Stxbp5 syntaxin binding protein 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Stxbp5provided by RGD
Official Full Name: syntaxin binding protein 5provided by RGD
Primary source: RGD:708517
See related: EnsemblRapid:ENSRNOG00000013351 AllianceGenome:RGD:708517
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
Summary: Enables syntaxin-1 binding activity. Involved in synaptic vesicle cycle. Is active in several cellular components, including Schaffer collateral - CA1 synapse; presynaptic cytosol; and synaptic vesicle. Is extrinsic component of presynaptic membrane. Orthologous to human STXBP5 (syntaxin binding protein 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 154.8), Kidney (RPKM 105.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1p13

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (6002738..6155528, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (4182489..4335290, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (3858917..4011684, complement)

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
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?

Tomo-1 overexpression increased dendritic spine density, whereas Tomo-1 knockdown (KD) decreased spine density.
Title: The ubiquitin-proteasome system functionally links neuronal Tomosyn-1 to dendritic morphology.
We suggest that tomosyn uses its CTD to arrest SNARE-dependent fusion reactions, whereas its NTD is required for the recruitment of tomosyn to vesicle fusion sites through syntaxin interaction.
Title: The N- and C-terminal domains of tomosyn play distinct roles in soluble N-ethylmaleimide-sensitive factor attachment protein receptor binding and fusion regulation.
Unstructured loops in the WD40 domain mediate tomosyn's binding to SNAP25 and are involved in tomosyn's organization on the plasma membrane.
Title: Differential interaction of tomosyn with syntaxin and SNAP25 depends on domains in the WD40 β-propeller core and determines its inhibitory activity.
Overexpression of transduced rat tomosyn 1 significantly impaired mouse hippocampus-dependent spatial memory & strategy in the water maze. It impaired paired-pulse facilitation in CA3 mossy fiber synapses.
Title: Neuron-specific expression of tomosyn1 in the mouse hippocampal dentate gyrus impairs spatial learning and memory.
multiple domains outside the R-SNARE of tomosyn are critical to the efficacy of inhibition by tomosyn on exocytotic secretion
Title: Structural and functional analysis of tomosyn identifies domains important in exocytotic regulation.
the interplay between tomosyn and synaptotagmin-1 underlies inhibitory control of Ca(2+)-dependent neurotransmitter release.
Title: Tomosyn inhibits synaptotagmin-1-mediated step of Ca2+-dependent neurotransmitter release through its N-terminal WD40 repeats.
tomosyn controls synaptic vesicle fusion positively by serving as a placeholder for VAMP2.
Title: The tail domain of tomosyn controls membrane fusion through tomosyn displacement by VAMP2.
conformational change of tomosyn mediated by the intramolecular interactions of the tail domain controls its inhibitory activity on the SNARE complex formation, leading to a regulated inhibition of neurotransmitter release.
Title: Reciprocal intramolecular interactions of tomosyn control its inhibitory activity on SNARE complex formation.
Tomosyn inhibits neurotransmitter release by catalyzing oligomerization of the SNARE complex through the N-terminal WD-40 repeat domain in addition to the inhibitory activity of the C-terminal (VAMP)-like domain.
Title: Dual inhibition of SNARE complex formation by tomosyn ensures controlled neurotransmitter release.
Can negatively regulate exocytosis independently of syntaxin.
Title: Amisyn regulates exocytosis and fusion pore stability by both syntaxin-dependent and syntaxin-independent mechanisms.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BF390393 (e-PCR)
- UniSTS:249454

