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C10orf90 Gene

protein-coding   GIFtS: 43
GCID: GC10M128113

Chromosome 10 Open Reading Frame 90

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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 10 Open Reading Frame 901 2
Fragile-Site Associated Tumor Suppressor Homolog2 3
FATS2 3
Fragile-Site Associated Tumor Suppressor1
bA422P15.22
Centrosomal Protein C10orf902

External Ids:    HGNC: 265631   Entrez Gene: 1186112   Ensembl: ENSG000001544937   UniProtKB: Q96M023   

Export aliases for C10orf90 gene to outside databases

Previous GC identifers: GC10M127687 GC10M128103 GC10M121800


(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 C10orf90 Gene:
C10orf90 (chromosome 10 open reading frame 90) is a protein-coding gene. GO annotations related to this gene include histone deacetylase binding. An important paralog of this gene is ALMS1.

UniProtKB/Swiss-Prot: CJ090_HUMAN, Q96M02
Function: Tumor suppressor that is required to sustain G2/M checkpoint after DNA damage. Mediates CDKN1A/p21
protein stability in a ubiquitin-independent manner (By similarity). May have a role in the assembly of primary
cilia




(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_000010.10  NT_030059.14  NC_018921.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C10orf90 gene promoter:
         HOXA9B   HOXA9   TBP   Meis-1b   E47   FOXL1   c-Rel   GATA-6   TFIID   Meis-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C10orf90

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C10orf90


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

Entrez Gene cytogenetic band: 10q26.2   Ensembl cytogenetic band:  10q26.2   HGNC cytogenetic band: 10q26.2

C10orf90 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C10orf90 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M128113:  view genomic region     (about GC identifiers)

Start:
128,113,566 bp from pter      End:
128,359,079 bp from pter
Size:
245,514 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: CJ090_HUMAN, Q96M02 (See protein sequence)
Recommended Name: Centrosomal protein C10orf90  
Size: 699 amino acids; 77910 Da
Subunit: Interacts with HDAC1; the interaction prevents binding of HDAC1 to CDKN1A/p21 and facilitates the
acetylation and stabilization of CDKN1A/p21 (By similarity)
Sequence caution: Sequence=AAM20911.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=CAI12409.1; Type=Erroneous gene model prediction; Sequence=CAI40680.1; Type=Erroneous gene model
prediction;
Secondary accessions: B9EIQ9 Q5JRP6 Q5T023 Q8NCV5 Q8WU75
Alternative splicing: 2 isoforms:  Q96M02-1   Q96M02-2   

Explore the universe of human proteins at neXtProt for C10orf90: NX_Q96M02

Explore proteomics data for C10orf90 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C10orf90 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001004298.2  
    ENSEMBL proteins: 
     ENSP00000411609   ENSP00000474753   ENSP00000349318   ENSP00000405995   ENSP00000474558  
     ENSP00000474615   ENSP00000444369   ENSP00000284694   ENSP00000398786   ENSP00000376459  

    C10orf90 Human Recombinant Protein Products:

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    Browse Proteins at Cloud-Clone Corp.

     
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    antibodies-online proteins for C10orf90 (2 products) 

     
    antibodies-online peptides for C10orf90

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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: Q96M02


    (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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CJ090_HUMAN, Q96M02
    Function: Tumor suppressor that is required to sustain G2/M checkpoint after DNA damage. Mediates CDKN1A/p21
    protein stability in a ubiquitin-independent manner (By similarity). May have a role in the assembly of primary
    cilia

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042826histone deacetylase binding IEA--
         
    Find genes that share ontologies with C10orf90           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for D7Ertd443e (no phenotypes)

    Find genes that share phenotypes with C10orf90           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for C10orf90

