U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 64474, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Hdlbpprovided by RGD
    Official Full Name
    high density lipoprotein binding proteinprovided by RGD
    Primary source
    RGD:620962
    See related
    EnsemblRapid:ENSRNOG00000031479 AllianceGenome:RGD:620962
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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 cytoplasm and nucleus. Predicted to be part of high-density lipoprotein particle. Orthologous to human HDLBP (high density lipoprotein binding protein). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 483.0), Heart (RPKM 467.3) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    vigilin
    Names
    HDL-binding protein
    lipoprotein-binding protein

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001432862.1 → NP_001419791.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    2. NM_001432863.1 → NP_001419792.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    3. NM_001432864.1 → NP_001419793.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    4. NM_001432865.1 → NP_001419794.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    5. NM_001432866.1 → NP_001419795.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    6. NM_001432867.1 → NP_001419796.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    7. NM_001432868.1 → NP_001419797.1  vigilin isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2

    8. NM_001432869.1 → NP_001419798.1  vigilin isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A0A0G2K8R4

    9. NM_001432870.1 → NP_001419799.1  vigilin isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A0A0G2K8R4

    10. NM_001432871.1 → NP_001419800.1  vigilin isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A0A0G2K8R4

    11. NM_001432872.1 → NP_001419801.1  vigilin isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6

    12. NM_172039.3 → NP_742036.2  vigilin isoform 1

      See identical proteins and their annotated locations for NP_742036.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q9Z1A6
      UniProtKB/TrEMBL
      A6JR00, A6JR01, Q3KRF2
      Related
      ENSRNOP00000048476.2, ENSRNOT00000051155.5
      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

      Related
      ENSRNOP00000074707.2, ENSRNOT00000085448.3

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

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

      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

    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

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

    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

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

      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

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

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Z1A6.1 GenPept UniProtKB/Swiss-Prot:Q9Z1A6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools