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Aliases for HDLBP Gene

Aliases for HDLBP Gene

  • High Density Lipoprotein Binding Protein 2 3 5
  • High Density Lipoprotein-Binding Protein 3 4
  • HDL-Binding Protein 3 4
  • HBP 3 4
  • VGL 3 4
  • Vigilin 2
  • PRO2900 3

External Ids for HDLBP Gene

Previous HGNC Symbols for HDLBP Gene

  • VGL

Previous GeneCards Identifiers for HDLBP Gene

  • GC02P239181
  • GC02P240038
  • GC02M242188
  • GC02M242489
  • GC02M242488
  • GC02M241888
  • GC02M233922
  • GC02M242166

Summaries for HDLBP Gene

Entrez Gene Summary for HDLBP Gene

  • The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 2016]

GeneCards Summary for HDLBP Gene

HDLBP (High Density Lipoprotein Binding Protein) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is BICC1.

UniProtKB/Swiss-Prot for HDLBP Gene

  • Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Gene Wiki entry for HDLBP Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HDLBP Gene

Genomics for HDLBP Gene

Regulatory Elements for HDLBP Gene

Promoters for HDLBP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HDLBP on UCSC Golden Path with GeneCards custom track

Genomic Location for HDLBP Gene

Chromosome:
2
Start:
241,227,264 bp from pter
End:
241,317,061 bp from pter
Size:
89,798 bases
Orientation:
Minus strand

Genomic View for HDLBP Gene

Genes around HDLBP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HDLBP Gene

Proteins for HDLBP Gene

  • Protein details for HDLBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q00341-VIGLN_HUMAN
    Recommended name:
    Vigilin
    Protein Accession:
    Q00341
    Secondary Accessions:
    • B4DTQ2
    • E7EM71
    • Q53QU2
    • Q9UCY3

    Protein attributes for HDLBP Gene

    Size:
    1268 amino acids
    Molecular mass:
    141456 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for HDLBP Gene

    Alternative splice isoforms for HDLBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDLBP Gene

Proteomics data for HDLBP Gene at MOPED

Post-translational modifications for HDLBP Gene

  • Ubiquitination at Lys 231
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for HDLBP Gene

Domains & Families for HDLBP Gene

Protein Domains for HDLBP Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HDLBP Gene

Graphical View of Domain Structure for InterPro Entry

Q00341

UniProtKB/Swiss-Prot:

VIGLN_HUMAN :
  • Contains 14 KH domains.
Domain:
  • Contains 14 KH domains.
genes like me logo Genes that share domains with HDLBP: view

No data available for Gene Families for HDLBP Gene

Function for HDLBP Gene

Molecular function for HDLBP Gene

GENATLAS Biochemistry:
vigilin,high density lipoprotein binding protein
UniProtKB/Swiss-Prot Function:
Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Gene Ontology (GO) - Molecular Function for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24725430
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with HDLBP: view
genes like me logo Genes that share phenotypes with HDLBP: view

Animal Model Products

  • Taconic Biosciences Mouse Models for HDLBP

miRNA for HDLBP Gene

miRTarBase miRNAs that target HDLBP

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HDLBP Gene

Localization for HDLBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for HDLBP Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HDLBP Gene COMPARTMENTS Subcellular localization image for HDLBP gene
Compartment Confidence
plasma membrane 5
cytosol 4
extracellular 4
nucleus 4
cytoskeleton 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034364 high-density lipoprotein particle IEA --
genes like me logo Genes that share ontologies with HDLBP: view

Pathways & Interactions for HDLBP Gene

SuperPathways for HDLBP Gene

No Data Available

Gene Ontology (GO) - Biological Process for HDLBP Gene

None

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

Drugs & Compounds for HDLBP Gene

(2) Drugs for HDLBP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for HDLBP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HDLBP: view

Transcripts for HDLBP Gene

Unigene Clusters for HDLBP Gene

High density lipoprotein binding protein:
Representative Sequences:

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

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e ^ 11a · 11b ·
SP1: - - - - - - - - - -
SP2:
SP3:
SP4: - - - - - - - -
SP5: - - - - - - - - -
SP6:
SP7: - - - - - - -
SP8:
SP9:
SP10: - - - - - - - - - - - - - - - - - - - - -
SP11: - - - - - - -
SP12: - - - -
SP13: - - - - -
SP14: - - - - - - - - - - - - -
SP15:
SP16: - - - - - - - - - - - - -
SP17:
SP18:
SP19:
SP20: - - -
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:

ExUns: 11c · 11d · 11e ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b · 18c ^ 19 ^ 20 ^ 21a · 21b ^ 22a · 22b · 22c ^ 23 ^ 24a ·
SP1: - - - -
SP2: - - - - - - -
SP3: - - -
SP4:
SP5:
SP6:
SP7:
SP8: - -
SP9: - - -
SP10: -
SP11:
SP12:
SP13:
SP14:
SP15: - - -
SP16:
SP17:
SP18: - -
SP19:
SP20:
SP21:
SP22: - -
SP23:
SP24:
SP25:
SP26:

ExUns: 24b ^ 25a · 25b · 25c · 25d ^ 26a · 26b ^ 27 ^ 28a · 28b ^ 29 ^ 30 ^ 31 ^ 32a · 32b ^ 33a · 33b ^ 34 ^ 35a · 35b · 35c ^ 36a · 36b ^ 37
SP1: - - - -
SP2: - - - - - - -
SP3: - - -
SP4:
SP5:
SP6: - -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18: - - - -
SP19: -
SP20:
SP21:
SP22:
SP23: -
SP24:
SP25:
SP26:

