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

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, Nov 2024]
Expression: Ubiquitous expression in testis adult (RPKM 20.0), ovary adult (RPKM 17.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

VARP and Rab9 Are Dispensable for the Rab32/BLOC-3 Dependent Salmonella Killing.
Title: VARP and Rab9 Are Dispensable for the Rab32/BLOC-3 Dependent Salmonella Killing.
results indicate that activation of Rab32/38 by HPS4 (or BLOC-3) is essential for melanogenesis of cultured melanocytes and that Rab9 likely regulates melanogenesis independently of HPS4
Title: The BLOC-3 subunit HPS4 is required for activation of Rab32/38 GTPases in melanogenesis, but its Rab9 activity is dispensable for melanogenesis.
VAMP7 mediates fusion of BLOC-1-dependent transport carriers with melanosomes, illuminate SNARE recycling from melanosomes as a critical BLOC-3-dependent step.
Title: BLOC-1 and BLOC-3 regulate VAMP7 cycling to and from melanosomes via distinct tubular transport carriers.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Spontaneous (1) 1 citation
Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU040608 (e-PCR)
- UniSTS:159422

NoName (e-PCR)
- UniSTS:235263

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

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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)

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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)

NM_001359853.1 → NP_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:15 → 121

Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

pfam19033
Location:561 → 662

Intu_longin_3; Intu longin-like domain 3
NM_138646.3 → NP_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:15 → 121

Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

pfam19033
Location:561 → 662

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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

112490849..112526290

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006534832.4 → XP_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:15 → 121

Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

pfam19033
Location:561 → 662

Intu_longin_3; Intu longin-like domain 3
XM_006534831.5 → XP_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:15 → 121

Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

pfam19033
Location:561 → 662

Intu_longin_3; Intu longin-like domain 3
XM_030254211.2 → XP_030110071.1 BLOC-3 complex member HPS4 isoform X1

UniProtKB/Swiss-Prot

Q99KG7

UniProtKB/TrEMBL

Q3TAF8, Q541V2, Q6P568

Conserved Domains (2) summary

pfam19031
Location:15 → 121

Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

pfam19033
Location:561 → 662

Intu_longin_3; Intu longin-like domain 3
XM_036164910.1 → XP_036020803.1 BLOC-3 complex member HPS4 isoform X1

UniProtKB/Swiss-Prot

Q99KG7

UniProtKB/TrEMBL

Q3TAF8, Q541V2, Q6P568

Conserved Domains (2) summary

pfam19031
Location:15 → 121

Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

pfam19033
Location:561 → 662

Intu_longin_3; Intu longin-like domain 3