Vipas39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vipas39provided by MGI
Official Full Name: VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homologprovided by MGI
Primary source: MGI:MGI:2144805
See related: Ensembl:ENSMUSG00000021038 AllianceGenome:MGI:2144805
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: Spe39; Vipar; SPE-39; hSPE-39; 6720456H09Rik; 9330175H22Rik
Summary: Acts upstream of or within several processes, including collagen fibril organization; collagen metabolic process; and peptidyl-lysine hydroxylation. Predicted to be located in Golgi apparatus and endosome. Predicted to be part of vesicle tethering complex. Predicted to be active in cytoplasm. Is expressed in several structures, including central nervous system; retina layer; and skeletal muscle. Used to study ARC syndrome. Human ortholog(s) of this gene implicated in arthrogryposis, renal dysfunction, and cholestasis 2. Orthologous to human VIPAS39 (VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E14 (RPKM 16.2), CNS E18 (RPKM 15.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 12 D2; 12 41.44 cM

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (87285647..87313426, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (87238875..87266378, complement)

Chromosome 12 - NC_000078.7 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?

VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function
Title: VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Mit34.1 (e-PCR), detects polymorphism
- UniSTS:131903

NoName (e-PCR)
- UniSTS:236915

RH98219 (e-PCR)
- UniSTS:88508

AI413782 (e-PCR)
- UniSTS:160238

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within collagen metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within collagen metabolic process	ISO Inferred from Sequence Orthology more info	PubMed
involved_in endosome to lysosome transport	IEA Inferred from Electronic Annotation more info
involved_in endosome to lysosome transport	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within peptidyl-lysine hydroxylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peptidyl-lysine hydroxylation	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within post-translational protein modification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in vacuolar transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in early endosome	IEA Inferred from Electronic Annotation more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	IEA Inferred from Electronic Annotation more info
located_in recycling endosome	ISO Inferred from Sequence Orthology more info
part_of vesicle tethering complex	IEA Inferred from Electronic Annotation more info
part_of vesicle tethering complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: spermatogenesis-defective protein 39 homolog

Names: VPS33B-interacting protein in apical-basolateral polarity regulator; VPS33B-interacting protein in polarity and apical restriction; protein spe-39 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)

NM_001142580.1 → NP_001136052.1 spermatogenesis-defective protein 39 homolog isoform a

See identical proteins and their annotated locations for NP_001136052.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).

Source sequence(s)

AK079055, AK082261, BB610654

Consensus CDS

CCDS49119.1

UniProtKB/Swiss-Prot

Q8BGQ1, Q8BL55, Q8CIK4, Q91YI3

UniProtKB/TrEMBL

Q3UM95

Related

ENSMUSP00000072527.8, ENSMUST00000072744.15

Conserved Domains (1) summary

pfam09787
Location:26 → 469

Golgin_A5; Golgin subfamily A member 5
NM_001142581.1 → NP_001136053.1 spermatogenesis-defective protein 39 homolog isoform b

See identical proteins and their annotated locations for NP_001136053.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform b, which is shorter than isoform a. Variants 2 and 3 both encode isoform b.

Source sequence(s)

AC151967

Consensus CDS

CCDS26074.1

UniProtKB/TrEMBL

Q3UM95

Related

ENSMUSP00000137190.2, ENSMUST00000179379.9

Conserved Domains (1) summary

pfam09787
Location:26 → 450

Golgin_A5; Golgin subfamily A member 5
NM_134044.3 → NP_598805.2 spermatogenesis-defective protein 39 homolog isoform b

See identical proteins and their annotated locations for NP_598805.2

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform b, which is shorter than isoform a. Variants 2 and 3 both encode isoform b.

Source sequence(s)

AC151967

Consensus CDS

CCDS26074.1

UniProtKB/TrEMBL

Q3UM95

Related

ENSMUSP00000021426.10, ENSMUST00000021426.10

Conserved Domains (1) summary

pfam09787
Location:26 → 450

Golgin_A5; Golgin subfamily A member 5

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_000078.7 Reference GRCm39 C57BL/6J

Range

87285647..87313426 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157150.1 → XP_036013043.1 spermatogenesis-defective protein 39 homolog isoform X2
XM_011243977.3 → XP_011242279.1 spermatogenesis-defective protein 39 homolog isoform X2

Conserved Domains (1) summary

pfam09787
Location:3 → 359

Golgin_A5; Golgin subfamily A member 5
XM_006515339.5 → XP_006515402.1 spermatogenesis-defective protein 39 homolog isoform X1

See identical proteins and their annotated locations for XP_006515402.1

UniProtKB/Swiss-Prot

Q8BGQ1, Q8BL55, Q8CIK4, Q91YI3

UniProtKB/TrEMBL

Q3UM95

Conserved Domains (1) summary

pfam09787
Location:26 → 469

Golgin_A5; Golgin subfamily A member 5
XM_011243976.4 → XP_011242278.1 spermatogenesis-defective protein 39 homolog isoform X1

See identical proteins and their annotated locations for XP_011242278.1

UniProtKB/Swiss-Prot

Q8BGQ1, Q8BL55, Q8CIK4, Q91YI3

UniProtKB/TrEMBL

Q3UM95

Conserved Domains (1) summary

pfam09787
Location:26 → 469

Golgin_A5; Golgin subfamily A member 5