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

Gene ID: 64474, updated on 6-Jun-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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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/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A0A0G2K8R4

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    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/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    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/Swiss-Prot
    Q9Z1A6
    UniProtKB/TrEMBL
    A6JR00, A6JR01, Q3KRF2

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

    UniProtKB/Swiss-Prot
    Q9Z1A6
    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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