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    Hps4 HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304555, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Hps4provided by RGD
    Official Full Name
    HPS4, biogenesis of lysosomal organelles complex 3 subunit 2provided by RGD
    Primary source
    RGD:1308070
    See related
    EnsemblRapid:ENSRNOG00000000661 AllianceGenome:RGD:1308070
    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 protein homodimerization activity and small GTPase binding activity. Predicted to contribute to guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including melanosome assembly; positive regulation of protein targeting to mitochondrion; and protein stabilization. Predicted to act upstream of or within blood coagulation and melanocyte differentiation. Predicted to be located in cytoplasmic vesicle; lysosome; and membrane. Predicted to be part of BLOC-3 complex. Predicted to be active in cytoplasmic vesicle and lysosomal membrane. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome; Hermansky-Pudlak syndrome 4; and schizophrenia. Orthologous to human HPS4 (HPS4 biogenesis of lysosomal organelles complex 3 subunit 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 30.7), Kidney (RPKM 29.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hps4 in Genome Data Viewer
    Location:
    12q16
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (49924444..49955201, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (44264037..44294791, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (50285239..50315893, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene seizure related 6 homolog like Neighboring gene coiled-coil domain containing 121 like 2 Neighboring gene aspartate beta-hydroxylase domain containing 2 Neighboring gene coiled-coil domain-containing protein 121-like Neighboring gene tuftelin interacting protein 11 Neighboring gene SRR1 domain containing Neighboring gene tyrosylprotein sulfotransferase 2

    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. Hermansky-Pudlak syndrome type 4 (HPS-4): clinical and molecular characteristics. Anderson PD, et al. Hum Genet, 2003 Jul. PMID 12664304
    2. An association study of the Hermansky-Pudlak syndrome type 4 gene in schizophrenic patients. Saito A, et al. Psychiatr Genet, 2013 Aug. PMID 23563589
    3. BLOC-3, a protein complex containing the Hermansky-Pudlak syndrome gene products HPS1 and HPS4. Martina JA, et al. J Biol Chem, 2003 Aug 1. PMID 12756248
    4. The Hermansky-Pudlak syndrome 1 (HPS1) and HPS4 proteins are components of two complexes, BLOC-3 and BLOC-4, involved in the biogenesis of lysosome-related organelles. Chiang PW, et al. J Biol Chem, 2003 May 30. PMID 12663659
    5. Assembly of the biogenesis of lysosome-related organelles complex-3 (BLOC-3) and its interaction with Rab9. Kloer DP, et al. J Biol Chem, 2010 Mar 5. PMID 20048159, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein dimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables small GTPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within blood coagulation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within melanocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in melanosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in melanosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein targeting to mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in protein stabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein targeting IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein targeting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of BLOC-3 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of BLOC-3 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in melanosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in platelet dense granule ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    BLOC-3 complex member HPS4
    Names
    Hermansky-Pudlak syndrome 4 homolog

    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_001107148.3 → NP_001100618.2  BLOC-3 complex member HPS4

      See identical proteins and their annotated locations for NP_001100618.2

      Status: VALIDATED

      Source sequence(s)
      BC168901, JAXUCZ010000012
      UniProtKB/TrEMBL
      A0A8J8YPH6
      Related
      ENSRNOP00000071892.3, ENSRNOT00000079256.3
      Conserved Domains (3) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam19031
      Location:15 → 121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:551 → 652
      Intu_longin_3; Intu longin-like domain 3

    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_086030.1 Reference GRCr8

      Range
      49924444..49955201 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039089506.2 → XP_038945434.1  BLOC-3 complex member HPS4 isoform X1

      UniProtKB/TrEMBL
      A0A8J8YPH6
      Conserved Domains (3) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam19031
      Location:15 → 121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:551 → 652
      Intu_longin_3; Intu longin-like domain 3

    2. XM_006249544.4 → XP_006249606.1  BLOC-3 complex member HPS4 isoform X1

      See identical proteins and their annotated locations for XP_006249606.1

      UniProtKB/TrEMBL
      A0A8J8YPH6
      Conserved Domains (3) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam19031
      Location:15 → 121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:551 → 652
      Intu_longin_3; Intu longin-like domain 3

    3. XM_006249542.5 → XP_006249604.1  BLOC-3 complex member HPS4 isoform X1

      See identical proteins and their annotated locations for XP_006249604.1

      UniProtKB/TrEMBL
      A0A8J8YPH6
      Conserved Domains (3) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam19031
      Location:15 → 121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:551 → 652
      Intu_longin_3; Intu longin-like domain 3

    4. XM_063271364.1 → XP_063127434.1  BLOC-3 complex member HPS4 isoform X2

      UniProtKB/TrEMBL
      A0A0G2K1L6

    5. XM_006249546.5 → XP_006249608.1  BLOC-3 complex member HPS4 isoform X3

      UniProtKB/TrEMBL
      A0A0G2K1L6
      Conserved Domains (1) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional

    6. XM_039089507.2 → XP_038945435.1  BLOC-3 complex member HPS4 isoform X4

      UniProtKB/TrEMBL
      A0A0G2K1L6
      Conserved Domains (2) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam19031
      Location:15 → 121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

    7. XM_006249543.5 → XP_006249605.1  BLOC-3 complex member HPS4 isoform X1

      See identical proteins and their annotated locations for XP_006249605.1

      UniProtKB/TrEMBL
      A0A8J8YPH6
      Conserved Domains (3) summary
      PHA03307
      Location:225 → 490
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam19031
      Location:15 → 121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:551 → 652
      Intu_longin_3; Intu longin-like domain 3

    8. XM_063271362.1 → XP_063127432.1  BLOC-3 complex member HPS4 isoform X1

      UniProtKB/TrEMBL
      A0A8J8YPH6

    9. XM_063271363.1 → XP_063127433.1  BLOC-3 complex member HPS4 isoform X1

      UniProtKB/TrEMBL
      A0A8J8YPH6

    RNA

    1. XR_358770.5 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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