Ykt6 YKT6 v-SNARE homolog [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ykt6provided by RGD
Official Full Name: YKT6 v-SNARE homologprovided by RGD
Primary source: RGD:70897
See related: EnsemblRapid:ENSRNOG00000014785 AllianceGenome:RGD:70897
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: Predicted to enable SNAP receptor activity and protein-cysteine S-palmitoyltransferase activity. Predicted to be involved in several processes, including endoplasmic reticulum to Golgi vesicle-mediated transport; retrograde transport, endosome to Golgi; and vesicle docking involved in exocytosis. Located in apical dendrite; basal dendrite; and neuronal cell body. Part of SNARE complex. Orthologous to human YKT6 (YKT6 v-SNARE homolog). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 258.1), Kidney (RPKM 248.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14q21

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (85041393..85057347)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (80832187..80843394)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (86196018..86207057)

Chromosome 14 - NC_086032.1 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?

Different conformational dynamics of SNARE protein Ykt6 among yeast and mammals.
Title: Different conformational dynamics of SNARE protein Ykt6 among yeast and mammals.
The un-lipidated rat Ykt6 adopts five major conformational states.
Title: A revisit of the conformational dynamics of SNARE protein rYkt6.
Dodecylphosphocholine-regulated intramolecular conformational dynamics of Ykt6 has been reported.
Title: Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6.
The ykt6 particles/aggregates may represent ykt6 engaged in a non-SNARE function(s) or else nonfunctional, stored and/or excess ykt6.
Title: R-SNARE ykt6 resides in membrane-associated protease-resistant protein particles and modulates cell cycle progression when over-expressed.
A posttranslationally attached farnesyl group can actively regulate Ykt6 fusion activity in addition to its anticipated membrane-anchoring role.
Title: Lipid-Induced conformational switch controls fusion activity of longin domain SNARE Ykt6.
Data suggest that GS15 exists in a distinct SNARE complex that contains syntaxin5, GS28, and Ykt6, and may be involved in both ER-to-Golgi and intra-Golgi transport.
Title: GS15 forms a SNARE complex with syntaxin 5, GS28, and Ykt6 and is implicated in traffic in the early cisternae of the Golgi apparatus.
ykt6 is a neuronal SNARE targeted to a specialized compartment by its profilin-like amino terminal domain
Title: Mammalian ykt6 is a neuronal SNARE targeted to a specialized compartment by its profilin-like amino terminal domain.
The Ykt6 intramolecular interactions would be predicted to create a compact, closed conformation of the SNARE that prevents promiscuous targeting interactions and premature insertion into membranes.
Title: Intramolecular protein-protein and protein-lipid interactions control the conformation and subcellular targeting of neuronal Ykt6.

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General gene information

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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	ISO Inferred from Sequence Orthology more info
enables protein-cysteine S-palmitoyltransferase activity	ISO Inferred from Sequence Orthology more info
enables protein-cysteine S-palmitoyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available 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	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in membrane fusion	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info
involved_in vesicle docking involved in exocytosis	ISO Inferred from Sequence Orthology more info
involved_in vesicle docking involved in exocytosis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in vesicle targeting	ISO Inferred from Sequence Orthology more info
involved_in vesicle targeting	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
located_in apical dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in basal dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle membrane	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 endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: synaptobrevin homolog YKT6

Names: YKT6 homolog; prenylated SNARE protein

NP_113880.2

EC 2.3.1.-

XP_038948322.1

EC 2.3.1.-

XP_063129646.1

EC 2.3.1.-

XP_063129647.1

EC 2.3.1.-

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_031692.3 → NP_113880.2 synaptobrevin homolog YKT6

See identical proteins and their annotated locations for NP_113880.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000014

UniProtKB/Swiss-Prot

O35487, Q5EGY4

UniProtKB/TrEMBL

A0A8I6G2X5, A6IKR3

Related

ENSRNOP00000020693.1, ENSRNOT00000020693.5

Conserved Domains (1) summary

COG5143
Location:3 → 198

SNC1; Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]

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_086032.1 Reference GRCr8

Range

85041393..85057347

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063273576.1 → XP_063129646.1 synaptobrevin homolog YKT6 isoform X1
XM_063273577.1 → XP_063129647.1 synaptobrevin homolog YKT6 isoform X2
XM_039092394.2 → XP_038948322.1 synaptobrevin homolog YKT6 isoform X3

UniProtKB/TrEMBL

A6IKR4

Conserved Domains (2) summary

COG5143
Location:4 → 147

SNC1; Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]

cd15867
Location:85 → 144

R-SNARE_YKT6; SNARE motif of YKT6