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HDLBP Gene

protein-coding   GIFtS: 62
GCID: GC02M242166

High Density Lipoprotein Binding Protein

(Previous name: vigilin)
(Previous symbol: VGL)
  See HDLBP-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
High Density Lipoprotein Binding Protein1 2     HBP2 3
VGL1 2 3 5     HDL-Binding Protein2 3
vigilin1 2     PRO29002
High Density Lipoprotein-Binding Protein2 3     

External Ids:    HGNC: 48571   Entrez Gene: 30692   Ensembl: ENSG000001156777   OMIM: 1426955   UniProtKB: Q003413   

Export aliases for HDLBP gene to outside databases

Previous GC identifers: GC02P239181 GC02P240038 GC02M242188 GC02M242489 GC02M242488 GC02M241888 GC02M233922


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. Diseases associated with HDLBP include familial hdl deficiency. GO annotations related to this gene include lipid binding and RNA binding. An important paralog of this gene is BICC1.

UniProtKB/Swiss-Prot: VIGLN_HUMAN, Q00341
Function: 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


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HDLBP gene promoter:
         Max1   Nkx3-1   Nkx3-1 v4   Nkx3-1 v1   Nkx3-1 v2   Max   Nkx3-1 v3   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HDLBP promoter sequence
   Search Chromatin IP Primers for HDLBP

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HDLBP


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q37.3   Ensembl cytogenetic band:  2q37.3   HGNC cytogenetic band: 2q37.3

HDLBP Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HDLBP gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M242166:  view genomic region     (about GC identifiers)

Start:
242,166,679 bp from pter      End:
242,256,476 bp from pter
Size:
89,798 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: VIGLN_HUMAN, Q00341 (See protein sequence)
Recommended Name: Vigilin  
Size: 1268 amino acids; 141456 Da
Selected PDB 3D structures from and Proteopedia for HDLBP (see all 8):
1VIG (3D)        1VIH (3D)        2CTE (3D)        2CTF (3D)        2CTJ (3D)        2CTK (3D)    
Secondary accessions: B4DTQ2 E7EM71 Q53QU2 Q9UCY3
Alternative splicing: 2 isoforms:  Q00341-1   Q00341-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HDLBP: NX_Q00341

Explore proteomics data for HDLBP at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys231
  • Modification sites at PhosphoSitePlus

  • See HDLBP Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001230829.1  NP_005327.1  NP_976221.1  

    ENSEMBL proteins: 
     ENSP00000375836   ENSP00000375837   ENSP00000312042   ENSP00000362389   ENSP00000411211  
     ENSP00000405180   ENSP00000388876   ENSP00000393766   ENSP00000403807   ENSP00000405109  
     ENSP00000413891   ENSP00000387782   ENSP00000416559   ENSP00000403913   ENSP00000396964  
     ENSP00000394205   ENSP00000390290   ENSP00000413805   ENSP00000390942   ENSP00000396202  
     ENSP00000403693   ENSP00000409868   ENSP00000408582   ENSP00000397799   ENSP00000396959  
     ENSP00000391773   ENSP00000399139  

    HDLBP Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for HDLBP
    OriGene Protein Over-expression Lysate for HDLBP
    OriGene MassSpec for HDLBP
    OriGene Custom Protein Services for HDLBP
    GenScript Custom Purified and Recombinant Proteins Services for HDLBP
    Novus Biologicals HDLBP Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for HDLBP

     
    Search eBioscience for Proteins for HDLBP 

     
    Search antibodies-online for proteins for HDLBP 

     
    antibodies-online peptides for HDLBP

    HDLBP Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    Cloud-Clone Corp. Antibodies for HDLBP
    ThermoFisher Antibody for HDLBP
    antibodies-online antibodies for HDLBP (48 products) 

    HDLBP Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for HDLBP
    Cloud-Clone Corp. CLIAs for HDLBP
    Search eBioscience for ELISAs for HDLBP 
    antibodies-online kits for HDLBP (10 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR004087 KH_dom
     IPR004088 KH_dom_type_1

    Graphical View of Domain Structure for InterPro Entry Q00341

    ProtoNet protein and cluster: Q00341

    2 Blocks protein domains:
    IPB004087 KH domain
    IPB004088 KH


    UniProtKB/Swiss-Prot: VIGLN_HUMAN, Q00341
    Similarity: Contains 14 KH domains


    Find genes that share domains with HDLBP           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VIGLN_HUMAN, Q00341
    Function: Appears to play a role in cell sterol metabolism. It may function to protect cells from
    over-accumulation of cholesterol