RH144675 (e-PCR)
- UniSTS:233920

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables myosin II binding	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info
enables syntaxin-1 binding	IDA Inferred from Direct Assay more info	PubMed
enables syntaxin-1 binding	IEA Inferred from Electronic Annotation more info
enables syntaxin-1 binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Golgi to plasma membrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within exocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exocytosis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of exocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exocytosis	TAS Traceable Author Statement more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of exocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic vesicle exocytosis	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic vesicle priming	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle priming	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle cycle	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle cycle	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in Schaffer collateral - CA1 synapse	IDA Inferred from Direct Assay more info	PubMed
part_of acetylcholine-gated channel complex	IEA Inferred from Electronic Annotation more info
part_of acetylcholine-gated channel complex	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in extrinsic component of neuronal dense core vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in extrinsic component of neuronal dense core vesicle membrane	ISO Inferred from Sequence Orthology more info
is_active_in extrinsic component of presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in hippocampal mossy fiber to CA3 synapse	IEA Inferred from Electronic Annotation more info
is_active_in hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
is_active_in neuromuscular junction	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	IEA Inferred from Electronic Annotation more info
is_active_in presynapse	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule	TAS Traceable Author Statement more info	PubMed
is_active_in synaptic vesicle	EXP Inferred from Experiment more info	PubMed
is_active_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: syntaxin-binding protein 5

Names: lethal(2) giant larvae protein homolog 3; tomosyn; tomosyn-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_030843.3 → NP_110470.1 syntaxin-binding protein 5 isoform m

See identical proteins and their annotated locations for NP_110470.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I6GF49, A6JP29

Conserved Domains (5) summary

COG2319
Location:47 → 275

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1049 → 1109

R-SNARE_STXBP5; SNARE domain of STXBP5

pfam08366
Location:277 → 384

LLGL; LLGL2

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

cl02567
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_178345.2 → NP_848035.1 syntaxin-binding protein 5 isoform b

See identical proteins and their annotated locations for NP_848035.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q9WU70, Q9WU71, Q9Z152

UniProtKB/TrEMBL

A0A8I6APW1, A6JP31

Related

ENSRNOP00000049322.4, ENSRNOT00000049699.8

Conserved Domains (5) summary

COG2319
Location:47 → 275

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1085 → 1145

R-SNARE_STXBP5; SNARE domain of STXBP5

pfam08366
Location:277 → 384

LLGL; LLGL2

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

cl02567
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_178346.2 → NP_848036.1 syntaxin-binding protein 5 isoform s

See identical proteins and their annotated locations for NP_848036.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I6GF49, A6JP28

Conserved Domains (5) summary

COG2319
Location:47 → 275

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1032 → 1092

R-SNARE_STXBP5; SNARE domain of STXBP5

pfam08366
Location:277 → 384

LLGL; LLGL2

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

cl02567
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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

6002738..6155528 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039091853.2 → XP_038947781.1 syntaxin-binding protein 5 isoform X1

UniProtKB/TrEMBL

A0A8L2QJB5, A0A8L2QLQ5, A6JP30

Related

ENSRNOP00000044738.4, ENSRNOT00000040559.7

Conserved Domains (5) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

cd15893
Location:1069 → 1129

R-SNARE_STXBP5; SNARE domain of STXBP5

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_063275001.1 → XP_063131071.1 syntaxin-binding protein 5 isoform X11
XM_063274990.1 → XP_063131060.1 syntaxin-binding protein 5 isoform X10

UniProtKB/TrEMBL

A0A8I6AIJ8

Related

ENSRNOP00000092947.1, ENSRNOT00000115103.2
XM_063274968.1 → XP_063131038.1 syntaxin-binding protein 5 isoform X2

Related

ENSRNOP00000099537.1, ENSRNOT00000133785.1
XM_063274970.1 → XP_063131040.1 syntaxin-binding protein 5 isoform X3
XM_039091879.2 → XP_038947807.1 syntaxin-binding protein 5 isoform X8

Conserved Domains (4) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_039091859.2 → XP_038947787.1 syntaxin-binding protein 5 isoform X4

Conserved Domains (4) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_039091874.2 → XP_038947802.1 syntaxin-binding protein 5 isoform X7

Conserved Domains (4) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_039091862.2 → XP_038947790.1 syntaxin-binding protein 5 isoform X5

Conserved Domains (4) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_039091865.2 → XP_038947793.1 syntaxin-binding protein 5 isoform X6

Conserved Domains (4) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_039091888.2 → XP_038947816.1 syntaxin-binding protein 5 isoform X9

Conserved Domains (4) summary

COG2319
Location:237 → 539

WD40; WD40 repeat [General function prediction only]

sd00039
Location:62 → 95

7WD40; WD40 repeat [structural motif]

pfam08366
Location:276 → 384

LLGL; LLGL2

cl29593
Location:62 → 280

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...