Aliases for DIRC3 Gene

Subcategory (RNA class) for DIRC3 Gene

lncRNA

Number of RNA Genes sources:

3 / 17

Aliases for DIRC3 Gene

  • Disrupted In Renal Carcinoma 3 2 3 5
  • DIRC3 2 5
  • NONHSAG030502.2 91
  • HSALNG0022192 164
  • Lnc-DIRC3-1 165
  • FLJ14199 2

External Ids for DIRC3 Gene

Previous GeneCards Identifiers for DIRC3 Gene

  • GC00U912756
  • GC02U900716
  • GC02M218174
  • GC02M218276
  • GC02M210003

Summaries for DIRC3 Gene

GeneCards Summary for DIRC3 Gene

DIRC3 (Disrupted In Renal Carcinoma 3) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with DIRC3 include Renal Cell Carcinoma, Nonpapillary and Breast Cancer.

Additional gene information for DIRC3 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DIRC3 Gene

Genomics for DIRC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DIRC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J217756 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 0.0 -47 0.3 HNRNPL CTCF KDM1A PATZ1 REST ZFX SCRT2 ARNT RAD21 ZXDB DIRC3 piR-42059-002 TNS1 TNP1
GH02J217433 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE CraniofacialAtlas 610.2 +322.3 322297 2 SP1 RFX5 POLR2A ZBTB20 RAD21 RUNX3 ZNF444 OSR2 ZBTB17 YY1 DIRC3 LINC01921 TNP1 ENSG00000231597 ENSG00000227021 LOC105373876 piR-47675-069 lnc-RUFY4-6 TNS1
GH02J217757 Enhancer 0.6 CraniofacialAtlas dbSUPER 600.7 +0.4 415 0.2 PRDM10 KDM1A ZFX CTCF L3MBTL2 DIRC3 lnc-RUFY4-5 ENSG00000224414 LOC100533848 TNS1 TNP1
GH02J217392 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 16.2 +362.5 362502 2.6 FOXA1 CEBPB ESRRA FOS CTCF BHLHE40 RCOR1 KDM1A RAD21 RFX5 DIRC3 piR-47675-069 lnc-IGFBP2-11 TNP1 TNS1
GH02J217402 Enhancer 1 Ensembl ENCODE dbSUPER 16.5 +352.7 352692 3 ZNF629 ZNF692 PATZ1 SP1 NFIC WT1 ZFHX2 FOSL2 ZNF184 ZFP69B DIRC3 AAMP RPL37A SMARCAL1 IGFBP5 piR-47675-069 lnc-IGFBP2-11 TNP1 TNS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DIRC3 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the DIRC3 gene promoter:
  • CREB
  • deltaCREB
  • E4BP4
  • Evi-1
  • FOXF2
  • FOXO4
  • GATA-1
  • GATA-2
  • GATA-3
  • Pbx1a

Genomic Locations for DIRC3 Gene

Genomic Locations for DIRC3 Gene
chr2:217,284,019-217,756,593
(GRCh38/hg38)
Size:
472,575 bases
Orientation:
Minus strand
chr2:218,148,742-218,621,316
(GRCh37/hg19)
Size:
472,575 bases
Orientation:
Minus strand

Genomic View for DIRC3 Gene

Genes around DIRC3 on UCSC Golden Path with GeneCards custom track
DIRC3 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
DIRC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DIRC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DIRC3 Gene

Proteins for DIRC3 Gene

No data available for DME Specific Peptides for DIRC3 Gene

Domains & Families for DIRC3 Gene

Gene Families for DIRC3 Gene

genes like me logo Genes that share domains with DIRC3: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for DIRC3 Gene

Function for DIRC3 Gene

Phenotypes From GWAS Catalog for DIRC3 Gene

Phenotypes for DIRC3 Gene

genes like me logo Genes that share phenotypes with DIRC3: view

Animal Model Products

CRISPR Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for DIRC3 Gene

Localization for DIRC3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DIRC3 gene
Compartment Confidence
extracellular 2
nucleus 2
plasma membrane 1
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for DIRC3 Gene

Pathways & Interactions for DIRC3 Gene

PathCards logo

SuperPathways for DIRC3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DIRC3 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for DIRC3 Gene

Drugs & Compounds for DIRC3 Gene

No Compound Related Data Available

Transcripts for DIRC3 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for DIRC3 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS0000CCDF88_9606 lncRNA 3910 2

