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C14orf39 Gene

protein-coding   GIFtS: 40
GCID: GC14M060863

Chromosome 14 Open Reading Frame 39

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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 14 Open Reading Frame 391 2
Six6 Opposite Strand Transcript 12 3
Six6os12
Protein SIX6OS12

External Ids:    HGNC: 198491   Entrez Gene: 3177612   Ensembl: ENSG000001790087   UniProtKB: Q8N1H73   

Export aliases for C14orf39 gene to outside databases

Previous GC identifers: GC14M054696 GC14M058853 GC14M058892 GC14M059972 GC14M041066


(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 C14orf39 Gene:
C14orf39 (chromosome 14 open reading frame 39) is a protein-coding gene.

UniProtKB/Swiss-Prot: S6OS1_HUMAN, Q8N1H7
Function: May be involved in eye development through regulation of the SIX6 transcription factor




(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_000014.8  NT_026437.13  NC_018925.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C14orf39 gene promoter:
         Nkx3-1   Nkx3-1 v4   RP58   GCNF   Nkx3-1 v1   C/EBPalpha   Nkx3-1 v2   FOXJ2 (long isoform)   Nkx3-1 v3   FOXJ2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C14orf39

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C14orf39


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

Entrez Gene cytogenetic band: 14q23.1   Ensembl cytogenetic band:  14q23.1   HGNC cytogenetic band: 14q23.1

C14orf39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C14orf39 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M060863:  view genomic region     (about GC identifiers)

Start:
60,863,187 bp from pter      End:
60,982,261 bp from pter
Size:
119,075 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: S6OS1_HUMAN, Q8N1H7 (See protein sequence)
Recommended Name: Protein SIX6OS1  
Size: 587 amino acids; 68166 Da
Secondary accessions: Q08AQ4

Explore the universe of human proteins at neXtProt for C14orf39: NX_Q8N1H7

Explore proteomics data for C14orf39 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C14orf39 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_777638.2  
    ENSEMBL proteins: 
     ENSP00000451937   ENSP00000324920   ENSP00000450476   ENSP00000451665   ENSP00000451441  

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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: Q8N1H7


    (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: S6OS1_HUMAN, Q8N1H7
    Function: May be involved in eye development through regulation of the SIX6 transcription factor

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    Find genes that share ontologies with C14orf39           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for C14orf39:
     Increased homologous recombina 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for C14orf39

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    hsa-mir-122-5p (MIRT023303)

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    hsa-miR-3671 hsa-miR-16-2* hsa-miR-3613-3p hsa-miR-195* hsa-miR-2116 hsa-miR-578 hsa-miR-551b*
    SwitchGear 3'UTR luciferase reporter plasmidC14orf39 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 COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton1
    cytosol1
    extracellular1
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--

    Find genes that share ontologies with C14orf39           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 C14orf39
    Interactions:

        Search GeneGlobe Interaction Network for C14orf39

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0051090regulation of sequence-specific DNA binding transcription factor activity NAS15703187

    Find genes that share ontologies with C14orf39           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 C14orf39 (S6OS1)



    (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 C14orf39 gene: 
    NM_174978.2  

    Unigene Cluster for C14orf39:

    Chromosome 14 open reading frame 39
    Hs.335754  [show with all ESTs]
    Unigene Representative Sequence: AL832219
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000498565 ENST00000321731(uc001xez.4 uc010apo.3) ENST00000557138
    ENST00000555476 ENST00000556799
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate C14orf39:
    hsa-miR-3671 hsa-miR-16-2* hsa-miR-3613-3p hsa-miR-195* hsa-miR-2116 hsa-miR-578 hsa-miR-551b*
    SwitchGear 3'UTR luciferase reporter plasmidC14orf39 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat C14orf39

    Additional mRNA sequence: 

    AK098187.1 AL832219.1 BC125070.1 BC125071.1 

    3 DOTS entries:

    DT.97779429  DT.120782768  DT.97815858 

    8 AceView cDNA sequences:

    AW188354 AI024589 NM_174978 BQ435611 AK098187 AL832219 AW511757 BF087559 

    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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    C14orf39 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTACAATTCT
    C14orf39 Expression
    About this image


    C14orf39 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Gonad
             XY Germ Cells Testis Cord
     
