Use1 (unconventional SNARE in the ER 1) - Rat Genome Database

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Gene: Use1 (unconventional SNARE in the ER 1) Rattus norvegicus
Analyze
Symbol: Use1
Name: unconventional SNARE in the ER 1
RGD ID: 1306660
Description: Predicted to enable SNAP receptor activity. Predicted to be involved in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Predicted to act upstream of or within endoplasmic reticulum tubular network organization and regulation of ER to Golgi vesicle-mediated transport. Located in COPI-coated vesicle. Part of SNARE complex. Orthologous to human USE1 (unconventional SNARE in the ER 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC499392; LOC290627; RGD1306660; similar to RIKEN cDNA 2010315L10; unconventional SNARE in the ER 1 homolog; unconventional SNARE in the ER 1 homolog (S. cerevisiae); vesicle transport protein USE1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,069,118 - 18,075,816 (+)NCBIGRCr8
mRatBN7.21618,038,284 - 18,041,826 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,039,173 - 18,041,826 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,090,802 - 18,093,451 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,223,356 - 19,226,011 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,143,723 - 18,146,372 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,762,202 - 19,765,781 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,762,938 - 19,765,782 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,622,280 - 19,625,903 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,528,286 - 18,530,994 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11618,528,291 - 18,530,992 (+)NCBI
Celera1618,246,778 - 18,249,398 (+)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Members of a mammalian SNARE complex interact in the endoplasmic reticulum in vivo and are found in COPI vesicles. Verrier SE, etal., Eur J Cell Biol. 2008 Nov;87(11):863-78. doi: 10.1016/j.ejcb.2008.07.003. Epub 2008 Oct 1.
Additional References at PubMed
PMID:12477932   PMID:15029241   PMID:19188447  


Genomics

Comparative Map Data
Use1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,069,118 - 18,075,816 (+)NCBIGRCr8
mRatBN7.21618,038,284 - 18,041,826 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,039,173 - 18,041,826 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,090,802 - 18,093,451 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,223,356 - 19,226,011 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,143,723 - 18,146,372 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,762,202 - 19,765,781 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,762,938 - 19,765,782 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,622,280 - 19,625,903 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,528,286 - 18,530,994 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11618,528,291 - 18,530,992 (+)NCBI
Celera1618,246,778 - 18,249,398 (+)NCBICelera
Cytogenetic Map16p14NCBI
USE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381917,215,357 - 17,219,829 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1917,215,346 - 17,220,237 (+)EnsemblGRCh38hg38GRCh38
GRCh371917,326,166 - 17,330,638 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361917,187,155 - 17,191,638 (+)NCBINCBI36Build 36hg18NCBI36
Celera1917,227,674 - 17,232,159 (+)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1916,893,593 - 16,898,078 (+)NCBIHuRef
CHM1_11917,325,672 - 17,330,156 (+)NCBICHM1_1
T2T-CHM13v2.01917,349,405 - 17,354,703 (+)NCBIT2T-CHM13v2.0
Use1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39871,819,329 - 71,822,376 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl871,819,492 - 71,822,376 (+)EnsemblGRCm39 Ensembl
GRCm38871,366,848 - 71,369,732 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl871,366,848 - 71,369,732 (+)EnsemblGRCm38mm10GRCm38
MGSCv37873,890,747 - 73,893,631 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36874,296,215 - 74,298,718 (+)NCBIMGSCv36mm8
Celera873,889,937 - 73,892,821 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.43NCBI
Use1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955524969,422 - 971,997 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955524969,181 - 973,469 (-)NCBIChiLan1.0ChiLan1.0
USE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22022,085,101 - 22,089,949 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11921,091,701 - 21,096,525 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01916,702,277 - 16,706,842 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11917,677,354 - 17,681,516 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1917,677,411 - 17,681,500 (+)Ensemblpanpan1.1panPan2
USE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12045,507,986 - 45,510,920 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2045,507,985 - 45,510,891 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2045,421,267 - 45,424,203 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02045,994,133 - 45,997,070 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2045,993,020 - 45,997,008 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12045,230,749 - 45,233,685 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02045,640,604 - 45,643,533 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02045,916,408 - 45,919,344 (-)NCBIUU_Cfam_GSD_1.0
Use1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118204,063,649 - 204,066,537 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365963,612,790 - 3,615,656 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365963,612,788 - 3,615,671 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl260,450,425 - 60,454,800 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1260,450,424 - 60,454,070 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2260,079,245 - 60,083,135 (+)NCBISscrofa10.2Sscrofa10.2susScr3
USE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1615,709,956 - 15,714,830 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl615,710,011 - 15,714,812 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660743,718,271 - 3,723,144 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Use1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624908684,458 - 687,222 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624908683,505 - 687,259 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Use1
7 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:35
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000022650
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000022650   ⟹   ENSRNOP00000022650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,039,173 - 18,041,826 (+)Ensembl
Rnor_6.0 Ensembl1619,762,938 - 19,765,782 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115892   ⟹   ENSRNOP00000084167
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,039,177 - 18,041,824 (+)Ensembl
RefSeq Acc Id: NM_001169100   ⟹   NP_001162571
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,073,164 - 18,075,816 (+)NCBI
mRatBN7.21618,039,178 - 18,041,826 (+)NCBI
Rnor_6.01619,763,129 - 19,765,781 (+)NCBI
Rnor_5.01619,622,280 - 19,625,903 (+)NCBI
RGSC_v3.41618,528,286 - 18,530,994 (+)RGD
Celera1618,246,778 - 18,249,398 (+)RGD
Sequence:
RefSeq Acc Id: XM_006252855   ⟹   XP_006252917
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,069,118 - 18,075,816 (+)NCBI
mRatBN7.21618,038,284 - 18,041,826 (+)NCBI
Rnor_6.01619,762,202 - 19,765,781 (+)NCBI
Rnor_5.01619,622,280 - 19,625,903 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001162571 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252917 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58813 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022650.7
  ENSRNOP00000084167.1
RefSeq Acc Id: NP_001162571   ⟸   NM_001169100
- UniProtKB: A6K9S0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252917   ⟸   XM_006252855
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A1D9 (UniProtKB/TrEMBL),   A6K9S0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000022650   ⟸   ENSRNOT00000022650
Ensembl Acc Id: ENSRNOP00000084167   ⟸   ENSRNOT00000115892

