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    Hps4 HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 [ Mus musculus (house mouse) ]

    Gene ID: 192232, updated on 9-Dec-2024

    Summary

    Official Symbol
    Hps4provided by MGI
    Official Full Name
    HPS4, biogenesis of lysosomal organelles complex 3 subunit 2provided by MGI
    Primary source
    MGI:MGI:2177742
    See related
    Ensembl:ENSMUSG00000042328 AllianceGenome:MGI:2177742
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    le; BLOC-3; mKIAA1667; 2010205O06Rik; C130020P05Rik
    Summary
    Enables small GTPase binding activity. Acts upstream of or within blood coagulation and melanocyte differentiation. Located in cytoplasmic vesicle. Is expressed in midgut and midgut loop. Used to study Hermansky-Pudlak syndrome 4 and platelet storage pool deficiency. 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
    Ubiquitous expression in testis adult (RPKM 20.0), ovary adult (RPKM 17.2) and 28 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Hps4 in Genome Data Viewer
    Location:
    5 F; 5 54.69 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (112490849..112526290)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (112342983..112378424)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:112714594-112714795 Neighboring gene STARR-positive B cell enhancer ABC_E3600 Neighboring gene protein-tyrosine sulfotransferase 2 Neighboring gene tuftelin interacting protein 11 Neighboring gene coiled-coil domain containing 121, retrogene 3 Neighboring gene SRR1 domain containing Neighboring gene predicted gene 20636 Neighboring gene aspartate beta-hydroxylase domain containing 2 Neighboring gene seizure related 6 homolog like Neighboring gene coiled-coil domain containing 121, retrogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Spontaneous (1)  1 citation
    • Targeted (1) 

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    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
     
    contributes_to guanyl-nucleotide exchange factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein dimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein dimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables small GTPase binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within blood coagulation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lysosome organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in lysosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    acts_upstream_of_or_within melanocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 melanosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in melanosome assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within organelle organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in platelet dense granule organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in protein stabilization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    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 protein targeting ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    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
     
    part_of BLOC-3 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in melanosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in melanosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in platelet dense granule IEA
    Inferred from Electronic Annotation
    more info
     
    located_in platelet dense granule ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    BLOC-3 complex member HPS4
    Names
    Hermansky-Pudlak syndrome 4 homolog
    hermansky-Pudlak syndrome 4 protein homolog
    light ear
    light-ear protein

    NCBI Reference Sequences (RefSeq)

    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_001359853.1NP_001346782.1  BLOC-3 complex member HPS4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC123848, AK147954
      Consensus CDS
      CCDS19540.1
      UniProtKB/Swiss-Prot
      Q99KG7
      UniProtKB/TrEMBL
      Q3TAF8, Q541V2, Q6P568
      Related
      ENSMUSP00000107978.3, ENSMUST00000112359.9
      Conserved Domains (2) summary
      pfam19031
      Location:15121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:561662
      Intu_longin_3; Intu longin-like domain 3
    2. NM_138646.3NP_619587.3  BLOC-3 complex member HPS4

      See identical proteins and their annotated locations for NP_619587.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AK129418, BE626904, BY741149
      Consensus CDS
      CCDS19540.1
      UniProtKB/Swiss-Prot
      Q99KG7
      UniProtKB/TrEMBL
      Q3TAF8, Q541V2, Q6P568
      Related
      ENSMUSP00000047920.4, ENSMUST00000035279.4
      Conserved Domains (2) summary
      pfam19031
      Location:15121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:561662
      Intu_longin_3; Intu longin-like domain 3

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      112490849..112526290
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006534832.4XP_006534895.1  BLOC-3 complex member HPS4 isoform X1

      See identical proteins and their annotated locations for XP_006534895.1

      UniProtKB/Swiss-Prot
      Q99KG7
      UniProtKB/TrEMBL
      Q3TAF8, Q541V2, Q6P568
      Related
      ENSMUST00000133708.2
      Conserved Domains (2) summary
      pfam19031
      Location:15121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:561662
      Intu_longin_3; Intu longin-like domain 3
    2. XM_006534831.5XP_006534894.1  BLOC-3 complex member HPS4 isoform X1

      See identical proteins and their annotated locations for XP_006534894.1

      UniProtKB/Swiss-Prot
      Q99KG7
      UniProtKB/TrEMBL
      Q3TAF8, Q541V2, Q6P568
      Conserved Domains (2) summary
      pfam19031
      Location:15121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:561662
      Intu_longin_3; Intu longin-like domain 3
    3. XM_030254211.2XP_030110071.1  BLOC-3 complex member HPS4 isoform X1

      UniProtKB/Swiss-Prot
      Q99KG7
      UniProtKB/TrEMBL
      Q3TAF8, Q541V2, Q6P568
      Conserved Domains (2) summary
      pfam19031
      Location:15121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:561662
      Intu_longin_3; Intu longin-like domain 3
    4. XM_036164910.1XP_036020803.1  BLOC-3 complex member HPS4 isoform X1

      UniProtKB/Swiss-Prot
      Q99KG7
      UniProtKB/TrEMBL
      Q3TAF8, Q541V2, Q6P568
      Conserved Domains (2) summary
      pfam19031
      Location:15121
      Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
      pfam19033
      Location:561662
      Intu_longin_3; Intu longin-like domain 3