Aliases for LINC01239 Gene

Data sources for LINC01239 Gene:

RNA type for LINC01239 Gene

lncRNA

Aliases for LINC01239 Gene

External Ids for LINC01239 Gene

Previous GeneCards Identifiers for LINC01239 Gene

  • GC09P022648
  • GC09P022238

Summaries for LINC01239 Gene

GeneCards Summary for LINC01239 Gene

LINC01239 (Long Intergenic Non-Protein Coding RNA 1239) is an RNA Gene, and is affiliated with the lncRNA class.

Additional gene information for LINC01239 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 LINC01239 Gene

Genomics for LINC01239 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LINC01239 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
GH09J022646 Promoter 0.3 EPDnew 250 +519.3 519286 0.1 LINC01239 lnc-CDKN2B-5 HSALNG0070412 DMRTA1
GH09J022684 Enhancer 0.8 Ensembl ENCODE 15.8 +556.5 556542 1.7 CEBPB FEZF1 EP300 STAT3 ZNF189 INSM2 ZSCAN23 ZNF24 JUND ZNF362 LINC01239 ENSG00000224549 piR-61580-630 lnc-DMRTA1-10 LOC107987054 DMRTA1 ENSG00000284418
GH09J022630 Enhancer 0.3 Ensembl 10.1 +504.1 504109 1.2 FOXA2 LINC01239 HSALNG0070412 lnc-CDKN2B-5 DMRTA1
GH09J022127 Enhancer 0.9 VISTA Ensembl ENCODE dbSUPER 0.7 +2.4 2355 3.1 EP300 FOXA2 POLR2A LINC01239 RF00017-6898 lnc-MTAP-7 HSALNG0070392-001 CDKN2B CDKN2B-AS1 DMRTA1
GH09J022156 Enhancer 1.2 Ensembl ENCODE dbSUPER 0.3 +32.6 32642 6.1 JUND CEBPA MXD4 CEBPB HOMEZ MAX EP300 THAP11 FOXA2 MAFF UBA52P6 CDKN2B RF00017-6898 LINC01239 lnc-CDKN2B-4 HSALNG0070392-001 CDKN2B-AS1 DMRTA1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINC01239 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for LINC01239 Gene

Latest Assembly
chr9:22,126,892-22,824,214
(GRCh38/hg38)
Size:
697,323 bases
Orientation:
Plus strand

Previous Assembly
chr9:22,646,199-22,824,212
(GRCh37/hg19 by Entrez Gene)
Size:
178,014 bases
Orientation:
Plus strand

chr9:22,646,199-22,824,212
(GRCh37/hg19 by Ensembl)
Size:
178,014 bases
Orientation:
Plus strand

Genomic View for LINC01239 Gene

Genes around LINC01239 on UCSC Golden Path with GeneCards custom track
LINC01239 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
LINC01239 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINC01239 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINC01239 Gene

Proteins for LINC01239 Gene

Post-translational modifications for LINC01239 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINC01239 Gene

Domains & Families for LINC01239 Gene

Gene Families for LINC01239 Gene

genes like me logo Genes that share domains with LINC01239: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LINC01239 Gene

Function for LINC01239 Gene

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LINC01239 Gene

Localization for LINC01239 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for LINC01239 Gene

Pathways & Interactions for LINC01239 Gene

PathCards logo

SuperPathways for LINC01239 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LINC01239 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for LINC01239 Gene

Drugs & Compounds for LINC01239 Gene

No Compound Related Data Available

Transcripts for LINC01239 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for LINC01239 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS00000E9163_9606 lncRNA 2347 4

RefSeq: NR_038977,

Ensembl: ENST00000436786 (view in UCSC) ,

LNCipedia: LINC01239:3,

NONCODE: NONHSAT130442.2,

URS0000EF2DE7_9606 lncRNA 1187 1

Ensembl: ENST00000669551 (view in UCSC) ,

URS0000152C9D_9606 lncRNA 325 3

LncBook: HSALNT0147498,

LNCipedia: LINC01239:5,

NONCODE: NONHSAT130444.2,

URS00008B7A14_9606 lncRNA 2954 2

LNCipedia: LINC01239:2,

NONCODE: NONHSAT130441.2,

URS00008B37BD_9606 lncRNA 1381 2

LNCipedia: LINC01239:6,

NONCODE: NONHSAT130449.2,

LINC01239 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for LINC01239 Gene