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LQ22-F1-model_v2 AlphaFold F1LQ22 1-270 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699993
Promoter ID:EPDNEW_R10517
Type:multiple initiation site
Name:Use1_1
Description:unconventional SNARE in the ER 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01619,763,126 - 19,763,186EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306660 AgrOrtholog
BioCyc Gene G2FUF-11858 BioCyc
Ensembl Genes ENSRNOG00000016619 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022650.8 UniProtKB/TrEMBL
  ENSRNOT00000115892.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7370655 IMAGE-MGC_LOAD
InterPro Vesicle_transport_protein_Use1 UniProtKB/TrEMBL
KEGG Report rno:290627 UniProtKB/TrEMBL
MGC_CLONE MGC:188248 IMAGE-MGC_LOAD
NCBI Gene 290627 ENTREZGENE
PANTHER PTHR13050 UniProtKB/TrEMBL
  VESICLE TRANSPORT PROTEIN USE1 UniProtKB/TrEMBL
Pfam Use1 UniProtKB/TrEMBL
PhenoGen Use1 PhenoGen
RatGTEx ENSRNOG00000016619 RatGTEx
UniProt A0A8I6A1D9 ENTREZGENE, UniProtKB/TrEMBL
  A6K9S0 ENTREZGENE, UniProtKB/TrEMBL
  B0BNG6_RAT UniProtKB/TrEMBL
  F1LQ22_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Use1  unconventional SNARE in the ER 1  Use1  unconventional SNARE in the ER 1 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Use1  unconventional SNARE in the ER 1 homolog (S. cerevisiae)  LOC499392  hypothetical LOC499392  Data merged from RGD:1597034 1643240 APPROVED
2008-03-07 Use1  unconventional SNARE in the ER 1 homolog (S. cerevisiae)  RGD1306660_predicted  similar to RIKEN cDNA 2010315L10 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC499392  hypothetical LOC499392      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1306660_predicted  similar to RIKEN cDNA 2010315L10 (predicted)  LOC290627_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290627_predicted  similar to RIKEN cDNA 2010315L10 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL