Vipas39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vipas39provided by RGD
Official Full Name: VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homologprovided by RGD
Primary source: RGD:1589291
See related: EnsemblRapid:ENSRNOG00000049223 AllianceGenome:RGD:1589291
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
Also known as: Spe39; Vipar; hSPE-39
Summary: Predicted to be involved in endosome to lysosome transport and intracellular protein transport. Predicted to act 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. 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: Biased expression in Thymus (RPKM 144.6), Heart (RPKM 138.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q31

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (112619228..112644089, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (106888284..106913139, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (111271283..111296013, complement)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

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
NOT involved_in autophagosome maturation	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in collagen metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen metabolic process	ISO Inferred from Sequence Orthology more info
involved_in endosome to lysosome transport	IEA Inferred from Electronic Annotation more info
NOT involved_in endosome to lysosome transport	ISO Inferred from Sequence Orthology 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
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intracellular protein transport	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within peptidyl-lysine hydroxylation	ISO Inferred from Sequence Orthology more info
involved_in post-translational protein modification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-translational protein modification	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
NOT part_of HOPS complex	ISO Inferred from Sequence Orthology more info
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.