Aliases for VLDLR-AS1 Gene

Data sources for VLDLR-AS1 Gene:

RNA type for VLDLR-AS1 Gene

lncRNA

Aliases for VLDLR-AS1 Gene

External Ids for VLDLR-AS1 Gene

Previous GeneCards Identifiers for VLDLR-AS1 Gene

  • GC09M002425
  • GC09M002426

Summaries for VLDLR-AS1 Gene

GeneCards Summary for VLDLR-AS1 Gene

VLDLR-AS1 (VLDLR Antisense RNA 1) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with VLDLR-AS1 include Cerebellar Ataxia, Mental Retardation, And Dysequilibrium Syndrome 1 and Hepatocellular Carcinoma. Among its related pathways are LncRNA-mediated mechanisms of therapeutic resistance.

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 VLDLR-AS1 Gene

Genomics for VLDLR-AS1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VLDLR-AS1 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
GH09J002620 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 250.4 +20.6 20581 4.4 MYC ZNF600 CEBPA POLR2A ZBTB10 MXD4 ZNF592 SIN3A ZNF341 RAD51 VLDLR HSALNG0069631-002 VLDLR-AS1 piR-54979 KCNV2
GH09J002570 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 250.2 +72.3 72286 1.6 ZNF600 ZNF580 ATF2 ZNF10 ATF3 NFIC ZIC2 CEBPB FEZF1 ZNF639 VLDLR-AS1 PUM3 ENSG00000236199 VLDLR ENSG00000231052 HSALNG0069631-001 HSALNG0069631-002 SMARCA2
GH09J002643 Promoter 0.3 EPDnew 250.7 0.0 -18 0.1 VLDLR-AS1 ENSG00000286670 VLDLR KCNV2
GH09J002725 Enhancer 1.1 Ensembl ENCODE 11 -84.7 -84741 5.8 BCLAF1 ZNF654 ZNF580 ATF2 CEBPA ATF3 YY1 REST TRIM22 ZNF639 VLDLR-AS1 VLDLR lnc-PUM3-3 KCNV2 piR-56785 PUM3
GH09J002602 Enhancer 0.9 Ensembl ENCODE 11.4 +40.4 40421 0.7 NFIC CEBPB FEZF1 ZNF217 CTBP1 PRDM1 RXRA TCF7L2 PRDM6 BHLHE40 VLDLR-AS1 HSALNG0069631-001 HSALNG0069631-002 VLDLR ENSG00000231052 SMARCA2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VLDLR-AS1 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for VLDLR-AS1 Gene

Latest Assembly
chr9:2,411,588-2,643,359
(GRCh38/hg38)
Size:
231,772 bases
Orientation:
Minus strand

Previous Assembly
chr9:2,535,652-2,622,373
(GRCh37/hg19 by Entrez Gene)
Size:
86,722 bases
Orientation:
Minus strand

chr9:2,422,702-2,641,395
(GRCh37/hg19 by Ensembl)
Size:
218,694 bases
Orientation:
Minus strand

Genomic View for VLDLR-AS1 Gene

Genes around VLDLR-AS1 on UCSC Golden Path with GeneCards custom track
VLDLR-AS1 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
VLDLR-AS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VLDLR-AS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VLDLR-AS1 Gene

Proteins for VLDLR-AS1 Gene

Post-translational modifications for VLDLR-AS1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for VLDLR-AS1 Gene

Domains & Families for VLDLR-AS1 Gene

Gene Families for VLDLR-AS1 Gene

genes like me logo Genes that share domains with VLDLR-AS1: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VLDLR-AS1 Gene

Function for VLDLR-AS1 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 VLDLR-AS1 Gene

Localization for VLDLR-AS1 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 VLDLR-AS1 Gene

Pathways & Interactions for VLDLR-AS1 Gene

PathCards logo

SuperPathways for VLDLR-AS1 Gene

genes like me logo Genes that share pathways with VLDLR-AS1: view

Pathways by source for VLDLR-AS1 Gene

1 BioSystems pathway for VLDLR-AS1 Gene

Gene Ontology (GO) - Biological Process for VLDLR-AS1 Gene

None

No data available for Interacting Proteins and SIGNOR curated interactions for VLDLR-AS1 Gene

Drugs & Compounds for VLDLR-AS1 Gene

No Compound Related Data Available

Transcripts for VLDLR-AS1 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for VLDLR-AS1 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS00002B0996_9606 lncRNA 750 4

