Vta1 vesicle trafficking 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vta1provided by RGD
Official Full Name: vesicle trafficking 1provided by RGD
Primary source: RGD:1305031
See related: EnsemblRapid:ENSRNOG00000011540 AllianceGenome:RGD:1305031
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: Lip5; RGD1305031
Summary: Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in multivesicular body. Orthologous to human VTA1 (vesicle trafficking 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 154.2), Kidney (RPKM 152.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1p13

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (10852966..10900764, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (9032861..9080635, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (8830405..8878191, complement)

Chromosome 1 - NC_086019.1 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?

LIP5 protein expression in a mouse tissue panel and various rodent and human tissues were studied.
Title: The lysosomal trafficking regulator interacting protein-5 localizes mainly in epithelial cells.

Submit: New GeneRIF Correction

General gene information

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Markers

RH133293 (e-PCR)
- UniSTS:216576

AU049296 (e-PCR)
- UniSTS:145744

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in late endosome to vacuole transport via multivesicular body sorting pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
is_active_in multivesicular body	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein VTA1 homolog

Names: Vps20-associated 1 homolog; lysosomal trafficking regulator interacting protein-5; vesicle (multivesicular body) trafficking 1

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_001025640.2 → NP_001020811.1 vacuolar protein sorting-associated protein VTA1 homolog isoform 2

See identical proteins and their annotated locations for NP_001020811.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I5ZX91, Q4KM55

Related

ENSRNOP00000061074.1, ENSRNOT00000064836.3

Conserved Domains (1) summary

pfam04652
Location:11 → 94

Vta1; Vta1 like
NM_001398685.1 → NP_001385614.1 vacuolar protein sorting-associated protein VTA1 homolog isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I6A5Y0, A6JP73

Related

ENSRNOP00000068514.3, ENSRNOT00000075850.4

Conserved Domains (3) summary

pfam03957
Location:182 → 253

Jun; Jun-like transcription factor

pfam04652
Location:22 → 152

Vta1; Vta1 like

pfam18097
Location:268 → 305

Vta1_C; Vta1 C-terminal domain