    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate C10orf90:
    hsa-miR-587 hsa-miR-548am hsa-miR-214 hsa-miR-548x hsa-miR-2116 hsa-miR-4273 hsa-miR-548c-3p hsa-miR-761
    SwitchGear 3'UTR luciferase reporter plasmidC10orf90 3' UTR sequence
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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
    CJ090_HUMAN, Q96M02: Cytoplasm. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.
    Note=Localizes to the actin cytoskeleton in a proportion of cells. Colocalizes with centriolar acetylated tubulin
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    nucleus3
    cytosol2
    plasma membrane1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--
    GO:0005813centrosome IDA--
    GO:0015629actin cytoskeleton IDA--

    Find genes that share ontologies with C10orf90           About GenesLikeMe


    (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 C10orf90
    Interactions:

        Search GeneGlobe Interaction Network for C10orf90

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for C10orf90 (Q96M023 ENSP000002846944) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
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    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006974cellular response to DNA damage stimulus ----
    GO:0007095mitotic G2 DNA damage checkpoint IEA--
    GO:0009411response to UV IEA--
    GO:0010212response to ionizing radiation IEA--
    GO:0030308negative regulation of cell growth IEA--

    Find genes that share ontologies with C10orf90           About GenesLikeMe



    (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 C10orf90 (CJ090)



    (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 C10orf90 gene: 
    NM_001004298.2  

    Unigene Cluster for C10orf90:

    Chromosome 10 open reading frame 90
    Hs.587663  [show with all ESTs]
    Unigene Representative Sequence: NM_001004298
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000424927 ENST00000480379 ENST00000356858(uc001ljp.3 uc010qum.2)
    ENST00000432642 ENST00000368674(uc001ljs.1) ENST00000488181 ENST00000463082
    ENST00000544758(uc009yao.2) ENST00000284694(uc001ljq.3) ENST00000454341
    ENST00000392694
    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate C10orf90:
    hsa-miR-587 hsa-miR-548am hsa-miR-214 hsa-miR-548x hsa-miR-2116 hsa-miR-4273 hsa-miR-548c-3p hsa-miR-761
    SwitchGear 3'UTR luciferase reporter plasmidC10orf90 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat C10orf90
      QuantiFast Probe-based Assays in human, mouse, rat C10orf90

    Additional mRNA sequence: 

    AF435960.1 AK057500.1 AK093093.1 AK297577.1 AK308357.1 AK309217.1 BC021140.1 BC034828.1 
    BC140898.1 BC146869.1 

    11 DOTS entries:

    DT.100746880  DT.97804391  DT.100015162  DT.99932776  DT.91789898  DT.40240116  DT.121264242  DT.121264260 
    DT.121264283  DT.40127119  DT.95121312 

    Selected AceView cDNA sequences (see all 45):

    BQ775403 CA429607 CB108421 BU618481 BQ214690 CR602784 NM_001004298 CR621517 
    CA423069 AX747917 BM907872 BM674479 BQ431025 AK093093 AA989352 BM717101 
    BQ681161 BU184717 BU629883 BU194912 AF435960 AK057500 BM994497 AI969684 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for C10orf90 (see all 8)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17
    SP1:                                -                 -                 -           -           -     -                     
    SP2:                                                  -     -     -     -           -           -     -                     
    SP3:                                                                    -           -           -     -                     
    SP4:                                                                                -           -     -                     
    SP5:              -     -           -                                                                                       


    ECgene alternative splicing isoforms for C10orf90

    (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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    C10orf90 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    C10orf90 Expression
    About this image

    C10orf90 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C10orf90 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.587663
        Custom PCR Arrays for C10orf90
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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 C10orf90 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia D7Ertd443e1 , 5 DNA segment, Chr 7, ERATO Doi 443, expressed1, 5 76.38(n)1
    67.83(a)1
      7 (78.40 cM)5
    710071  NM_001199941.11  NP_001186870.11 
     1342662625 
    chicken
    (Gallus gallus)
    Aves C6H10ORF901 chromosome 6 open reading frame, human C10orf90 53.69(n)
    40.35(a)
      423959  XM_004942350.1  XP_004942407.1 
    lizard
    (Anolis carolinensis)
    Reptilia C10orf906
    chromosome 10 open reading frame 90
    42(a)
    1 ↔ 1
    3(52659348-52723320)
    zebrafish
    (Danio rerio)
    Actinopterygii C12H10orf906
    chromosome 10 open reading frame 90
    15(a)
    1 ↔ 1
    12(45467869-45518511) ENSDARG00000089024