         Genatlas biochemistry entry for HDLBP:
    vigilin,high density lipoprotein binding protein

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding ----
    GO:0008289lipid binding TAS1318310
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with HDLBP           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for HDLBP:
     Synthetic lethal with c-Myc af 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for HDLBP

    miRNA
    Products:
        
    miRTarBase miRNAs that target HDLBP:
    hsa-mir-423-3p (MIRT042633), hsa-mir-34a-5p (MIRT025358), hsa-mir-484 (MIRT042063), hsa-mir-1301-3p (MIRT035959), hsa-mir-877-3p (MIRT036841), hsa-mir-615-3p (MIRT039778), hsa-mir-222-3p (MIRT046605), hsa-mir-7-5p (MIRT025699), hsa-mir-365a-3p (MIRT044029), hsa-mir-548d-5p (MIRT037779)

    Block miRNA regulation of human, mouse, rat HDLBP using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HDLBP (see all 64):
    hsa-miR-759 hsa-miR-10b* hsa-miR-642b hsa-miR-92b hsa-miR-761 hsa-miR-4324 hsa-miR-3688-3p hsa-miR-425
    SwitchGear 3'UTR luciferase reporter plasmidHDLBP 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HDLBP
    Predesigned siRNA for gene silencing in human, mouse, rat HDLBP

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HDLBP

    Clone
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    OriGene clones in human, mouse for HDLBP (see all 12)
    OriGene ORF clones in mouse, rat for HDLBP
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): HDLBP (NM_203346)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HDLBP
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDLBP

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for HDLBP
    Browse ESI BIO Cell Lines and PureStem Progenitors for HDLBP 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HDLBP


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VIGLN_HUMAN, Q00341: Cytoplasm. Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    endoplasmic reticulum4
    plasma membrane4
    extracellular3
    cytoskeleton1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IDA--
    GO:0005886plasma membrane TAS1318310
    GO:0034364high-density lipoprotein particle IEA--

    Find genes that share ontologies with HDLBP           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Pathway & Disease-focused RT2 Profiler PCR Array including HDLBP: 
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for HDLBP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for HDLBP (Q003412, 3 ENSP000003120424) via UniProtKB, MINT, STRING, and/or I2D (see all 1045)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006869lipid transport IEA--
    GO:0008203cholesterol metabolic process IEA--

    Find genes that share ontologies with HDLBP           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HDLBP (VIGLN)

    4 Novoseek inferred chemical compound relationships for HDLBP gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    trna 58.7 10 12792806 (2), 10657246 (2), 9445390 (2), 14618268 (1)
    cholesterol 30.5 14 12941645 (2), 1318310 (2), 9409201 (2), 10638200 (1) (see all 6)
    estrogen 5.77 4 9632784 (2), 11050168 (1)
    lipid 0 2 12941645 (2)



    Find genes that share compounds with HDLBP           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for HDLBP gene (3 alternative transcripts): 
    NM_001243900.1  NM_005336.4  NM_203346.3  

    Unigene Cluster for HDLBP:

    High density lipoprotein binding protein
    Hs.471851  [show with all ESTs]
    Unigene Representative Sequence: NM_005336
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 47):
    ENST00000391975(uc021vzg.1 uc002waz.3 uc002wba.3) ENST00000391976(uc010fzn.1)
    ENST00000310931 ENST00000487169 ENST00000373292 ENST00000484412 ENST00000442730
    ENST00000494862 ENST00000488013 ENST00000470482 ENST00000479894 ENST00000483086
    ENST00000479169 ENST00000427487 ENST00000459788 ENST00000471294 ENST00000452931
    ENST00000460826
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat HDLBP using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HDLBP (see all 64):
    hsa-miR-759 hsa-miR-10b* hsa-miR-642b hsa-miR-92b hsa-miR-761 hsa-miR-4324 hsa-miR-3688-3p hsa-miR-425
    SwitchGear 3'UTR luciferase reporter plasmidHDLBP 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for HDLBP
    Predesigned siRNA for gene silencing in human, mouse, rat HDLBP
    Clone
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    OriGene clones in human, mouse for HDLBP (see all 12)
    OriGene ORF clones in mouse, rat for HDLBP
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): HDLBP (NM_203346)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HDLBP
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDLBP
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for HDLBP
    OriGene qSTAR qPCR primer pairs in human, mouse for HDLBP
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HDLBP
      QuantiTect SYBR Green Assays in human, mouse, rat HDLBP
      QuantiFast Probe-based Assays in human, mouse, rat HDLBP

