Stx5 syntaxin 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Stx5provided by RGD
Official Full Name: syntaxin 5provided by RGD
Primary source: RGD:68426
See related: EnsemblRapid:ENSRNOG00000018847 AllianceGenome:RGD:68426
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: Stx5a
Summary: Predicted to enable SNAP receptor activity and SNARE binding activity. Involved in endoplasmic reticulum to Golgi vesicle-mediated transport and vesicle fusion with Golgi apparatus. Located in Golgi membrane. Part of SNARE complex. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation type II. Orthologous to human STX5 (syntaxin 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 171.2), Thymus (RPKM 164.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (215066532..215082685)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (205637401..205653563)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (224939497..224955658)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

O3 exposure (0.25 ppm) induced a significant increase of Syntaxin 5 and accumulation of betaA42 peptide in the reticulum in cells of the dentate gyrus
Title: Syntaxin 5 Overexpression and β-Amyloid 1-42 Accumulation in Endoplasmic Reticulum of Hippocampal Cells in Rat Brain Induced by Ozone Exposure.
Syx5 plays important roles in beta-amyloid precursor protein processing and in the endoplasmic reticulum stress response.
Title: ER stress response in NG108-15 cells involves upregulation of syntaxin 5 expression and reduced amyloid β peptide secretion.
depletion of GM130 by RNA interference slows the rate of ER to Golgi trafficking in vivo; interactions of GM130 with syntaxin 5 and Rab1 are regulated by mitotic phosphorylation
Title: Coordination of golgin tethering and SNARE assembly: GM130 binds syntaxin 5 in a p115-regulated manner.
elucidated the structure in solution of the isolated N-terminal domain of rat Sly1 and analyzed its complex with an N-terminal peptide of rat syntaxin 5 by NMR spectroscopy
Title: Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BE457658 (e-PCR)
- UniSTS:209437

AU024903 (e-PCR)
- UniSTS:115789

RH124618 (e-PCR)
- UniSTS:161440

RH134005 (e-PCR)
- UniSTS:217287

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables SNAP receptor activity	IEA Inferred from Electronic Annotation more info
enables SNAP receptor activity	ISO Inferred from Sequence Orthology more info
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi disassembly	ISO Inferred from Sequence Orthology more info
involved_in early endosome to Golgi transport	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed
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
involved_in membrane fusion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of Golgi organization	ISO Inferred from Sequence Orthology more info
involved_in retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
involved_in vesicle docking	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion with Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum-Golgi intermediate compartment membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in vesicle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: syntaxin-5

Names: syntaxin 5a

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_031704.2 → NP_113892.2 syntaxin-5

See identical proteins and their annotated locations for NP_113892.2

Status: VALIDATED

Source sequence(s)

BC127489

UniProtKB/Swiss-Prot

A0JPL4, O55200, Q08851

UniProtKB/TrEMBL

A0A8L2QDM8, A6HZT3

Conserved Domains (3) summary

COG5325
Location:80 → 324

COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]

cd15844
Location:266 → 338

SNARE_syntaxin5; SNARE motif of syntaxin 5

pfam11416
Location:52 → 73

Syntaxin-5_N; Syntaxin-5 N-terminal, Sly1p-binding domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

215066532..215082685

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006230997.4 → XP_006231059.1 syntaxin-5 isoform X1

See identical proteins and their annotated locations for XP_006231059.1

UniProtKB/Swiss-Prot

A0JPL4, O55200, Q08851

UniProtKB/TrEMBL

A0A8L2QDM8, A6HZT3

Related

ENSRNOP00000025664.6, ENSRNOT00000025664.7

Conserved Domains (3) summary

COG5325
Location:80 → 324

COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]

cd15844
Location:266 → 338

SNARE_syntaxin5; SNARE motif of syntaxin 5

pfam11416
Location:52 → 73

Syntaxin-5_N; Syntaxin-5 N-terminal, Sly1p-binding domain
XM_039089892.2 → XP_038945820.1 syntaxin-5 isoform X1

UniProtKB/Swiss-Prot

A0JPL4, O55200, Q08851

UniProtKB/TrEMBL

A0A8L2QDM8, A6HZT3

Conserved Domains (3) summary

COG5325
Location:80 → 324

COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]

cd15844
Location:266 → 338

SNARE_syntaxin5; SNARE motif of syntaxin 5

pfam11416
Location:52 → 73

Syntaxin-5_N; Syntaxin-5 N-terminal, Sly1p-binding domain