Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LINC00339 Gene

Subcategory (RNA class) for LINC00339 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for LINC00339 Gene

  • Long Intergenic Non-Protein Coding RNA 339 2 3 5
  • Non-Protein Coding RNA 339 2
  • NCRNA00339 3
  • HSPC157 3

External Ids for LINC00339 Gene

Previous HGNC Symbols for LINC00339 Gene

  • NCRNA00339

Previous GeneCards Identifiers for LINC00339 Gene

  • GC01P022353
  • GC01P022025

Summaries for LINC00339 Gene

GeneCards Summary for LINC00339 Gene

LINC00339 (Long Intergenic Non-Protein Coding RNA 339) is an RNA Gene, and is affiliated with the non-coding RNA class. Diseases associated with LINC00339 include Pancreatic Ductal Adenocarcinoma and Astrocytoma.

Additional gene information for LINC00339 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LINC00339 Gene

Genomics for LINC00339 Gene

GeneHancer (GH) Regulatory Elements for LINC00339 Gene

Promoters and enhancers for LINC00339 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J022023 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 706.6 +1.2 1180 3.8 ZNF652 SP1 CC2D1A ZFX ELF3 ZKSCAN8 CBFA2T2 NKRF POLR2A MLLT1 LINC00339 LINC01635 CDC42 ZBTB40 KDM1A USP48 CDC42-IT1 ENSG00000271428 HSPG2 NBPF3
GH01J022022 Enhancer 0.8 ENCODE 600.7 -1.5 -1525 0.2 ZNF652 CTCF MLLT1 ZSCAN21 SP7 PPARG ZNF644 RAD21 MTA1 GMEB1 LINC00339 HSPG2 WNT4 RNU6-776P ENSG00000285959
GH01J022051 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 45.3 +28.8 28814 3.3 HDGF ZNF652 SP1 CC2D1A ZFX ELF3 MNT ZNF148 NKRF POLR2A CDC42 CDC42-AS1 ZBTB40 KDM1A USP48 LINC00339 CDC42-IT1 NBPF3 ENSG00000271428 NBPF2P
GH01J022037 Enhancer 1.5 FANTOM5 ENCODE dbSUPER 48 +16.1 16143 6.7 SP1 CBFA2T2 ZNF121 GTF2F1 ZNF687 CREM MLLT1 SMARCA4 MTA1 IKZF1 LINC00339 HSPG2 ZBTB40 LDLRAD2 LINC01635 CDC42-IT1 USP48 GC01M022038 CDC42-AS1 CDC42
GH01J022133 Enhancer 1.2 Ensembl ENCODE dbSUPER 40.4 +108.6 108643 3.2 CC2D1A CTCF NFIB RAD21 GLIS2 ARID2 ZBTB8A ZNF600 ZIC2 ZNF143 LINC00339 CDC42 PIR60757 LOC105376845 WNT4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINC00339 on UCSC Golden Path with GeneCards custom track

Genomic Locations for LINC00339 Gene

Genomic Locations for LINC00339 Gene
6,667 bases
Plus strand
6,036 bases
Plus strand

Genomic View for LINC00339 Gene

Genes around LINC00339 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LINC00339 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINC00339 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINC00339 Gene

Proteins for LINC00339 Gene

Post-translational modifications for LINC00339 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINC00339 Gene

Domains & Families for LINC00339 Gene

Graphical View of Domain Structure for InterPro Entry

No data available for Gene Families , Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for LINC00339 Gene

Function for LINC00339 Gene

Phenotypes From GWAS Catalog for LINC00339 Gene

Phenotypes for LINC00339 Gene

genes like me logo Genes that share phenotypes with LINC00339: 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 LINC00339 Gene

Localization for LINC00339 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 LINC00339 Gene

Pathways & Interactions for LINC00339 Gene

PathCards logo

SuperPathways for LINC00339 Gene

No Data Available

Interacting Proteins for LINC00339 Gene

Gene Ontology (GO) - Biological Process for LINC00339 Gene


No data available for Pathways by source and SIGNOR curated interactions for LINC00339 Gene

Drugs & Compounds for LINC00339 Gene

No Compound Related Data Available

Transcripts for LINC00339 Gene

mRNA/cDNA for LINC00339 Gene

(9) Additional mRNA sequences :
(13) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(6) RNA Central transcripts :

Unigene Clusters for LINC00339 Gene

Long intergenic non-protein coding RNA 339:
Representative Sequences:

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for LINC00339 Gene

No ASD Table

Relevant External Links for LINC00339 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LINC00339 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LINC00339 Gene

mRNA differential expression in normal tissues according to GTEx for LINC00339 Gene

This gene is overexpressed in Pancreas (x7.5).

NURSA nuclear receptor signaling pathways regulating expression of LINC00339 Gene:


SOURCE GeneReport for Unigene cluster for LINC00339 Gene:

genes like me logo Genes that share expression patterns with LINC00339: view

Primer Products

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 LINC00339 Gene

Orthologs for LINC00339 Gene

Evolution for LINC00339 Gene

Gene Tree for LINC00339 (if available)
Gene Tree for LINC00339 (if available)

No data available for Orthologs for LINC00339 Gene

Paralogs for LINC00339 Gene

No data available for Paralogs for LINC00339 Gene

Variants for LINC00339 Gene

Sequence variations from dbSNP and Humsavar for LINC00339 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000077250 -- 22,031,222(+) A/G non_coding_transcript_variant
rs1000874989 -- 22,030,915(+) G/C non_coding_transcript_variant
rs1000973725 -- 22,025,280(+) T/C genic_upstream_transcript_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1001043236 -- 22,026,758(+) T/C intron_variant
rs1001252446 -- 22,024,407(+) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LINC00339 Gene

Variant ID Type Subtype PubMed ID
esv2758927 CNV loss 17122850
esv2764236 CNV gain+loss 21179565
nsv528664 CNV gain 19592680
nsv545745 CNV loss 21841781
nsv834413 CNV loss 17160897

Additional Variant Information for LINC00339 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for LINC00339 Gene

Disorders for LINC00339 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LINC00339 Gene - From: LncRNADisease and DISEASES

Disorder Aliases PubMed IDs
pancreatic ductal adenocarcinoma
  • ductal adenocarcinoma of the pancreas
  • astrocytic tumor
breast cancer
  • breast tumor
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LINC00339

genes like me logo Genes that share disorders with LINC00339: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LINC00339 Gene

Publications for LINC00339 Gene

  1. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. (PMID: 29706346) Chen XF … Yang TL (American journal of human genetics 2018) 2 3 58
  2. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang QH … Chen Z (Genome research 2000) 2 3 58
  3. Long non-coding RNA LINC00339 facilitates the tumorigenesis of non-small cell lung cancer by sponging miR-145 through targeting FOXM1. (PMID: 29906749) Yuan Y … Xin H (Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2018) 3 58
  4. Endometriosis risk alleles at 1p36.12 act through inverse regulation of CDC42 and LINC00339. (PMID: 28171565) Powell JE … Montgomery GW (Human molecular genetics 2016) 3 58
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for LINC00339 Gene

Sources for LINC00339 Gene

Loading form....