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CASC16 Gene

RNA gene   GIFtS: 15
GCID: GC16M052587

Cancer Susceptibility Candidate 16 (Non-Protein Coding)

(Previous name: long intergenic non-protein coding RNA 918)
(Previous symbol: LINC00918)
  See CASC16-related disease
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 3

Aliases
Cancer Susceptibility Candidate 16 (Non-Protein Coding)1 2
LINC009181 2
Long Intergenic Non-Protein Coding RNA 9181

External Ids:    HGNC: 486081   Entrez Gene: 6437142   Ensembl: ENSG000002492317   
ORGUL members:         

Export aliases for CASC16 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 CASC16 Gene:
CASC16 (cancer susceptibility candidate 16 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with CASC16 include breast cancer susceptibility.


(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 CASC16
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CASC16


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

Entrez Gene cytogenetic band: 16q12.1   Ensembl cytogenetic band:  16q12.2   HGNC cytogenetic band: 16q12.1

CASC16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CASC16 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M052587:  view genomic region     (about GC identifiers)

Start:
52,585,999 bp from pter      End:
52,686,017 bp from pter
Size:
100,019 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for CASC16

(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 CASC16
Interactions:

    Search GeneGlobe Interaction Network for CASC16

(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
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Browse Tocris compounds for CASC16



(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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3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000565755(lincRNA) ENST00000510238(lincRNA)(uc002egx.3) ENST00000563844(lincRNA)
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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 CASC16:none

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

CASC16 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for CASC16
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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 CASC16 (if available)
TreeFam Gene Tree for CASC16 (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 CASC16 (see all 1240)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs456112411,2
C--52585678(+) ACAGAT/CACATA 1 -- ds50012Minor allele frequency- C:0.01EU NA 200
rs753756351,2
C--52585682(+) ATACAT/CAGTAA 1 -- ds50012Minor allele frequency- C:0.07CSA WA 120
rs746965771,2
C--52585851(+) GTGCAA/GTTTTC 1 -- ds50012Minor allele frequency- G:0.07CSA WA 120
rs455324321,2
C,F--52585878(+) GCCTTA/-AAAAA 1 -- ds50011Minor allele frequency- -:0.44EU 78
rs802559011,2
C--52585886(+) AAAAAA/TTTTGT 1 -- ds50010--------
rs791448531,2
C,F--52585981(+) ACAGCG/ATGTTT 1 -- ds50011Minor allele frequency- A:0.03WA 118
rs1896037231,2
--52586042(+) TTCACA/GATAAG 1 -- nc-transcript-variant0--------
rs456060401,2
C,F--52586298(+) TCTTCG/ACAAAT 1 -- nc-transcript-variant2Minor allele frequency- A:0.01EU NA 208
rs1912907301,2
--52586335(+) TCTTCG/TCTAAG 1 -- nc-transcript-variant0--------
rs38036621,2
C,F,A,H--52586341(-) CTGTCT/CCTTAG 1 -- nc-transcript-variant39Minor allele frequency- C:0.49EA NA NS EU WA CSA 4804

HapMap Linkage Disequilibrium report for CASC16 (52585999 - 52686017 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for CASC16: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing CASC16
DNA2.0 Custom Variant and Variant Library Synthesis for CASC16

(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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1 disease for CASC16:    
About MalaCards
breast cancer susceptibility


Find genes that share disorders with CASC16           About GenesLikeMe


Export disorders for CASC16 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 CASC16 gene, integrated from 10 sources (see all 18):
(articles sorted by number of sources associating them with CASC16)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. (PubMed id 23535729)1 Michailidou K....Easton D.F. (Nat. Genet. 2013)
  2. Genome-wide association studies identify four ER negative-specific breast cancer risk loci. (PubMed id 23535733)1 Garcia-Closas M....Kraft P. (Nat. Genet. 2013)
  3. Genome-wide association study identifies a common variant in RAD51B associated with male breast cancer risk. (PubMed id 23001122)1 Orr N....Swerdlow A.J. (Nat. Genet. 2012)
  4. A combined analysis of genome-wide association studies in breast cancer. (PubMed id 20872241)1 Li J....Hall P. (Breast Cancer Res. Treat. 2011)
  5. Genome-wide association study identifies novel restless legs syndrome susceptibility loci on 2p14 and 16q12.1. (PubMed id 21779176)1 Winkelmann J....Meitinger T. (PLoS Genet. 2011)
  6. Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study. (PubMed id 21263130)1 Fletcher O....Peto J. (J. Natl. Cancer Inst. 2011)
  7. Birth weight, breast cancer susceptibility loci, and breast cancer risk. (PubMed id 20054709)1 Tamimi R.M....Hall P. (amp 2010)
  8. Fine scale mapping of the breast cancer 16q12 locus. (PubMed id 20332101)1 Udler M.S....Dunning A.M. (Hum. Mol. Genet. 2010)
  9. Genetic variants in trinucleotide repeat-containing 9 (TNRC9) are associated with risk of estrogen receptor positive breast cancer in a Chinese population. (PubMed id 20213080)1 Liang J....Shen H. (Breast Cancer Res. Treat. 2010)
  10. Polymorphisms in the TOX3/LOC643714 locus and risk of breast cancer in African-American women. (PubMed id 20406955)1 Ruiz-NarvA!ez E.A....Palmer J.R. (amp 2010)

(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: 643714 HGNC: 48608 Ensembl:ENSG00000249231 euGenes: HUgn643714 ECgene: CASC16
H-InvDB: CASC16

(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 CASC16 gene:
Search GeneIP for patents involving CASC16

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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