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    Hdlbp high density lipoprotein binding protein [ Rattus norvegicus (Norway rat) ]

    Gene ID: 64474, updated on 2-May-2024

    Summary

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    Official Symbol
    Hdlbpprovided by RGD
    Official Full Name
    high density lipoprotein binding proteinprovided by RGD
    Primary source
    RGD:620962
    See related
    Ensembl:ENSRNOG00000031479 AllianceGenome:RGD:620962
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable mRNA binding activity. Predicted to be involved in cholesterol metabolic process and lipid transport. Predicted to be located in cytosol. Predicted to be part of polysome. Predicted to be active in cytoplasm and nucleus. Orthologous to human HDLBP (high density lipoprotein binding protein). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Liver (RPKM 483.0), Heart (RPKM 467.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hdlbp in Genome Data Viewer
    Location:
    9q36
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (101395491..101465446, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (93948099..94018040, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (100554574..100624707, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene protein phosphatase 1, regulatory subunit 7 Neighboring gene anoctamin 7 Neighboring gene uncharacterized LOC120094809 Neighboring gene septin 2 Neighboring gene FERM, ARH/RhoGEF and pleckstrin domain protein 2 Neighboring gene 5S ribosomal RNA

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Expression of high density lipoprotein-binding protein messenger ribonucleic acid in the rat ovary and its regulation by gonadotropin. Chen Z, et al. Endocrinology, 1994 Jun. PMID 7514997
    2. Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. Moser K, et al. J Proteome Res, 2006 Jan. PMID 16396499
    3. E-cadherin interactome complexity and robustness resolved by quantitative proteomics. Guo Z, et al. Sci Signal, 2014 Dec 2. PMID 25468996, Free PMC Article
    4. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC124559

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of high-density lipoprotein particle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vigilin
    Names
    HDL-binding protein
    lipoprotein-binding protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_172039.2 → NP_742036.2  vigilin

      See identical proteins and their annotated locations for NP_742036.2

      Status: PROVISIONAL

      Source sequence(s)
      BC105748
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2
      Related
      ENSRNOP00000048476.2, ENSRNOT00000051155.4
      Conserved Domains (1) summary
      cd02394
      Location:583 → 644
      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: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      101395491..101465446 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063267684.1 → XP_063123754.1  vigilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K8R4

    2. XM_063267685.1 → XP_063123755.1  vigilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K8R4

    3. XM_017596623.3 → XP_017452112.1  vigilin isoform X1

      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2
      Conserved Domains (1) summary
      cd02394
      Location:583 → 644
      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_063267678.1 → XP_063123748.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    5. XM_063267682.1 → XP_063123752.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    6. XM_063267683.1 → XP_063123753.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    7. XM_063267674.1 → XP_063123744.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    8. XM_063267677.1 → XP_063123747.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    9. XM_063267680.1 → XP_063123750.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    10. XM_063267681.1 → XP_063123751.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    11. XM_017596624.3 → XP_017452113.1  vigilin isoform X1

      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2
      Conserved Domains (1) summary
      cd02394
      Location:583 → 644
      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 ...

    12. XM_039084167.2 → XP_038940095.1  vigilin isoform X2

      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A0A0G2K8R4
      Related
      ENSRNOP00000074707.2

    13. XM_006245548.3 → XP_006245610.1  vigilin isoform X1

      See identical proteins and their annotated locations for XP_006245610.1

      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2
      Conserved Domains (1) summary
      cd02394
      Location:583 → 644
      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 ...

    14. XM_063267679.1 → XP_063123749.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    15. XM_063267676.1 → XP_063123746.1  vigilin isoform X1

      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Z1A6.1 GenPept UniProtKB/Swiss-Prot:Q9Z1A6

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