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CRNDE Gene

RNA gene   GIFtS: 23
GCID: GC16M054953

Colorectal Neoplasia Differentially Expressed (Non-Protein...

  See related diseases
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
Colorectal Neoplasia Differentially Expressed (Non-Protein Coding)1 2
Long Intergenic Non-Protein Coding RNA 1801
LINC001802
NCRNA001802

External Ids:    HGNC: 370781   Entrez Gene: 6439112   Ensembl: ENSG000002456947   OMIM: 6156245   

Export aliases for CRNDE gene to outside databases

Previous GC identifers: GC16M053512 GC16M040838


(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 CRNDE Gene:
CRNDE (colorectal neoplasia differentially expressed (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with CRNDE include adenoma, and adenocarcinoma.


(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:
NC_000016.10  NC_018927.2  NT_010498.16  
Regulatory elements:
   Search for regulatory transcription factor binding sites for CRNDE
         Other transcription factors

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


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

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

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

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M054953:  view genomic region     (about GC identifiers)

Start:
54,952,775 bp from pter      End:
54,963,101 bp from pter
Size:
10,327 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for CRNDE

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, 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 CRNDE
Interactions:

    Search GeneGlobe Interaction Network for CRNDE

(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 CRNDE



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for CRNDE:

Colorectal neoplasia differentially expressed (non-protein coding)
Hs.237396  [show with all ESTs]
Unigene Representative Sequence: BQ431041
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000501177(lincRNA)(uc010vhb.2) ENST00000559598(lincRNA)(uc010vhc.2) ENST00000560029(lincRNA)
ENST00000502066(lincRNA)(uc002ehu.2) ENST00000558031(lincRNA) ENST00000559432(lincRNA) ENST00000560912(lincRNA)
ENST00000558952(lincRNA) ENST00000560208(lincRNA) ENST00000557792(lincRNA)
miRNA
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Additional mRNA sequence: 

AF275804.1 FJ466685.1 FJ466686.1 NR_034105.2 NR_034106.1 

9 DOTS entries:

DT.97770909  DT.455174  DT.87046257  DT.100035576  DT.100035575  DT.95131063  DT.75153908  DT.92419926 
DT.99945836 

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 CRNDE:none

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


CRNDE expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Adipose (Muscoskeletal System)
         HyStem+BMP4-induced E15 cells
 
 Bone (Muscoskeletal System)
         HyStem+BMP4-induced E15 cells
 
 Cartilage (Muscoskeletal System)
         HyStem+BMP4-induced E15 cells
CRNDE Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.237396
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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 CRNDE (if available)
TreeFam Gene Tree for CRNDE (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 CRNDE (see all 156)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs50060751,2
C,F--54952312(+) CCTTTG/CTGGAC 2 -- int12Minor allele frequency- C:0.25WA 120
rs1878793171,2
--54952385(+) CAAAGA/TGGCTA 2 -- int10--------
rs1925108471,2
--54952436(+) GCTGCC/TACAAA 2 -- int10--------
rs1844455851,2
--54952636(+) AGGGAC/TTATTA 2 -- int10--------
rs1886921081,2
--54952808(+) AAACAG/TTCATT 2 -- nc-transcript-variant0--------
rs1915979291,2
--54952869(+) ATTTTC/TCCTAT 2 -- nc-transcript-variant0--------
rs1844199401,2
--54952939(+) ACTGGC/TAATCA 2 -- nc-transcript-variant0--------
rs1439396611,2
--54953071(+) TCTTTA/GCATCT 2 -- nc-transcript-variant0--------
rs1887969261,2
C--54953113(+) ACCAAC/TGGCTG 2 -- nc-transcript-variant0--------
rs1155155941,2
C,F--54953114(+) CCAACG/AGCTGA 2 -- nc-transcript-variant2Minor allele frequency- A:0.04WA NA 238

HapMap Linkage Disequilibrium report for CRNDE (54952775 - 54963101 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for CRNDE:    About this table    
Variant IDTypeSubtypePubMed ID
nsv827657CNV Gain20364138

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

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 615624    OMIM disorders: --

2 diseases for CRNDE:    About MalaCards
adenoma    adenocarcinoma


CRNDE for disorders           About GeneDecksing


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

  1. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. (PubMed id 24381249)1, 3 Sauvageau M....Rinn J.L. (Elife 2013)
  2. CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment. (PubMed id 23226159)1, 3 Ellis B.C....Graham L.D. (Front Genet 2012)
  3. CRNDE, a long non-coding RNA responsive to insulin/IGF signaling, regulates genes involved in central metabolism. (PubMed id 24184209)1 Ellis B.C....Molloy P.L. (Biochim. Biophys. Acta 2014)
  4. SF3B1 mutations are associated with alternative splicing in uveal melanoma. (PubMed id 23861464)1 Furney S.J....Marais R. (Cancer Discov 2013)
  5. Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas. (PubMed id 22393467)1 Graham L.D....Molloy P.L. (amp 2011)
  6. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)
  7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

(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: 643911 HGNC: 37078 Ensembl:ENSG00000245694 euGenes: HUgn643911 ECgene: CRNDE
H-InvDB: CRNDE

(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 CRNDE 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 CRNDE gene:
Search GeneIP for patents involving CRNDE

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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