    Additional mRNA sequence: 

    AF116718.1 AK026138.1 AK127833.1 AK296684.1 AK300312.1 AK309075.1 AK312335.1 BC001179.1 
    BC007961.2 BC009422.1 BC014305.2 BC021817.1 BC038965.1 BC058826.1 BC113120.1 BX647759.1 
    M64098.1 

    Selected DOTS entries (see all 120):

    DT.100060166  DT.100891495  DT.405195  DT.91777154  DT.100891477  DT.97861017  DT.95165709  DT.100891497 
    DT.95293553  DT.100891486  DT.120964777  DT.100891484  DT.120964528  DT.91777150  DT.91773953  DT.420593 
    DT.95165778  DT.100891501  DT.120964358  DT.120964485  DT.454461  DT.120964637  DT.100055634  DT.100891492 

    Selected AceView cDNA sequences (see all 56):

    BQ071302 BI858125 BM801822 BG254246 BM851227 BP362839 BC014305 H42603 
    BM803941 CB131582 BP335239 BM772516 BU147158 BQ940873 NM_203346 CA429273 
    BC009422 BF872528 AF116718 AI276755 CK430628 BM771003 NM_005336 F02903 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for HDLBP (see all 26)    About this scheme

    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:              -     -     -     -     -     -     -     -     -                                                                                             

    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:                                                                                                                                                            

    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:                                                                                                                                                


    ECgene alternative splicing isoforms for HDLBP

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HDLBP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACCTCAGGAA
    HDLBP Expression
    About this image


    HDLBP expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 23) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebral Cortex
     
     Testis (Reproductive System)
             Testis Somatic Cells Primitive Gonad
     
     Ovary (Reproductive System)
             Oviduct
     
     Limb (Muscoskeletal System)
             Limb Bud
     
     Gonad (Reproductive System)
             Testis Somatic Cells Primitive Gonad
    HDLBP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HDLBP Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.471851
        Pathway & Disease-focused RT2 Profiler PCR Array including HDLBP: 
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for HDLBP gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hdlbp1 , 5 high density lipoprotein (HDL) binding protein1, 5 89.67(n)1
    97.95(a)1
      1 (47.24 cM)5
    1106111  NM_133808.41  NP_598569.11 
     934059405 
    chicken
    (Gallus gallus)
    Aves HDLBP1 high density lipoprotein binding protein 79.77(n)
    87.53(a)
      395984  NM_205096.1  NP_990427.1 
    lizard
    (Anolis carolinensis)
    Reptilia HDLBP6
    high density lipoprotein binding protein
    89(a)
    1 ↔ 1
    3(30209683-30281114)
    African clawed frog
    (Xenopus laevis)
    Amphibia hdlbp-prov2 high density lipoprotein binding protein (vigilin) 77.15(n)    BC044314.1 
    zebrafish
    (Danio rerio)
    Actinopterygii hdlbp2 high density lipoprotein-binding protein (vigilin) 76.84(n)   323312  BC051153.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Dp11 , 3 single-stranded DNA binding3
    Dodeca-satellite-binding protein 11
    39(a)3
    54.86(n)1
    49.75(a)1
      55C83
    371161  NM_166282.11  NP_725787.11 
    worm
    (Caenorhabditis elegans)
    Secernentea C08H9.23
    CELE_C08H9.21
    high-density lipoprotein-binding
    protein3
    CELE_C08H9.21
    38(a)3
    49.22(n)1
    40.3(a)1
      II(9886952-9890851)3
    1745431  NM_063735.61  NP_496136.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SCP160(YJL080C)4 Essential RNA-binding G protein effector of mating more   --   10(289226-285558) 853365  NP_012455.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HDLBP gene
    BICC12  
    1 SIMAP similar gene for HDLBP using alignment to 27 protein entries:     VIGLN_HUMAN (see all proteins):
    DKFZp686L08115