    ENSEMBL Gene Tree for C10orf90 (if available)
    TreeFam Gene Tree for C10orf90 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C10orf90 gene
    ALMS12  

    Find genes that share paralogs with C10orf90           About GenesLikeMe



    (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 C10orf90 (see all 2174)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1477355341,2
    Cuntested1128174221(+) AACCTC/TGGAAA 1 -- int10--------
    rs1400076761,2
    C--128113211(+) GCAGCA/GGGAGG 1 -- int10--------
    rs109016091,2
    C,F,A,H--128113320(+) GTAAGA/GTTTAG 1 -- int121Minor allele frequency- G:0.16NS EA NA WA 2350
    rs2017350781,2
    C--128113373(+) CTTTTC/GTCTTA 1 -- int10--------
    rs760575611,2
    C,F--128113430(+) CAAGTA/GCTTCC 1 -- int11Minor allele frequency- G:0.33EA 120
    rs38126781,2
    C,F--128113585(-) AAATGC/TAATTA 1 -- ut316Minor allele frequency- T:0.18WA NA CSA EA 364
    rs1444460561,2
    C--128113625(+) GTTCTC/TAGCTT 1 -- ut310--------
    rs1395073551,2
    C--128113681(+) AAGAAC/TAGACA 1 -- ut310--------
    rs1451786461,2
    C--128113739(+) TGGGGC/TGGGGC 1 -- ut310--------
    rs38126771,2
    C,F,A,H--128113799(-) AAGAAT/GCCATT 1 -- ut319Minor allele frequency- G:0.19EA NA WA 1820

    HapMap Linkage Disequilibrium report for C10orf90 (128113566 - 128359079 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for C10orf90:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2677894CNV Deletion23128226
    esv2743062CNV Deletion23290073
    nsv7602CNV Loss18451855
    nsv525054CNV Loss19592680
    nsv521809CNV Loss19592680

    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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    Find genes that share disorders with C10orf90           About GenesLikeMe

    Genetic Association Database (GAD): C10orf90

    Export disorders for C10orf90 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 C10orf90 gene, integrated from 10 sources (see all 17):
    (articles sorted by number of sources associating them with C10orf90)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. An HDAC1-binding domain within FATS bridges p21 turnover to radiation-induced tumorigenesis. (PubMed id 20154723)1, 3 Li Z....Cai W.W. (Oncogene 2010)
    2. FATS is a transcriptional target of p53 and associated with antitumor activity. (PubMed id 20843368)1, 3 Zhang X....Li Z. (Mol. Cancer 2010)
    3. Centriolar association of ALMS1 and likely centrosomal functions of the ALMS motif-containing proteins C10orf90 and KIAA1731. (PubMed id 20844083)1, 2 Knorz V.J.... Hearn T. (Mol. Biol. Cell 2010)
    4. 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)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (Nature 2004)
    7. FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage. (PubMed id 24240685)1 Yan S....Li Z. (Oncogene 2013)
    8. Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. (PubMed id 23319000)1 Luykx J.J....Ophoff R.A. (Mol. Psychiatry 2013)
    9. Expression level of novel tumor suppressor gene FATS is associated with the outcome of node positive breast cancer. (PubMed id 22040499)1 Zhang J....Li Z. (Chin. Med. J. 2011)
    10. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 118611 HGNC: 26563 AceView: C10orf90 Ensembl:ENSG00000154493 euGenes: HUgn118611
    ECgene: C10orf90 H-InvDB: C10orf90

    (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 C10orf90 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for C10orf90 gene:
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