     Ovary (Reproductive System)
             XX Germ Cells Ovigerous Cord
     
     Testis (Reproductive System)
             XY Germ Cells Testis Cord
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
    C14orf39 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C14orf39 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.335754

    UniProtKB/Swiss-Prot: S6OS1_HUMAN, Q8N1H7
    Tissue specificity: Highest expression in retina, skeletal muscle and colon

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C14orf39

    (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 C14orf39 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 4930447C04Rik1 , 5 RIKEN cDNA 4930447C04 gene1, 5 82.35(n)1
    70.21(a)1
      12 (30.30 cM)5
    758011  NM_029444.21  NP_083720.11 
     728811095 
    chicken
    (Gallus gallus)
    Aves LOC1017480501 protein SIX6OS1-like 63.14(n)
    44.93(a)
      101748050  XM_004936537.1  XP_004936594.1 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004863241 chromosome unknown open reading frame, human C14orf39 53.53(n)
    32.12(a)
      100486324  XM_002933746.2  XP_002933792.2 


    ENSEMBL Gene Tree for C14orf39 (if available)
    TreeFam Gene Tree for C14orf39 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C14orf39 gene
    1 SIMAP similar gene for C14orf39 using alignment to 4 protein entries:     G3V257_HUMAN (see all proteins):
    SIX6OS1

    Find genes that share paralogs with C14orf39           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 C14orf39 (see all 1002)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs12690271,2
    C,F,A,H--41886782(+) AACTGA/TGATAA 1 -- ds500116Minor allele frequency- T:0.50NS EA NA WA CSA 786
    rs1895395581,2
    --41886791(+) AATTTC/GTAGAC 1 -- ds50010--------
    rs733052671,2
    C,F--41886837(+) TTGATT/GTGCAT 1 -- ds50014Minor allele frequency- G:0.16WA CSA 122
    rs12543171,2
    C,F,H--41887004(+) AGGGGG/TTGGGC 1 -- ds500117Minor allele frequency- T:0.26NS EA NA WA CSA 2077
    rs12543181,2
    C,F--41887033(+) TGTGGT/CTTGAA 1 -- ds50016Minor allele frequency- C:0.17WA CSA NA EA 364
    rs1465526611,2
    --41887125(+) GTTAGG/TTTTAA 1 -- ds50010--------
    rs1812683991,2
    --41887169(+) CAAACC/GCTTTA 1 -- ut310--------
    rs1863703611,2
    --41887247(+) CAGAAG/TTTCAT 1 -- ut310--------
    rs1400058171,2
    C--41887498(+) TAGAAC/TTGTAC 1 -- ut310--------
    rs1911298081,2
    --41887617(+) ACCCAA/GTAATT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for C14orf39 (60863187 - 60982261 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for C14orf39:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1942n71CNV Loss21882294
    nsv902000CNV Loss21882294
    nsv1294CNV Loss18451855
    nsv901999CNV 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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with C14orf39           About GenesLikeMe

    Genetic Association Database (GAD): C14orf39

    Export disorders for C14orf39 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 C14orf39 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C14orf39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Natural antisense transcripts associated with genes involved in eye development. (PubMed id 15703187)1, 2 Alfano G.... Banfi S. (Hum. Mol. Genet. 2005)
    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. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. (PubMed id 23563607)1 Berndt S.I....Ingelsson E. (Nat. Genet. 2013)
    4. Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. (PubMed id 23396134)1 Verhoeven V.J....Hammond C.J. (Nat. Genet. 2013)
    5. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)4 Lango Allen H....Hirschhorn J.N. (Nature 2010)
    6. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PubMed id 17903301)4 Vasan R.S....Benjamin E.J. (BMC Med. Genet. 2007)
    7. Framingham Heart Study genome-wide association: results for pulmonary function measures. (PubMed id 17903307)4 Wilk J.B....O'Connor G.T. (BMC Med. Genet. 2007)
    8. 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)
    9. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)2 Heilig R.... Weissenbach J. (Nature 2003)
    10. 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: 317761 HGNC: 19849 AceView: C14orf39 Ensembl:ENSG00000179008 euGenes: HUgn317761
    ECgene: C14orf39 H-InvDB: C14orf39

    (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 C14orf39 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 C14orf39 gene:
    Search GeneIP for patents involving C14orf39

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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