    Find genes that share paralogs with HDLBP           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for HDLBP
    PGOHUM00000244869


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HDLBP (see all 2002)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0360534
    A breast cancer sample4--see VAR_0360532 D V mis40--------
    VAR_0360524
    A breast cancer sample4--see VAR_0360522 K N mis40--------
    rs714046881,2
    C--241537716(+) ACCTT-/GGG   
      
    /GGGGG
    GGGGG
    6 -- int1 cds11NA 2
    rs621863601,2
    C--242166212(+) AGGAAC/TACCTA 3 -- ds50016Minor allele frequency- T:0.25NA WA EA 364
    rs1145495161,2
    F--242166283(+) CTCAAC/TGCCCC 3 -- ds50011Minor allele frequency- T:0.02WA 118
    rs16771,2
    C,F,H--242166550(-) CCACAT/CTGAGG 3 -- ds500128Minor allele frequency- C:0.18EA MN NS NA WA CSA 4388
    rs67262261,2
    C,F--242166568(+) GGGGCT/CGTTGA 3 -- ds50013Minor allele frequency- C:0.33WA CSA 6
    rs38321491,2
    C--242166574(-) ACTGT-/GTTCAAC 3 -- ds50010--------
    rs1818632021,2
    --242166577(+) GAACAC/GAGTGT 3 -- ds50010--------
    rs1408959231,2
    C--242166613(+) AAAGAC/TGAACT 3 -- ds50010--------

    HapMap Linkage Disequilibrium report for HDLBP (242166679 - 242256476 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for HDLBP:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2675219CNV Deletion23128226
    nsv508900CNV Insertion20534489
    nsv3242CNV Insertion18451855
    nsv215143CNV Loss16902084
    dgv4492n71CNV Loss21882294
    nsv876116CNV Loss21882294
    nsv470532CNV Loss18288195
    nsv524008CNV Gain19592680

    Human Gene Mutation Database (HGMD): HDLBP
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing HDLBP
    DNA2.0 Custom Variant and Variant Library Synthesis for HDLBP

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 142695    OMIM disorders: --

    1 disease for HDLBP:    
    About MalaCards
    familial hdl deficiency


    Find genes that share disorders with HDLBP           About GenesLikeMe

    Genetic Association Database (GAD): HDLBP
    Human Genome Epidemiology (HuGE) Navigator: HDLBP (5 documents)

    Export disorders for HDLBP gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for HDLBP gene, integrated from 10 sources (see all 94):
    (articles sorted by number of sources associating them with HDLBP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and expression of a cellular high density lipoprotein-binding protein that is up-regulated by cholesterol loading of cells. (PubMed id 1318310)1, 2, 3, 9 McKnight G.L.... Oram J.F. (J. Biol. Chem. 1992)
    2. Follow-up of potential novel Graves' disease susceptibility loci, identified in the UK WTCCC genome-wide nonsynonymous SNP study. (PubMed id 20442750)1, 4 Newby P.R....Gough S.C. (Eur. J. Hum. Genet. 2010)
    3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    4. Candidate genetic analysis of plasma high-density lipoprotein-cholesterol and severity of coronary atherosclerosis. (PubMed id 19878569)1, 4 Chen S.N....Marian A.J. (BMC Med. Genet. 2009)
    5. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PubMed id 15592455)1, 2 Rush J.... Comb M.J. (Nat. Biotechnol. 2005)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Vigilin contains a functional nuclear localisation sequence and is present in both the cytoplasm and the nucleus. (PubMed id 8605996)1, 2 Kugler S....Kruse C. (FEBS Lett. 1996)
    9. Localization of the gene for high-density lipoprotein binding protein (HDLBP) to human chromosome 2q37. (PubMed id 8390966)1, 3 Xia Y.R....Lusis A.J. (Genomics 1993)
    10. High-density lipoprotein-binding protein (HBP)/vigilin is expressed in human atherosclerotic lesions and colocalizes with apolipoprotein E. (PubMed id 9409201)1, 9 Chiu D.S....O'Brien K.D. (Arterioscler. Thromb. Vasc. Biol. 1997)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3069 HGNC: 4857 AceView: HDLBP Ensembl:ENSG00000115677 euGenes: HUgn3069
    ECgene: HDLBP H-InvDB: HDLBP

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for HDLBP Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HDLBP gene:
    Search GeneIP for patents involving HDLBP

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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