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DIRC3 Gene

protein-coding   GIFtS: 32
GCID: GC02M218174

Disrupted In Renal Carcinoma 3

  See DIRC3-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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Disrupted In Renal Carcinoma 31 2

External Ids:    HGNC: 178051   Entrez Gene: 7295822   Ensembl: ENSG000002316727   OMIM: 6082625   UniProtKB: C9JPN64   
ORGUL members:         

Export aliases for DIRC3 gene to outside databases

Previous GC identifers: GC00U912756 GC02U900716 GC02M218276 GC02M210003


(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 DIRC3 Gene:
DIRC3 (disrupted in renal carcinoma 3) is a protein-coding gene. Diseases associated with DIRC3 include familial renal cell carcinoma, and follicular thyroid carcinoma.


(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_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the DIRC3 gene promoter:
         GATA-3   FOXF2   Pbx1a   E4BP4   Evi-1   GATA-1   GATA-2   CREB   deltaCREB   FOXO4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for DIRC3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DIRC3


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

Entrez Gene cytogenetic band: 2q35   Ensembl cytogenetic band:  2q35   HGNC cytogenetic band: 2q35

DIRC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DIRC3 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M218174:  view genomic region     (about GC identifiers)

Start:
218,148,742 bp from pter      End:
218,621,316 bp from pter
Size:
472,575 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for DIRC3

(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/TrEMBL: C9JPN6 (See protein sequence)
Recommended Name: Protein DIRC3  
Size: 131 amino acids; 14375 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data


ENSEMBL proteins: 
 ENSP00000389455  

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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: C9JPN6


(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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular2
cytosol1
nucleus1
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 DIRC3
Interactions:

    Search GeneGlobe Interaction Network for DIRC3

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for DIRC3 (ENSP000003894554) via UniProtKB, MINT, STRING, and/or I2D (see all 190)
InteractantInteraction Details
GeneCardExternal ID(s)
GTPBP4ENSP000003540404STRING: ENSP00000354040
RPF1ENSP000003596884STRING: ENSP00000359688
RPL18ENSP000000847954STRING: ENSP00000084795
RPL24ENSP000003776404STRING: ENSP00000377640
RPL27AENSP000003460154STRING: ENSP00000346015
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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 DIRC3



(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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Unigene Cluster for DIRC3:

Disrupted in renal carcinoma 3
Hs.572788  [show with all ESTs]
Unigene Representative Sequence: NR_026597
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000474063(uc002vgn.2 uc002vgo.3) ENST00000486365 ENST00000484635
ENST00000423123
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Additional mRNA sequence: 

AK024261.1 AK090954.1 NR_026597.1 

3 DOTS entries:

DT.309715  DT.100745263  DT.40313650 

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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DIRC3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAGAAACTTA
DIRC3 Expression
About this image

DIRC3 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.572788
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In Situ
Assay Products:
 

 
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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 human and chimp.

Orthologs for DIRC3 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia DIRC36
disrupted in renal carcinoma 3
98(a)
1 ↔ 1
2B(222754314-222807022)


ENSEMBL Gene Tree for DIRC3 (if available)
TreeFam Gene Tree for DIRC3 (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 DIRC3 (see all 9339)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs665354631,2
C--210112837(+) CCTCA-/CC/CCC
        
CCCCC
1 -- int12NA CSA 4
rs340783081,2
C--210373534(+) CTTTT-/CTATTTT 1 -- int11Minor allele frequency- CT:0.00NA 2
rs343719501,2
C--217799119(+) ATCTC-/AAAAAAAA 1 -- int10--------
rs606481291,2
C--217978493(+) TTTTT-/TTTGAGAT 1 -- int11Minor allele frequency- TTT:0.00NA 2
rs1823995111,2
--218148256(+) TCACAA/TAAATC 1 -- ds50010--------
rs1869796521,2
--218148425(+) TCCCAC/TGCACT 1 -- ds50010--------
rs1430642711,2
--218148426(+) CCCACA/GCACTC 1 -- ds50010--------
rs1460513391,2
--218148590(+) CCACAA/TGATGT 1 -- ds50010--------
rs1134709111,2
C--218148766(+) AGTAAA/GTTTTA 1 -- nc-transcript-variant0--------
rs1827467201,2
--218148793(+) AGATTC/GTAATC 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for DIRC3 (218148742 - 218398742 bp, first 250kb of DIRC3)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for DIRC3 (see all 22):    About this table    
Variant IDTypeSubtypePubMed ID
esv993506CNV Deletion20482838
esv2721469CNV Deletion23290073
esv2721468CNV Deletion23290073
esv2668873CNV Deletion23128226
esv2661099CNV Deletion23128226
esv2721467CNV Deletion23290073
esv2721466CNV Deletion23290073
esv2721470CNV Deletion23290073
esv2450238CNV Deletion19546169
esv269834CNV Insertion20981092

Human Gene Mutation Database (HGMD): DIRC3
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing DIRC3
DNA2.0 Custom Variant and Variant Library Synthesis for DIRC3

(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 gene information: 608262    OMIM disorders: --

2 diseases for DIRC3:    
About MalaCards
familial renal cell carcinoma    follicular thyroid carcinoma


Find genes that share disorders with DIRC3           About GenesLikeMe

Genetic Association Database (GAD): DIRC3

Export disorders for DIRC3 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 DIRC3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with DIRC3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Discovery of common variants associated with low TSH levels and thyroid cancer risk. (PubMed id 22267200)1, 4 Gudmundsson J....Stefansson K. (Nat. Genet. 2012)
  2. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PubMed id 21998595)1, 4 N'Diaye A....Haiman C.A. (PLoS Genet. 2011)
  3. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)1, 4 Lango Allen H....Hirschhorn J.N. (Nature 2010)
  4. Disruption of a novel gene, DIRC3, and expression of DIRC3-HSPBAP1 fusion transcripts in a case of familial renal cell cancer and t(2;3)(q35;q21). (PubMed id 12939738)1, 3 Bodmer D....Geurts van Kessel A. (Genes Chromosomes Cancer 2003)
  5. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. (PubMed id 23535729)1 Michailidou K....Easton D.F. (Nat. Genet. 2013)
  6. Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. (PubMed id 23319000)1 Luykx J.J....Ophoff R.A. (Mol. Psychiatry 2013)
  7. Genome-wide association study on differentiated thyroid cancer. (PubMed id 23894154)1 KAPhler A....FAPrsti A. (J. Clin. Endocrinol. Metab. 2013)
  8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)

(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: 729582 HGNC: 17805 Ensembl:ENSG00000231672 euGenes: HUgn729582 ECgene: DIRC3
H-InvDB: DIRC3

(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 DIRC3 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for DIRC3 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for DIRC3 gene:
Search GeneIP for patents involving DIRC3

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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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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