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Aliases for HDLBP Gene

Aliases for HDLBP Gene

  • High Density Lipoprotein Binding Protein 2 3
  • VGL 3 4 6
  • High Density Lipoprotein-Binding Protein 3 4
  • HDL-Binding Protein 3 4
  • Vigilin 2 3
  • HBP 3 4
  • 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. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

GeneCards Summary for HDLBP Gene

HDLBP (High Density Lipoprotein Binding Protein) is a Protein Coding gene. GO annotations related to this gene include RNA binding and lipid 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

Genomic Location for HDLBP Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 Lys231
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HDLBP Gene

Domains 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 :
  • Q00341
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:0003676 nucleic acid binding --
GO:0003723 RNA binding --
GO:0005515 protein binding IPI 24725430
GO:0008289 lipid binding TAS 1318310
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with HDLBP: view

Phenotypes for HDLBP Gene

GenomeRNAi human phenotypes for HDLBP:
genes like me logo Genes that share phenotypes with HDLBP: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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
nucleus 5
cytosol 4
endoplasmic reticulum 4
plasma membrane 4
extracellular 3
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IDA --
GO:0005886 plasma membrane TAS 1318310
GO:0034364 high-density lipoprotein particle IEA --
genes like me logo Genes that share ontologies with HDLBP: view

Pathways for HDLBP Gene

SuperPathways for HDLBP Gene

No Data Available

Gene Ontology (GO) - Biological Process for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006869 lipid transport IEA --
GO:0008203 cholesterol metabolic process IEA --
genes like me logo Genes that share ontologies with HDLBP: view

No data available for Pathways by source for HDLBP Gene

Compounds for HDLBP Gene

(4) Novoseek inferred chemical compound relationships for HDLBP Gene

Compound -log(P) Hits PubMed IDs
trna 58.7 7
cholesterol 30.5 9
estrogen 5.77 3
lipid 0 2
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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with HDLBP: view

No data available for 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
chimpanzee
(Pan troglodytes)
Mammalia HDLBP 35
  • 99.58 (n)
  • 99.84 (a)
HDLBP 36
  • 100 (a)
OneToOne
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
oppossum
(Monodelphis domestica)
Mammalia HDLBP 36
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HDLBP 36
  • 76 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hdlbp 35
  • 89.46 (n)
  • 97.87 (a)
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
African clawed frog
(Xenopus laevis)
Amphibia hdlbp-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia hdlbp 35
  • 74.93 (n)
  • 83.99 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10616 35
zebrafish
(Danio rerio)
Actinopterygii hdlbp 35
hdlbpa 35
  • 74.17 (n)
  • 80.4 (a)
hdlbpa 36
  • 78 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005467 35
  • 56.62 (n)
  • 52.08 (a)
fruit fly
(Drosophila melanogaster)
Insecta Dp1 35
  • 54.86 (n)
  • 49.75 (a)
Dp1 36
  • 45 (a)
OneToOne
Dp1 37
  • 39 (a)
worm
(Caenorhabditis elegans)
Secernentea C08H9.2 36
  • 38 (a)
OneToOne
CELE_C08H9.2 35
  • 49.22 (n)
  • 40.3 (a)
C08H9.2 37
  • 38 (a)
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 MAF
rs1677 -- 241,227,135(-) CCACA(C/T)TGAGG downstream-variant-500B
rs10892 -- 241,227,748(+) GATTG(C/G)GGGGA utr-variant-3-prime
rs12281 - 241,229,617(-) CCCTT(G/T)GGGCC reference, missense, intron-variant
rs14345 -- 241,228,073(-) CAGAC(G/T)CGAAT utr-variant-3-prime
rs15129 -- 241,229,561(-) GACCC(A/G)AACCC utr-variant-3-prime, intron-variant

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

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

No data available for UniProtKB/Swiss-Prot 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
  2. Vigilin is a cytoplasmic protein. A study on its expression in primary cells and in established cell lines of different species. (PMID: 8477745) Neu-Yilik G. … MA1ller P.K. (Eur. J. Biochem. 1993) 3 23
  3. Two additional 5' exons in the human Vigilin gene distinguish it from the chicken gene and provide the structural basis for differential routes of gene expression. (PMID: 8681952) KA1gler S. … MA1ller P.K. (Eur. J. Biochem. 1996) 3 23
  4. High-density lipoprotein-binding protein (HBP)/vigilin is expressed in human atherosclerotic lesions and colocalizes with apolipoprotein E. (PMID: 9409201) Chiu D.S. … O'Brien K.D. (Arterioscler. Thromb. Vasc. Biol. 1997) 3 23
  5. Characterization of a 95 kDa high affinity human high density lipoprotein-binding protein. (PMID: 11284697) Bocharov A.V. … Eggerman T.L. (Biochemistry 2001) 3 23

Products for HDLBP Gene

Sources for HDLBP Gene

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