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CASC15 Gene

RNA gene   GIFtS: 17
GCID: GC06P021669

Cancer Susceptibility Candidate 15 (Non-Protein Coding)

(Previous name: long intergenic non-protein coding RNA 340)
(Previous symbol: LINC00340)
  Search for CASC15
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): lncRNA

Quality score for this RNA gene is 5.4

Aliases
Cancer Susceptibility Candidate 15 (Non-Protein Coding)1 2
LINC003401 2
Long Intergenic Non-Protein Coding RNA 3401

External Ids:    HGNC: 282451   Entrez Gene: 4012372   Ensembl: ENSG000002721687   
ORGUL members:    fRNAdb10:FR114375 FR055353 FR327226 FR058372 FR004332      
H-InvDB12:HIT000218399 HIT000024721 HIT000067334    
NCBI13:U17618 AL117559 AF086455    
NONCODE14:n386406 n387392 n384833 n387391 n344556 see all 9    
RNAdb15:RNZ28965 EVF29666 RNZ28972 EVF23768 RNZ28967 see all 42    

Export aliases for CASC15 gene to outside databases


(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 CASC15 Gene:
CASC15 (cancer susceptibility candidate 15 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class.

fRNAdb sequence ontologies for CASC15 - the ORGUL cluster for this gene includes several descriptions:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
antisense_RNA - Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for CASC15

(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for CASC15
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for CASC15

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CASC15


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

Entrez Gene cytogenetic band: 6p22.3   Ensembl cytogenetic band:  6p22.3   HGNC cytogenetic band: 6p22.3

CASC15 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CASC15 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P021669:  view genomic region     (about GC identifiers)

Start:
21,665,003 bp from pter      End:
22,214,734 bp from pter
Size:
549,732 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for CASC15

(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: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(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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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 CASC15
Interactions:

    Search GeneGlobe Interaction Network for CASC15

(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 Tocris compounds for CASC15



(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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5/30 fRNAdb Secondary structures (see all 30):


6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000606336(lincRNA) ENST00000606851(lincRNA) ENST00000607048(lincRNA) ENST00000444265(lincRNA)(uc003ndj.3 uc011djk.2 uc003ndl.3)
ENST00000606197(lincRNA) ENST00000605917(lincRNA)
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Selected AceView cDNA sequences (see all 29):

AA054524 BF514382 AW296751 CD674380 BF515357 AK096633 BM564069 BF515228 
CD644417 AI085314 AW005902 AA301354 AA131967 AI634087 AI655859 AI638532 
AW196268 BQ358653 BF884629 AU127831 BQ358650 AA088598 AW235185 BC044235 

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 CASC15:H-invDB

CASC15 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
CASC15 Expression
About this image

CASC15 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for CASC15
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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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ENSEMBL Gene Tree for CASC15 (if available)
TreeFam Gene Tree for CASC15 (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 CASC15 (see all 11610)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs609681011,2
C--21590433(+) AAAAA-/A/AA  
        
GGAAA
1 -- int11NA 2
rs17408661,2
C,A,H--21664729(-) CCGGCA/CACGCG 1 -- us2k111Minor allele frequency- C:0.24MN NA WA CSA EA 554
rs1829206251,2
C--21665229(+) CATAGC/TCCCCA 1 -- us2k10--------
rs1861000111,2
--21665256(+) TCTACC/TTCATC 1 -- us2k10--------
rs1168787401,2
C,F--21665291(+) CCGAAA/GGGATT 1 -- us2k11Minor allele frequency- G:0.03EA 120
rs1913406311,2
--21665332(+) GGTGGA/TGGCAA 1 -- us2k10--------
rs788708161,2
C,F--21665363(+) ACCAAC/TTGGAG 1 -- us2k12Minor allele frequency- T:0.14WA NA 238
rs1832199531,2
--21665389(+) TGAAAC/TGTTTT 1 -- us2k10--------
rs94661381,2
C--21665590(+) TGGGGT/CCCCAA 1 -- us2k12Minor allele frequency- C:0.05WA 120
rs737375661,2
C,F--21665639(+) GGGTCG/CGGAGC 1 -- us2k12Minor allele frequency- C:0.04WA 120

HapMap Linkage Disequilibrium report for CASC15 (21665003 - 21915003 bp, first 250kb of CASC15)

Structural Variations
      Database of Genomic Variants (DGV) variations for CASC15: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing CASC15
DNA2.0 Custom Variant and Variant Library Synthesis for CASC15

(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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OMIM information: 606701 603001 606025 606409 601403 300408 122550 143400 604519 608545 602272 604098 607257 105590 601741    

Find genes that share disorders with CASC15           About GenesLikeMe


Export disorders for CASC15 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 CASC15 gene, integrated from 10 sources (see all 14):
(articles sorted by number of sources associating them with CASC15)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma. (PubMed id 22941191)1 Diskin S.J....Maris J.M. (Nat. Genet. 2012)
  2. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. (PubMed id 23284291)1 Hancock D.B....London S.J. (PLoS Genet. 2012)
  3. Integrative genomics identifies LMO1 as a neuroblastoma oncogene. (PubMed id 21124317)1 Wang K....Maris J.M. (Nature 2011)
  4. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. (PubMed id 21946350)1 Soler Artigas M....Tobin M.D. (Nat. Genet. 2011)
  5. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. (PubMed id 18463370)1 Maris J.M....Hakonarson H. (N. Engl. J. Med. 2008)
  6. A third approach to gene prediction suggests thousands of additional human transcribed regions. (PubMed id 16543943)1 Glusman G....Smit A.F. (PLoS Comput. Biol. 2006)
  7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  8. 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)
  9. (PubMed id 16273071)10 
  10. (PubMed id 15608161)10 

(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: 401237 HGNC: 28245 AceView: LOC401237 Ensembl:ENSG00000272168 euGenes: HUgn401237
ECgene: CASC15 H-InvDB: CASC15

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for CASC15 gene:
Search GeneIP for patents involving CASC15

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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