele frequency- A:0.03CSA WA 120
rs174572021,2
C,F,H--132081380(+) AGGGGG/ACCACG 1 -- us2k18Minor allele frequency- A:0.13NS EA NA WA 778
rs1404477251,2
--132081437(+) ATGCCA/GGGGAG 1 -- us2k10--------
rs175176441,2
C,F,H--132081528(+) CCTCCC/TCTGGC 1 -- us2k1 tfbs34Minor allele frequency- T:0.02NS EA 418
rs1131092421,2
F--132081582(+) CGACCG/CCTCTC 1 -- us2k11Minor allele frequency- C:0.50CSA 2
rs1394795681,2
--132081611(+) TCAAAA/CGCGCC 1 -- us2k10--------
rs108195001,2
C,F,A,H--132081623(+) GCTGCG/AGGGCT 1 -- us2k120Minor allele frequency- A:0.44NS EA NA WA CSA 2024
rs1896442681,2
--132081652(+) CCAGAA/GCCTGC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for C9orf106 (132083295 - 132087184 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for C9orf106:    About this table    
Variant IDTypeSubtypePubMed ID
nsv6726CNV Insertion18451855
nsv527231CNV Loss19592680
nsv893910CNV Loss21882294
nsv893909CNV Loss21882294
nsv893911CNV Gain21882294

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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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C9orf106 for disorders           About GeneDecksing

Genetic Association Database (GAD): C9orf106

Export disorders for C9orf106 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 C9orf106 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C9orf106)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  2. Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. (PubMed id 22041458)4 Clark S.L....van den Oord E.J. (Psychol Med 2012)
  3. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
  4. 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: 414318 HGNC: 31370 Ensembl:ENSG00000179082 euGenes: HUgn414318 ECgene: C9orf106
H-InvDB: C9orf106

(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 C9orf106 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 C9orf106 gene:
Search GeneIP for patents involving C9orf106

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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