Format

Send to:

Choose Destination

HDLBP high density lipoprotein binding protein [ Homo sapiens (human) ]

Gene ID: 3069, updated on 4-Nov-2018

Summary

Official Symbol
HDLBPprovided by HGNC
Official Full Name
high density lipoprotein binding proteinprovided by HGNC
Primary source
HGNC:HGNC:4857
See related
Ensembl:ENSG00000115677 MIM:142695; Vega:OTTHUMG00000133391
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HBP; VGL; PRO2900
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 89.6), thyroid (RPKM 63.1) and 25 other tissues See more
Orthologs

Genomic context

See HDLBP in Genome Data Viewer
Location:
2q37.3
Exon count:
35
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (241227264..241315842, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242166682..242255116, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene PAS domain containing serine/threonine kinase Neighboring gene uncharacterized LOC105373971 Neighboring gene protein phosphatase 1 regulatory subunit 7 Neighboring gene uncharacterized LOC105376810 Neighboring gene anoctamin 7 Neighboring gene basic proline-rich protein-like Neighboring gene septin 2 Neighboring gene uncharacterized LOC105373973 Neighboring gene FERM, ARH/RhoGEF and pleckstrin domain protein 2 Neighboring gene microRNA 3133

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Cellular biotinylated high density lipoprotein binding protein (HDLBP, Vigilin) is incorporated into HIV-1 Gag virus-like particles PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • HDL-mediated lipid transport, organism-specific biosystem (from REACTOME)
    HDL-mediated lipid transport, organism-specific biosystemHDL particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and e...
  • Lipid digestion, mobilization, and transport, organism-specific biosystem (from REACTOME)
    Lipid digestion, mobilization, and transport, organism-specific biosystemProcesses annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids thr...
  • Lipoprotein metabolism, organism-specific biosystem (from REACTOME)
    Lipoprotein metabolism, organism-specific biosystemBecause of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport ...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ16432

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
cadherin binding HDA PubMed 
lipid binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cholesterol metabolic process IEA
Inferred from Electronic Annotation
more info
 
high-density lipoprotein particle clearance TAS
Traceable Author Statement
more info
 
lipid transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
high-density lipoprotein particle IEA
Inferred from Electronic Annotation
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vigilin
Names
HDL-binding protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001243900.2NP_001230829.1  vigilin isoform b

    See identical proteins and their annotated locations for NP_001230829.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses a downstream promoter compared to variant 1.
    Source sequence(s)
    AC104841, AI434711, AK300312, BP359370
    Consensus CDS
    CCDS58760.1
    UniProtKB/Swiss-Prot
    Q00341
    Related
    ENSP00000399139.2, ENST00000427183.6
    Conserved Domains (1) summary
    cd02394
    Location:622684
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  2. NM_001320965.1NP_001307894.1  vigilin isoform a

    Status: REVIEWED

    Source sequence(s)
    AC104841, AI434711, AK312335, DC400438
    Consensus CDS
    CCDS2547.1
    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5, B2R5V9
    Related
    ENSP00000375837.2, OTTHUMP00000200288, ENST00000391976.6, OTTHUMT00000323294
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  3. NM_001320966.1NP_001307895.1  vigilin isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses a downstream promoter compared to variant 1.
    Source sequence(s)
    AC104841, AI434711, AK312335, BP283713
    Consensus CDS
    CCDS2547.1
    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5, B2R5V9
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  4. NM_001320967.1NP_001307896.1  vigilin isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses a downstream promoter compared to variant 1.
    Source sequence(s)
    AC104841, AI434711, AK312335, BP359370, DB282620
    UniProtKB/TrEMBL
    B2R5V9
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  5. NM_005336.5NP_005327.1  vigilin isoform a

    See identical proteins and their annotated locations for NP_005327.1

    Status: REVIEWED

    Source sequence(s)
    AC104841, AI434711, AK312335, BG720303, DC424146
    Consensus CDS
    CCDS2547.1
    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5, B2R5V9
    Related
    ENSP00000312042.4, OTTHUMP00000200289, ENST00000310931.8, OTTHUMT00000323295
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  6. NM_203346.4NP_976221.1  vigilin isoform a

    See identical proteins and their annotated locations for NP_976221.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a downstream promoter compared to variant 1.
    Source sequence(s)
    AC104841, AI434711, AK312335, BP359370, DB282620
    Consensus CDS
    CCDS2547.1
    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5, B2R5V9
    Related
    ENSP00000375836.1, OTTHUMP00000164572, ENST00000391975.5, OTTHUMT00000257245
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    241227264..241315842 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003941.2XP_016859430.1  vigilin isoform X2

    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  2. XM_017003942.1XP_016859431.1  vigilin isoform X2

    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  3. XM_011511060.3XP_011509362.1  vigilin isoform X1

    See identical proteins and their annotated locations for XP_011509362.1

    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  4. XM_011511058.3XP_011509360.1  vigilin isoform X1

    See identical proteins and their annotated locations for XP_011509360.1

    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  5. XM_024452833.1XP_024308601.1  vigilin isoform X1

    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  6. XM_005247002.4XP_005247059.2  vigilin isoform X1

    See identical proteins and their annotated locations for XP_005247059.2

    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  7. XM_006712475.4XP_006712538.1  vigilin isoform X1

    See identical proteins and their annotated locations for XP_006712538.1

    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  8. XM_024452832.1XP_024308600.1  vigilin isoform X1

    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
  9. XM_017003940.2XP_016859429.1  vigilin isoform X1

    UniProtKB/Swiss-Prot
    Q00341
    UniProtKB/TrEMBL
    A0A024R4E5
    Conserved Domains (1) summary
    cd02394
    Location:655717
    vigilin_like_KH; K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has ...
Support Center