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C6orf58 Gene

protein-coding   GIFtS: 41
GCID: GC06P127840

Chromosome 6 Open Reading Frame 58

  Search for C6orf58
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 6 Open Reading Frame 581 2
UPF0762 Protein C6orf582

External Ids:    HGNC: 209601   Entrez Gene: 3529992   Ensembl: ENSG000001845307   UniProtKB: Q6P5S23   
ORGUL members:         

Export aliases for C6orf58 gene to outside databases

Previous GC identifers: GC06U900113 GC06P127941 GC06P125474


(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 C6orf58 Gene:
C6orf58 (chromosome 6 open reading frame 58) 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 at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_025741.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the C6orf58 gene promoter:
         TBP   RelA   MEF-2A   AREB6   SRY   TFIID   aMEF-2   NF-kappaB1   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C6orf58

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C6orf58


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

Entrez Gene cytogenetic band: 6q22.33   Ensembl cytogenetic band:  6q22.33   HGNC cytogenetic band: 6q22.33

C6orf58 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C6orf58 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P127840:  view genomic region     (about GC identifiers)

Start:
127,840,600 bp from pter      End:
127,912,962 bp from pter
Size:
72,363 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: CF058_HUMAN, Q6P5S2 (See protein sequence)
Recommended Name: UPF0762 protein C6orf58 precursor  
Size: 330 amino acids; 37926 Da
Secondary accessions: B4E1I0 Q5VUP2

Explore the universe of human proteins at neXtProt for C6orf58: NX_Q6P5S2

Explore proteomics data for C6orf58 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn24, Asn69

  • See C6orf58 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001010905.1  
    ENSEMBL proteins: 
     ENSP00000328069  

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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:
     IPR008499 DUF781

    Graphical View of Domain Structure for InterPro Entry Q6P5S2

    ProtoNet protein and cluster: Q6P5S2

    UniProtKB/Swiss-Prot: CF058_HUMAN, Q6P5S2
    Similarity: Belongs to the UPF0762 family


    Find genes that share domains with C6orf58           About GenesLikeMe


    (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, 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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    Phenotypes:
         1 GenomeRNAi human phenotype for C6orf58:
     Increased HPV18 LCR reporter a 

    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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    Subcellular locations from UniProtKB/Swiss-Prot
    CF058_HUMAN, Q6P5S2: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    lysosome1
    nucleus1
    plasma membrane1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region ----
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with C6orf58           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 C6orf58
    Interactions:

        Search GeneGlobe Interaction Network for C6orf58

    (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 C6orf58 (CF058)



    (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 C6orf58 gene: 
    NM_001010905.2  

    Unigene Cluster for C6orf58:

    Chromosome 6 open reading frame 58
    Hs.226268  [show with all ESTs]
    Unigene Representative Sequence: BC062712
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000498112 ENST00000329722(uc003qbh.3)
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    Additional mRNA sequence: 

    AK303850.1 BC062712.1 

    4 DOTS entries:

    DT.75105754  DT.121376475  DT.92423725  DT.121376473 

    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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    C6orf58 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAGTTTATTC
    C6orf58 Expression
    About this image

    C6orf58 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C6orf58 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.226268
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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 C6orf58 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 2310057J18Rik5 RIKEN cDNA 2310057J18 gene   --   10 (16.46 cM) 28972288 
    chicken
    (Gallus gallus)
    Aves C6orf586
    chromosome 6 open reading frame 58
    34(a)
    1 ↔ 1
    3(58527005-58539770)
    lizard
    (Anolis carolinensis)
    Reptilia C6orf586
    chromosome 6 open reading frame 58
    38(a)
    1 ↔ 1
    GL343358.1(147821-164887)
    zebrafish
    (Danio rerio)
    Actinopterygii C20H6orf58 (1 of 2)6
    C20H6orf58 (2 of 2)6
    chromosome 6 open reading frame 58
    30(a)
    29(a)
    many → 1
    many → 1
    20(1422043-1444314) ENSDARG00000090722
    20(1421873-1429617) ENSDARG00000095751


    ENSEMBL Gene Tree for C6orf58 (if available)
    TreeFam Gene Tree for C6orf58 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C6orf58 gene

    Find genes that share paralogs with C6orf58           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for C6orf58
    PGOHUM00000243355


    (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 C6orf58 (see all 334)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1500239161,2
    Cuntested1127911308(+) CAGTCA/C/TTCTTT 2 L F mis11NA 4548
    rs1163902361,2
    F--127896492(+) AATTAA/GCATGT 1 -- us2k11Minor allele frequency- G:0.07WA 118
    rs1480552661,2
    --127896524(+) GAAACA/TTTGTA 1 -- us2k10--------
    rs93728761,2
    C,F,A--127896543(+) AAACTG/ATTCAA 1 -- us2k18Minor allele frequency- A:0.49NA WA EA 368
    rs1167953781,2
    C,F--127896711(+) TAGTAA/GTTTAG 1 -- us2k11Minor allele frequency- G:0.01WA 118
    rs69420971,2
    C,F,A,H--127896761(+) CTTCTG/AGTTTA 1 -- us2k115Minor allele frequency- A:0.19NS EA NA WA CSA 761
    rs778640861,2
    C,F--127896807(+) ATAAGG/AGAAAG 1 -- us2k11Minor allele frequency- A:0.05NA 120
    rs1879036851,2
    --127896948(+) TTAAAG/TGAGTG 1 -- us2k10--------
    rs14480551,2
    C,F,A,H--127896979(-) CAGATC/TGTTCT 1 -- us2k118Minor allele frequency- T:0.19NS EA NA WA CSA 901
    rs1408425611,2
    --127897009(+) CACATC/TTTACA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for C6orf58 (127840600 - 127912962 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for C6orf58:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv5469CNV Insertion18451855
    nsv830798CNV Loss17160897

    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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      --

    (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 C6orf58 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C6orf58)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. (PubMed id 16740002)1, 2 Ramachandran P....Loo J.A. (J. Proteome Res. 2006)
    2. 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)
    3. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    4. Large-scale proteomics and phosphoproteomics of urinary exosomes. (PubMed id 19056867)1 Gonzales P.A....Knepper M.A. (J. Am. Soc. Nephrol. 2009)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. 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: 352999 HGNC: 20960 Ensembl:ENSG00000184530 euGenes: HUgn352999 ECgene: C6orf58
    H-InvDB: C6orf58

    (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 C6orf58 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 C6orf58 gene:
    Search GeneIP for patents involving C6orf58

    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, eBioscience, 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
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