Ensembl: ENST00000424605 (view in UCSC) ,

LncBook: HSALNT0146036,

LNCipedia: VLDLR-AS1:9,

NONCODE: NONHSAT130000.2,

URS000041FE6A_9606 lncRNA 3167 3

Ensembl: ENST00000416826 (view in UCSC) ,

LNCipedia: VLDLR-AS1:7,

NONCODE: NONHSAT129994.2,

URS000006873D_9606 lncRNA 887 3

Ensembl: ENST00000453601 (view in UCSC) ,

LNCipedia: VLDLR-AS1:3,

NONCODE: NONHSAT129999.2,

URS0000A85E0F_9606 lncRNA 1346 2

Ensembl: ENST00000599229 (view in UCSC) ,

LNCipedia: VLDLR-AS1:1,

URS0000EF0496_9606 lncRNA 4519 1

Ensembl: ENST00000671040 (view in UCSC) ,

VLDLR-AS1 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for VLDLR-AS1 Gene

5 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for VLDLR-AS1 Gene

No ASD Table

Relevant External Links for VLDLR-AS1 Gene

GeneLoc Exon Structure for
VLDLR-AS1

Expression for VLDLR-AS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VLDLR-AS1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VLDLR-AS1

genes like me logo Genes that share expression patterns with VLDLR-AS1: 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 VLDLR-AS1 Gene

Orthologs for VLDLR-AS1 Gene

Evolution for VLDLR-AS1 Gene

ENSEMBL:
Gene Tree for VLDLR-AS1 (if available)
TreeFam:
Gene Tree for VLDLR-AS1 (if available)
Alliance of Genome Resources:
Additional Orthologs for VLDLR-AS1

No data available for Orthologs for VLDLR-AS1 Gene

Paralogs for VLDLR-AS1 Gene

No data available for Paralogs for VLDLR-AS1 Gene

Variants for VLDLR-AS1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VLDLR-AS1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
912497 Uncertain Significance: Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 2,621,887(-) C/G
NM_003383.5(VLDLR):c.-303C>G
FIVE_PRIME_UTR
912498 Uncertain Significance: Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 2,621,888(-) T/C
NM_003383.5(VLDLR):c.-302T>C
FIVE_PRIME_UTR
912499 Uncertain Significance: Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 2,621,983(-) G/A
NM_003383.5(VLDLR):c.-207G>A
FIVE_PRIME_UTR
913612 Uncertain Significance: Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 2,622,036(-) C/G
NM_003383.5(VLDLR):c.-154C>G
FIVE_PRIME_UTR
913613 Uncertain Significance: Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 2,622,091(-) C/G
NM_003383.5(VLDLR):c.-99C>G
FIVE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VLDLR-AS1 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 VLDLR-AS1 Gene

Variant ID Type Subtype PubMed ID
esv1360174 CNV insertion 17803354
esv3619295 CNV loss 21293372
nsv1020530 CNV gain 25217958
nsv1029876 CNV gain 25217958
nsv1033424 CNV gain 25217958
nsv1133705 CNV deletion 24896259
nsv466078 CNV gain 19166990
nsv466081 CNV gain 19166990
nsv518550 CNV loss 19592680
nsv525208 CNV loss 19592680
nsv527298 CNV loss 19592680
nsv613126 CNV gain 21841781
nsv613132 CNV gain 21841781
nsv824819 CNV gain 20364138

Additional Variant Information for VLDLR-AS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VLDLR-AS1
Leiden Open Variation Database (LOVD)
VLDLR-AS1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for VLDLR-AS1 Gene

Disorders for VLDLR-AS1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VLDLR-AS1 Gene - From: LNC, CVR, and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for VLDLR-AS1

genes like me logo Genes that share disorders with VLDLR-AS1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VLDLR-AS1 Gene

Publications for VLDLR-AS1 Gene

  1. Involvement of extracellular vesicle long noncoding RNA (linc-VLDLR) in tumor cell responses to chemotherapy. (PMID: 24874432) Takahashi K … Patel T (Molecular cancer research : MCR 2014) 2 3 72
  2. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. (PMID: 21057500) Loewer S … Rinn JL (Nature genetics 2010) 2 3
  3. Effects of long noncoding RNA (linc-VLDLR) existing in extracellular vesicles on the occurrence and multidrug resistance of esophageal cancer cells. (PMID: 30606658) Chen Y … Liu J (Pathology, research and practice 2019) 3
  4. Genome-wide association study of a quantitative disordered gambling trait. (PMID: 22780124) Lind PA … Slutske WS (Addiction biology 2013) 3
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K … Sugano S (Genome research 2006) 3

Products for VLDLR-AS1 Gene

Sources for VLDLR-AS1 Gene