Aliases for LINC01539 Gene

Data sources for LINC01539 Gene:

Subcategory (RNA class) for LINC01539 Gene

lncRNA

Aliases for LINC01539 Gene

External Ids for LINC01539 Gene

Summaries for LINC01539 Gene

GeneCards Summary for LINC01539 Gene

LINC01539 (Long Intergenic Non-Protein Coding RNA 1539) is an RNA Gene, and is affiliated with the lncRNA class.

Additional gene information for LINC01539 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 LINC01539 Gene

Genomics for LINC01539 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LINC01539 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
GH18J056137 Promoter 0.3 EPDnew 250.7 +0.0 8 0.1 ENSG00000267732 LINC01539 LOC105372132 LOC642484 TCF4 WDR7
GH18J056112 Enhancer 0.8 Ensembl 0.3 +22.6 22636 5.4 BCL11A IRF4 EBF1 FOSL1 CBFB SPI1 BHLHE40 BATF STAT5A ZNF24 ENSG00000201816 LINC01539 ENSG00000267732 HSALNG0121713 LOC642484 LINC01905 TCF4 WDR7
GH18J056127 Enhancer 0.5 FANTOM5 Ensembl 0.4 +9.9 9935 1.6 CEBPB NFIC ENSG00000267732 LINC01539 HSALNG0121713 LOC642484 LINC01905 TCF4 WDR7
GH18J056123 Enhancer 0.6 Ensembl ENCODE 0.4 +13.1 13136 1.2 BHLHE40 CEBPB FOS LINC01539 ENSG00000267732 HSALNG0121713 LOC642484 LINC01905 TCF4 WDR7
GH18J056082 Enhancer 0.6 Ensembl ENCODE 0.2 +54.1 54135 4 CTCF RAD21 NR2F2 LOC642484 HSALNG0121713 ENSG00000267732 LINC01539 LINC01905 TCF4 WDR7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINC01539 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for LINC01539 Gene

Latest Assembly
chr18:56,083,355-56,137,536
(GRCh38/hg38)
Size:
54,182 bases
Orientation:
Minus strand

Previous Assembly
chr18:53,750,587-53,804,767
(GRCh37/hg19 by Entrez Gene)
Size:
54,181 bases
Orientation:
Minus strand

chr18:53,750,587-53,804,767
(GRCh37/hg19 by Ensembl)
Size:
54,181 bases
Orientation:
Minus strand

Genomic View for LINC01539 Gene

Genes around LINC01539 on UCSC Golden Path with GeneCards custom track
LINC01539 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
LINC01539 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINC01539 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINC01539 Gene

Proteins for LINC01539 Gene

Post-translational modifications for LINC01539 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINC01539 Gene

Domains & Families for LINC01539 Gene

Gene Families for LINC01539 Gene

genes like me logo Genes that share domains with LINC01539: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LINC01539 Gene

Function for LINC01539 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 LINC01539 Gene

Localization for LINC01539 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 LINC01539 Gene

Pathways & Interactions for LINC01539 Gene

PathCards logo

SuperPathways for LINC01539 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LINC01539 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for LINC01539 Gene

Drugs & Compounds for LINC01539 Gene

No Compound Related Data Available

Transcripts for LINC01539 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for LINC01539 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS0000759985_9606 lncRNA 2093 4

RefSeq: NR_040025,

LncBook: HSALNT0251609,

LNCipedia: LINC01539:5,

NONCODE: NONHSAT059405.2,

URS0000158AB6_9606 lncRNA 1893 4

RefSeq: NR_040026,

Ensembl: ENST00000591974 (view in UCSC) ,

LNCipedia: LINC01539:6,

NONCODE: NONHSAT059406.2,

URS0000455D3F_9606 lncRNA 681 4

Ensembl: ENST00000593282 (view in UCSC) ,

LncBook: HSALNT0251615,

LNCipedia: LINC01539:14,

NONCODE: NONHSAT059409.2,

URS00002BF94D_9606 lncRNA 575 4

Ensembl: ENST00000589447 (view in UCSC) ,

LncBook: HSALNT0251625,

LNCipedia: LINC01539:15,

NONCODE: NONHSAT059415.2,

URS00002F406C_9606 lncRNA 2068 3

Ensembl: ENST00000587904 (view in UCSC) ,

LncBook: HSALNT0251610,

LNCipedia: LINC01539:7,

LINC01539 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for LINC01539 Gene

2 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for LINC01539 Gene

No ASD Table

Relevant External Links for LINC01539 Gene

GeneLoc Exon Structure for
LINC01539

Expression for LINC01539 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LINC01539 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LINC01539

genes like me logo Genes that share expression patterns with LINC01539: 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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LINC01539 Gene

Orthologs for LINC01539 Gene

Evolution for LINC01539 Gene

ENSEMBL:
Gene Tree for LINC01539 (if available)
TreeFam:
Gene Tree for LINC01539 (if available)

No data available for Orthologs for LINC01539 Gene

Paralogs for LINC01539 Gene

No data available for Paralogs for LINC01539 Gene

Variants for LINC01539 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LINC01539 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 LINC01539 Gene

Variant ID Type Subtype PubMed ID
dgv1611n106 CNV deletion 24896259
dgv1612n106 CNV deletion 24896259
dgv202e215 CNV deletion 23714750
esv1107800 CNV deletion 17803354
esv2506493 CNV deletion 19546169
esv25232 CNV loss 19812545
esv2677523 CNV deletion 23128226
esv2717134 CNV deletion 23290073
esv2717135 CNV deletion 23290073
esv3309728 CNV mobile element insertion 20981092
esv3405855 CNV insertion 20981092
esv3642604 CNV loss 21293372
nsv1126363 CNV deletion 24896259
nsv1141911 CNV deletion 24896259
nsv1146590 CNV deletion 26484159
nsv477130 CNV novel sequence insertion 20440878
nsv833661 CNV gain 17160897

Additional Variant Information for LINC01539 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINC01539

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 LINC01539 Gene

Disorders for LINC01539 Gene

Additional Disease Information for LINC01539

No disorders were found for LINC01539 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LINC01539 Gene

Publications for LINC01539 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3

Products for LINC01539 Gene

Sources for LINC01539 Gene