HGNC: 17805,

RefSeq: NR_026597,

URS00008B597D_9606 lncRNA 2582 2

Ensembl: ENST00000486365 (view in UCSC) ,

LNCipedia: lnc-DIRC3-1:1,

URS00008B8147_9606 lncRNA 660 2

Ensembl: ENST00000484635 (view in UCSC) ,

LNCipedia: lnc-DIRC3-1:5,

URS0000EF5298_9606 lncRNA 3959 1

Ensembl: ENST00000663562 (view in UCSC) ,

URS0000DB9008_9606 lncRNA 3078 1

Ensembl: ENST00000474063 (view in UCSC) ,

DIRC3 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for DIRC3 Gene

2 NCBI additional mRNA sequence :

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for DIRC3 Gene

No ASD Table

Relevant External Links for DIRC3 Gene

GeneLoc Exon Structure for
DIRC3

Expression for DIRC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DIRC3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DIRC3

SOURCE GeneReport for Unigene cluster for DIRC3 Gene:

Hs.572788

Phenotype-based relationships between genes and organs from Gene ORGANizer for DIRC3 Gene

Germ Layers:
  • endoderm
  • mesoderm
Systems:
  • endocrine
  • urinary
Regions:
Head and neck:
  • neck
  • thyroid
Abdomen:
  • kidney
genes like me logo Genes that share expression patterns with DIRC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for DIRC3 Gene

Orthologs for DIRC3 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for DIRC3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia DIRC3 31
  • 98 (a)
OneToOne
Species where no ortholog for DIRC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for DIRC3 Gene

ENSEMBL:
Gene Tree for DIRC3 (if available)
TreeFam:
Gene Tree for DIRC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DIRC3: view image

Paralogs for DIRC3 Gene

No data available for Paralogs for DIRC3 Gene

Variants for DIRC3 Gene

Additional dbSNP identifiers (rs#s) for DIRC3 Gene

Structural Variations from Database of Genomic Variants (DGV) for DIRC3 Gene

Variant ID Type Subtype PubMed ID
dgv1215e212 CNV loss 25503493
dgv4174n100 CNV gain 25217958
dgv763e214 CNV gain 21293372
esv1156929 CNV insertion 17803354
esv1580867 CNV insertion 17803354
esv2450238 CNV deletion 19546169
esv2661099 CNV deletion 23128226
esv2668873 CNV deletion 23128226
esv2721466 CNV deletion 23290073
esv2721467 CNV deletion 23290073
esv2721468 CNV deletion 23290073
esv2721469 CNV deletion 23290073
esv2721470 CNV deletion 23290073
esv3306418 CNV mobile element insertion 20981092
esv3310024 CNV mobile element insertion 20981092
esv3310286 CNV mobile element insertion 20981092
esv3329205 CNV insertion 20981092
esv3336572 CNV insertion 20981092
esv3451297 CNV insertion 20981092
esv3594312 CNV loss 21293372
esv3594314 CNV loss 21293372
esv3594318 CNV loss 21293372
esv3594319 CNV loss 21293372
esv3594320 CNV loss 21293372
esv3594323 CNV loss 21293372
esv3594324 CNV loss 21293372
esv993506 CNV deletion 20482838
nsv1006953 CNV gain 25217958
nsv1010775 CNV loss 25217958
nsv1127799 CNV deletion 24896259
nsv460101 CNV loss 19166990
nsv472963 CNV novel sequence insertion 20440878
nsv478858 CNV novel sequence insertion 20440878
nsv508129 OTHER sequence alteration 20534489
nsv523924 CNV loss 19592680
nsv527935 CNV loss 19592680
nsv584485 CNV loss 21841781
nsv834539 CNV gain 17160897
nsv834540 CNV gain 17160897
nsv962111 CNV deletion 23825009

Variation tolerance for DIRC3 Gene

Gene Damage Index Score: 6.30; 76.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DIRC3 Gene

Human Gene Mutation Database (HGMD)
DIRC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DIRC3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DIRC3 Gene

Disorders for DIRC3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for DIRC3 Gene - From: LncRNADisease, Orphanet, and DISEASES

Disorder Aliases PubMed IDs
renal cell carcinoma, nonpapillary
  • rcc
breast cancer
  • breast lobular carcinoma
differentiated thyroid carcinoma
  • papillary or follicular thyroid carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search DIRC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for DIRC3

genes like me logo Genes that share disorders with DIRC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DIRC3 Gene

Publications for DIRC3 Gene

  1. Discovery of common variants associated with low TSH levels and thyroid cancer risk. (PMID: 22267200) Gudmundsson J … Stefansson K (Nature genetics 2012) 3 41
  2. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PMID: 21998595) N'Diaye A … Haiman CA (PLoS genetics 2011) 3 41
  3. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PMID: 20881960) Lango Allen H … Hirschhorn JN (Nature 2010) 3 41
  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). (PMID: 12939738) Bodmer D … Geurts van Kessel A (Genes, chromosomes & cancer 2003) 2 3
  5. The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor. (PMID: 31881017) Coe EA … Vance KW (PLoS genetics 2019) 3

Products for DIRC3 Gene

Sources for DIRC3 Gene