Ykt6 (YKT6 v-SNARE homolog (S. cerevisiae)) - Rat Genome Database

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Gene: Ykt6 (YKT6 v-SNARE homolog (S. cerevisiae)) Mus musculus
Analyze
Symbol: Ykt6
Name: YKT6 v-SNARE homolog (S. cerevisiae)
RGD ID: 735771
MGI Page MGI
Description: 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. Predicted to act upstream of or within protein transport and vesicle-mediated transport. Predicted to be located in several cellular components, including dendrite; endosome; and neuronal cell body. Predicted to be part of SNARE complex. Predicted to be active in Golgi apparatus. Is expressed in coelomic epithelium of testis; embryo; and ovary. Orthologous to human YKT6 (YKT6 v-SNARE homolog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 0610042I15Rik; 1810013M05Rik; AW105923; prenylated SNARE protein (Ykt6); RP23-340E18.4; synaptobrevin homolog YKT6; YKT6 homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm11501   Gm5757  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39115,905,779 - 5,917,780 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl115,905,693 - 5,917,780 (+)EnsemblGRCm39 Ensembl
GRCm38115,955,758 - 5,967,780 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl115,955,693 - 5,967,780 (+)EnsemblGRCm38mm10GRCm38
MGSCv37115,855,761 - 5,867,783 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36115,855,835 - 5,867,783 (+)NCBIMGSCv36mm8
Celera116,447,816 - 6,459,840 (+)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.89NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:9211930   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11323436   PMID:12477932   PMID:14595844   PMID:15489334   PMID:15782199   PMID:16141072   PMID:16141073  
PMID:21267068   PMID:21677750   PMID:21873635   PMID:24457600   PMID:32325033   PMID:32554809   PMID:36417873   PMID:38187761  


Genomics

Comparative Map Data
Ykt6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39115,905,779 - 5,917,780 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl115,905,693 - 5,917,780 (+)EnsemblGRCm39 Ensembl
GRCm38115,955,758 - 5,967,780 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl115,955,693 - 5,967,780 (+)EnsemblGRCm38mm10GRCm38
MGSCv37115,855,761 - 5,867,783 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36115,855,835 - 5,867,783 (+)NCBIMGSCv36mm8
Celera116,447,816 - 6,459,840 (+)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.89NCBI
YKT6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38744,200,978 - 44,214,294 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl744,200,959 - 44,214,294 (+)EnsemblGRCh38hg38GRCh38
GRCh37744,240,577 - 44,253,893 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,207,103 - 44,220,418 (+)NCBINCBI36Build 36hg18NCBI36
Build 34744,013,817 - 44,027,132NCBI
Celera744,338,544 - 44,351,859 (+)NCBICelera
Cytogenetic Map7p13NCBI
HuRef744,125,857 - 44,139,172 (+)NCBIHuRef
CHM1_1744,244,442 - 44,257,752 (+)NCBICHM1_1
T2T-CHM13v2.0744,359,565 - 44,372,881 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2744,280,084 - 44,293,399 (+)NCBI
Ykt6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81485,041,393 - 85,057,347 (+)NCBIGRCr8
mRatBN7.21480,832,187 - 80,843,394 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1480,832,187 - 80,843,385 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1485,234,395 - 85,243,714 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01486,474,492 - 86,483,811 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01482,923,806 - 82,933,125 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01486,196,018 - 86,207,057 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,195,892 - 86,205,712 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01486,880,204 - 86,889,524 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,619,828 - 86,629,148 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11486,638,972 - 86,648,293 (+)NCBI
Celera1479,716,098 - 79,725,418 (+)NCBICelera
Cytogenetic Map14q21NCBI
Ykt6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554567,763,982 - 7,776,153 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554567,764,125 - 7,776,429 (-)NCBIChiLan1.0ChiLan1.0
YKT6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2649,111,738 - 49,125,662 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1797,436,478 - 97,450,400 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0744,915,181 - 44,928,001 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1744,975,782 - 44,996,195 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl744,982,748 - 44,994,183 (+)Ensemblpanpan1.1panPan2
YKT6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha162,131,031 - 2,140,443 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01614,721,412 - 14,730,822 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1614,721,419 - 14,730,907 (-)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.01614,352,875 - 14,362,275 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01614,333,138 - 14,342,549 (-)NCBIUU_Cfam_GSD_1.0
Ykt6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511899,954,485 - 99,967,329 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647819,166,153 - 19,179,719 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647819,166,225 - 19,179,060 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YKT6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1850,960,113 - 50,971,384 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11850,961,451 - 50,971,384 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21855,855,334 - 55,865,266 (-)NCBISscrofa10.2Sscrofa10.2susScr3
YKT6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12114,454,126 - 14,467,452 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2114,452,968 - 14,467,417 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660628,048,115 - 8,061,488 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ykt6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247407,832,114 - 7,845,149 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247407,832,436 - 7,844,416 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ykt6
334 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:709
Count of miRNA genes:490
Interacting mature miRNAs:568
Transcripts:ENSMUST00000002818, ENSMUST00000143834
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357722Vtbt11_mvertebral trabecular bone trait 11 (mouse)Not determined11123880487Mouse
1300768Tshp9_mtooth shape 9 (mouse)Not determined11125976374Mouse
1301765Skull15_mskull morphology 15 (mouse)Not determined11125976374Mouse
1300661Lmr6_mleishmaniasis resistance 6 (mouse)Not determined11125976374Mouse
10044008Hbnr15_mHeligmosomoides bakeri nematode resistance 15 (mouse)Not determined1122705234227232Mouse
1300599Cocrb11_mcocaine related behavior 11 (mouse)Not determined11267035536671472Mouse
27095914Pglq16_mpelvic girdle length QTL 16, 16 week (mouse)11325000018150000Mouse
27095919Pglq10_mpelvic girdle length QTL 10, 10 week (mouse)11325000018450000Mouse
27095925Pglq5_mpelvic girdle length QTL 5, 5 week (mouse)11325000019750000Mouse
27095904Scvln12_msacral vertebrae length 2, 10 week (mouse)11325000034495048Mouse
27095909Scvln6_msacral vertebrae length 2, 5 week (mouse)11325000044090827Mouse
27226798Scvln18_msacral vertebrae length 2, 16 week (mouse)11325000060690826Mouse
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
10053676Eae44a_mexperimental allergic encephalomyelitis susceptibility 44a (mouse)Not determined11450789621379532Mouse
27226741Metcl5_mmetatarsal-calcaneal length 5, 5 week (mouse)11465000046290827Mouse
27226735Metcl16_mmetatarsal-calcaneal length 16, 16 week (mouse)11525000035090827Mouse

