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C19orf60 Gene

protein-coding   GIFtS: 42
GCID: GC19P018699

Chromosome 19 Open Reading Frame 60

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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 19 Open Reading Frame 601 2
Uncharacterized Protein C19orf602

External Ids:    HGNC: 260981   Entrez Gene: 550492   Ensembl: ENSG000000060157   UniProtKB: Q96EN93   
ORGUL members:         

Export aliases for C19orf60 gene to outside databases

Previous GC identifers: GC19P018561 GC19P018262


(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 C19orf60 Gene:
C19orf60 (chromosome 19 open reading frame 60) 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_000019.9  NT_011295.12  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C19orf60 gene promoter:
         AhR   Lmo2   AP-4   HNF-4alpha2   AP-2gamma   Arnt   HNF-4alpha1   CREB   NF-kappaB1   MRF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C19orf60

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C19orf60


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

Entrez Gene cytogenetic band: 19p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.11

C19orf60 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C19orf60 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P018699:  view genomic region     (about GC identifiers)

Start:
18,699,495 bp from pter      End:
18,703,147 bp from pter
Size:
3,653 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., 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: CS060_HUMAN, Q96EN9 (See protein sequence)
Recommended Name: Uncharacterized protein C19orf60  
Size: 201 amino acids; 22599 Da
Sequence caution: Sequence=BAA91400.1; Type=Frameshift; Positions=107;
Secondary accessions: E9PAS0 Q8NAX4 Q9NWI0
Alternative splicing: 3 isoforms:  Q96EN9-1   Q96EN9-2   Q96EN9-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C19orf60: NX_Q96EN9

Explore proteomics data for C19orf60 at MOPED


See C19orf60 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001093888.1  NP_001093889.1  

ENSEMBL proteins: 
 ENSP00000351422   ENSP00000398467   ENSP00000471429   ENSP00000469859  

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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: Q96EN9


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

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI16189514
     
Find genes that share ontologies with C19orf60           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for C19orf60:
 Synthetic lethal with Ras 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for C19orf60

miRNA
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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
cytosol2
nucleus2
extracellular1
mitochondrion1
plasma membrane1

(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 C19orf60
Interactions:

    Search GeneGlobe Interaction Network for C19orf60

STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

Selected Interacting proteins for C19orf60 (Q96EN91, 2, 3 ENSP000003514224) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
InteractantInteraction Details
GeneCardExternal ID(s)
SMN1Q166372, 3MINT-8270904 I2D: score=2 
SMN2Q166372, 3MINT-8270904 I2D: score=2 
OSGEPQ9NPF42, 3MINT-8265098 I2D: score=2 
TK1P041832, 3MINT-8273026 I2D: score=2 
MDFIQ997501, 2, 3, ENSP000002303214EBI-745810,EBI-724076 MINT-66725 I2D: score=5 STRING: ENSP00000230321
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(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 C19orf60 (CS060)



(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 C19orf60 gene (3 alternative transcripts): 
NM_017967.2  NM_001100418.1  NM_001100419.1  

Unigene Cluster for C19orf60:

Chromosome 19 open reading frame 60
Hs.655317  [show with all ESTs]
Unigene Representative Sequence: AK094710
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000598375 ENST00000358607(uc002nju.2 uc002njv.4) ENST00000450195(uc010ebs.3)
ENST00000600997 ENST00000601736 ENST00000597371 ENST00000595490 ENST00000595077

miRNA
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hsa-miR-1207-3p
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Inhib. RNA
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Primer
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Additional mRNA sequence: 

AK000857.1 AK054670.1 AK091925.1 AK094710.1 BC012078.1 

16 DOTS entries:

DT.100845537  DT.86852028  DT.121499149  DT.95189254  DT.40111085  DT.100845535  DT.121499185  DT.102838526 
DT.75168885  DT.100026653  DT.100845538  DT.95189260  DT.95189261  DT.121499147  DT.100845534  DT.95293310 

Selected AceView cDNA sequences (see all 173):