1 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for LINC01239 Gene

No ASD Table

Relevant External Links for LINC01239 Gene

GeneLoc Exon Structure for
LINC01239

Expression for LINC01239 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LINC01239 Gene

mRNA differential expression in normal tissues according to GTEx for LINC01239 Gene

This gene is overexpressed in Adipose - Subcutaneous (x9.9) and Breast - Mammary Tissue (x5.9).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LINC01239

genes like me logo Genes that share expression patterns with LINC01239: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LINC01239 Gene

Orthologs for LINC01239 Gene

Evolution for LINC01239 Gene

ENSEMBL:
Gene Tree for LINC01239 (if available)
TreeFam:
Gene Tree for LINC01239 (if available)
Alliance of Genome Resources:
Additional Orthologs for LINC01239

No data available for Orthologs for LINC01239 Gene

Paralogs for LINC01239 Gene

No data available for Paralogs for LINC01239 Gene

Variants for LINC01239 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LINC01239 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LINC01239 Gene

Variant ID Type Subtype PubMed ID
dgv3968n106 CNV deletion 24896259
dgv7476n100 CNV loss 25217958
esv2142565 CNV deletion 18987734
esv2591956 CNV deletion 19546169
esv2657957 CNV deletion 23128226
esv2658099 CNV deletion 23128226
esv2666665 CNV deletion 23128226
esv2667071 CNV deletion 23128226
esv2675508 CNV deletion 23128226
esv2738287 CNV deletion 23290073
esv2738288 CNV deletion 23290073
esv2738289 CNV deletion 23290073
esv2738290 CNV deletion 23290073
esv2759681 CNV gain 17122850
esv2761290 CNV loss 21179565
esv2761508 CNV gain 21179565
esv29499 CNV gain 19812545
esv34240 CNV loss 17911159
esv3544663 CNV deletion 23714750
esv3544664 CNV deletion 23714750
esv3573170 CNV loss 25503493
esv3619989 CNV loss 21293372
esv3619990 CNV loss 21293372
esv3619991 CNV loss 21293372
esv3619992 CNV loss 21293372
esv3619993 CNV loss 21293372
esv3619995 CNV loss 21293372
esv3619996 CNV loss 21293372
esv3619997 CNV loss 21293372
esv3891634 CNV gain 25118596
esv3891635 CNV loss 25118596
esv5075 CNV loss 18987735
nsv1016983 CNV gain 25217958
nsv1019512 CNV gain 25217958
nsv1020027 CNV loss 25217958
nsv1022751 CNV loss 25217958
nsv1030670 CNV loss 25217958
nsv1130890 CNV deletion 24896259
nsv1140962 CNV deletion 24896259
nsv1153828 CNV deletion 26484159
nsv511407 CNV loss 21212237
nsv512092 CNV loss 21212237
nsv519091 CNV loss 19592680
nsv613786 CNV loss 21841781
nsv613787 CNV loss 21841781
nsv613788 CNV loss 21841781
nsv613789 CNV loss 21841781
nsv820957 CNV deletion 20802225
nsv824880 CNV gain 20364138
nsv824881 CNV gain 20364138
nsv824882 CNV loss 20364138
nsv8427 CNV loss 18304495
nsv972655 CNV duplication 23825009

Additional Variant Information for LINC01239 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINC01239
Leiden Open Variation Database (LOVD)
LINC01239

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for LINC01239 Gene

Disorders for LINC01239 Gene

Additional Disease Information for LINC01239

No disorders were found for LINC01239 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LINC01239 Gene

Publications for LINC01239 Gene

  1. Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. (PMID: 23453885) Cross-Disorder Group of the Psychiatric Genomics Consortium (Lancet (London, England) 2013) 3
  2. Genomewide association study of movement-related adverse antipsychotic effects. (PMID: 19875103) Aberg K … van den Oord EJ (Biological psychiatry 2010) 3
  3. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. (PMID: 19197348) Lowe JK … Friedman JM (PLoS genetics 2009) 3
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3
  5. Generation and analysis of 280,000 human expressed sequence tags. (PMID: 8889549) Hillier LD … Marra M (Genome research 1996) 3

Products for LINC01239 Gene

Sources for LINC01239 Gene