Relevant External Links for HDLBP Gene

GeneLoc Exon Structure for
HDLBP
ECgene alternative splicing isoforms for
HDLBP

Expression for HDLBP Gene

mRNA expression in normal human tissues for HDLBP Gene

Protein differential expression in normal tissues from HIPED for HDLBP Gene

This gene is overexpressed in Bone marrow stromal cell (15.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HDLBP Gene



SOURCE GeneReport for Unigene cluster for HDLBP Gene Hs.471851

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

Protein tissue co-expression partners for HDLBP Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HDLBP Gene

Orthologs for HDLBP Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HDLBP Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HDLBP 35
  • 88.41 (n)
  • 96.3 (a)
HDLBP 36
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HDLBP 35
  • 90.06 (n)
  • 97.4 (a)
HDLBP 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hdlbp 35
  • 89.67 (n)
  • 97.95 (a)
Hdlbp 16
Hdlbp 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia HDLBP 35
  • 99.58 (n)
  • 99.84 (a)
HDLBP 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hdlbp 35
  • 89.46 (n)
  • 97.87 (a)
oppossum
(Monodelphis domestica)
Mammalia HDLBP 36
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HDLBP 36
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves HDLBP 35
  • 79.77 (n)
  • 87.53 (a)
HDLBP 36
  • 91 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HDLBP 36
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hdlbp 35
  • 74.93 (n)
  • 83.99 (a)
African clawed frog
(Xenopus laevis)
Amphibia hdlbp-prov 35
zebrafish
(Danio rerio)
Actinopterygii hdlbp 35
hdlbpa 35
  • 74.17 (n)
  • 80.4 (a)
hdlbpa 36
  • 78 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10616 35
fruit fly
(Drosophila melanogaster)
Insecta Dp1 37
  • 39 (a)
Dp1 35
  • 54.86 (n)
  • 49.75 (a)
Dp1 36
  • 45 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005467 35
  • 56.62 (n)
  • 52.08 (a)
worm
(Caenorhabditis elegans)
Secernentea C08H9.2 37
  • 38 (a)
CELE_C08H9.2 35
  • 49.22 (n)
  • 40.3 (a)
C08H9.2 36
  • 38 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCP160 36
  • 4 (a)
OneToMany
SCP160 38
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4245 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4516 36
  • 48 (a)
OneToOne
Species with no ortholog for HDLBP:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for HDLBP Gene

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

Paralogs for HDLBP Gene

Paralogs for HDLBP Gene

Pseudogenes.org Pseudogenes for HDLBP Gene

genes like me logo Genes that share paralogs with HDLBP: view

Variants for HDLBP Gene

Sequence variations from dbSNP and Humsavar for HDLBP Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs7578199 - 241,253,433(+) CCACA(C/G/T)TGACA reference, missense
VAR_029279 -
VAR_036052 A breast cancer sample
VAR_036053 A breast cancer sample
rs11891776 - 241,264,501(+) TCCAG(A/C/G/T)GGGTT reference, missense

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

Variant ID Type Subtype PubMed ID
nsv876116 CNV Loss 21882294
dgv4492n71 CNV Loss 21882294
nsv508900 CNV Insertion 20534489
nsv524008 CNV Gain 19592680
nsv470532 CNV Loss 18288195
nsv3242 CNV Insertion 18451855
nsv215143 CNV Loss 16902084
esv2675219 CNV Deletion 23128226

Variation tolerance for HDLBP Gene

Residual Variation Intolerance Score: 3.57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.43; 42.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HDLBP Gene

HapMap Linkage Disequilibrium report
HDLBP
Human Gene Mutation Database (HGMD)
HDLBP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDLBP Gene

Disorders for HDLBP Gene

Relevant External Links for HDLBP

Genetic Association Database (GAD)
HDLBP
Human Genome Epidemiology (HuGE) Navigator
HDLBP
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HDLBP

No disorders were found for HDLBP Gene.

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

Publications for HDLBP Gene

  1. Cloning and expression of a cellular high density lipoprotein-binding protein that is up-regulated by cholesterol loading of cells. (PMID: 1318310) McKnight G.L. … Oram J.F. (J. Biol. Chem. 1992) 2 3 4 23 67
  2. [VIGILIN involves in regulation of imprinting gene IGF2 and H19 in human hepatocellular carcinoma cell]. (PMID: 19950580) Ge Y.J. … Qin Y. (Sichuan Da Xue Xue Bao Yi Xue Ban 2009) 3 23
  3. On the mechanism of induction of heterochromatin by the RNA-binding protein vigilin. (PMID: 18648073) Zhou J. … Carmichael G.G. (RNA 2008) 3 23
  4. Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. (PMID: 15723802) Wang Q. … Carmichael G.G. (Curr. Biol. 2005) 3 23
  5. Vigilin is co-localized with 80S ribosomes and binds to the ribosomal complex through its C-terminal domain. (PMID: 15109574) Vollbrandt T. … Kruse C. (Int. J. Biochem. Cell Biol. 2004) 3 23

Products for HDLBP Gene

Sources for HDLBP Gene

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