BM128521 BF591405 BU844497 BF939241 CR625418 AI223191 CB047779 CD673861 
CK299281 D20857 AW075602 CB177427 CB137039 CB155247 AI380546 AV707942 
AI433538 BM725708 CA422953 CR616719 BC012078 BQ002322 AI888992 BV175167 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for C19orf60 (see all 7)    About this scheme

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d
SP1:                                -                       -     -           -                     
SP2:                                -     -                 -     -           -                     
SP3:                                -     -     -     -     -     -           -                     
SP4:                                                                                                
SP5:                                                        -     -           -                     


ECgene alternative splicing isoforms for C19orf60

(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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C19orf60 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAGGCGATCA
C19orf60 Expression
About this image

C19orf60 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C19orf60 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.655317
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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 C19orf60 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 2810428I15Rik1 , 5 RIKEN cDNA 2810428I15 gene1, 5 80.5(n)1
73.58(a)1
  8 (34.15 cM)5
664621  NM_025577.21  NP_079853.11 
 705042925 
zebrafish
(Danio rerio)
Actinopterygii C22H19orf606
chromosome 19 open reading frame 60
31(a)
1 ↔ 1
22(21488870-21498043) ENSDARG00000073867


ENSEMBL Gene Tree for C19orf60 (if available)
TreeFam Gene Tree for C19orf60 (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 C19orf60 (see all 154)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1907085661,2
--18697655(+) GGCTTA/CTTCCA 2 -- us2k10--------
rs48088221,2
C,F,A,H--18697778(+) actgcA/Tgatgg 2 -- us2k1 tfbs325Minor allele frequency- T:0.40NS EA NA WA 2530
rs1817828781,2
--18697840(+) CTGCCA/GGCCCA 2 -- us2k10--------
rs1396591221,2
--18697852(+) ACCCGA/GACGTT 2 -- us2k10--------
rs1858686721,2
--18697878(+) TCTCAC/TGAGGA 2 -- us2k10--------
rs48088231,2
C,F,A,H--18698019(+) TTTACC/TGGGCA 2 -- us2k123Minor allele frequency- T:0.40NS EA NA WA CSA 2320
rs124628901,2
C,H--18698165(+) cgaggT/Cgggcg 2 -- us2k13Minor allele frequency- C:0.17NA WA 6
rs104073221,2
C,F,H--18698221(+) aacccC/Tgcctc 2 -- us2k18Minor allele frequency- T:0.20NA WA CSA 15
rs72455371,2
C--18698418(+) aaaaaA/Caaaaa 2 -- us2k12Minor allele frequency- C:0.25NA 4
rs65122761,2
C,A--18698419(+) aaaacA/Caaaaa 2 -- us2k1 trp31Minor allele frequency- C:0.00NA 2

HapMap Linkage Disequilibrium report for C19orf60 (18699495 - 18703147 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for C19orf60:    About this table    
Variant IDTypeSubtypePubMed ID
dgv3785n71CNV Loss21882294
nsv833776CNV Loss17160897
nsv911290CNV Loss21882294
dgv3784n71CNV Loss21882294
nsv911282CNV Loss21882294
nsv911288CNV Loss21882294
nsv911281CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing C19orf60
DNA2.0 Custom Variant and Variant Library Synthesis for C19orf60

(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 C19orf60 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with C19orf60)
    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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
  4. A directed protein interaction network for investigating intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (Sci Signal 2011)
  5. A novel human protein is able to interact with hepatitis B virus core deletion mutant but not with the wild-type protein. (PubMed id 19770013)1 Razanskas R. and Sasnauskas K. (Virus Res. 2009)
  6. An empirical framework for binary interactome mapping. (PubMed id 19060904)1 Venkatesan K....Vidal M. (Nat. Methods 2009)
  7. Defining the human deubiquitinating enzyme interaction landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (Cell 2009)
  8. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  10. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)

(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: 55049 HGNC: 26098 AceView: FLJ20850 Ensembl:ENSG00000006015 euGenes: HUgn55049
ECgene: C19orf60 H-InvDB: C19orf60

(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 C19orf60 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 C19orf60 gene:
Search GeneIP for patents involving C19orf60

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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