Markers in Region
AW105923  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38115,967,489 - 5,967,575UniSTSGRCm38
MGSCv37115,867,492 - 5,867,578UniSTSGRCm37
Celera116,459,549 - 6,459,635UniSTS
Cytogenetic Map11A1UniSTS
Whitehead/MRC_RH1162.65UniSTS
RH143696  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38115,967,125 - 5,967,264UniSTSGRCm38
GRCm381192,794,652 - 92,794,794UniSTSGRCm38
MGSCv371192,655,966 - 92,656,108UniSTSGRCm37
MGSCv37115,867,128 - 5,867,267UniSTSGRCm37
Celera116,459,185 - 6,459,324UniSTS
Celera11102,388,723 - 102,388,865UniSTS
Cytogenetic Map11A1UniSTS
Cytogenetic Map11DUniSTS
AI324827  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38115,966,223 - 5,966,351UniSTSGRCm38
MGSCv37115,866,226 - 5,866,354UniSTSGRCm37
Celera116,458,283 - 6,458,411UniSTS
Cytogenetic Map11A1UniSTS
Whitehead/MRC_RH1125.43UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000002818   ⟹   ENSMUSP00000002818
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl115,905,693 - 5,917,780 (+)Ensembl
GRCm38.p6 Ensembl115,955,693 - 5,967,780 (+)Ensembl
RefSeq Acc Id: ENSMUST00000143834
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl115,909,304 - 5,913,201 (+)Ensembl
GRCm38.p6 Ensembl115,959,304 - 5,963,201 (+)Ensembl
RefSeq Acc Id: NM_019661   ⟹   NP_062635
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39115,905,779 - 5,917,780 (+)NCBI
GRCm38115,955,758 - 5,967,780 (+)ENTREZGENE
MGSCv37115,855,761 - 5,867,783 (+)RGD
Celera116,447,816 - 6,459,840 (+)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_062635   ⟸   NM_019661
- UniProtKB: O88595 (UniProtKB/Swiss-Prot),   Q9CQW1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000002818   ⟸   ENSMUST00000002818
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9CQW1-F1-model_v2 AlphaFold Q9CQW1 1-198 view protein structure

Promoters
RGD ID:6822483
Promoter ID:MM_KWN:6332
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:OTTMUST00000011413
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36115,855,451 - 5,855,951 (+)MPROMDB
RGD ID:8673876
Promoter ID:EPDNEW_M14968
Type:initiation region
Name:Ykt6_1
Description:Mus musculus YKT6 v-SNARE homolog , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38115,955,779 - 5,955,839EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1927550 AgrOrtholog
Ensembl Genes ENSMUSG00000002741 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000002818 ENTREZGENE
  ENSMUST00000002818.9 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.5.110 UniProtKB/Swiss-Prot
  Longin domain UniProtKB/Swiss-Prot
InterPro Longin-like_dom_sf UniProtKB/Swiss-Prot
  Longin_dom UniProtKB/Swiss-Prot
  R-SNARE_YKT6 UniProtKB/Swiss-Prot
  V_SNARE_CC UniProtKB/Swiss-Prot
KEGG Report mmu:56418 UniProtKB/Swiss-Prot
MGD MGI:1927550 ENTREZGENE
NCBI Gene 56418 ENTREZGENE
PANTHER SYNAPTOBREVIN HOMOLOG YKT6 UniProtKB/Swiss-Prot
  SYNAPTOBREVIN HOMOLOG YKT6 UniProtKB/Swiss-Prot
Pfam Longin UniProtKB/Swiss-Prot
  Synaptobrevin UniProtKB/Swiss-Prot
PhenoGen Ykt6 PhenoGen
PROSITE LONGIN UniProtKB/Swiss-Prot
  V_SNARE UniProtKB/Swiss-Prot
SMART Longin UniProtKB/Swiss-Prot
Superfamily-SCOP SNARE fusion complex UniProtKB/Swiss-Prot
  SSF64356 UniProtKB/Swiss-Prot
UniProt O88595 ENTREZGENE
  Q9CQW1 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O88595 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-22 Ykt6  YKT6 v-SNARE homolog (S. cerevisiae)    YKT6 homolog (S. Cerevisiae)  Symbol and/or name change 5135510 APPROVED