Vta1 (vesicle trafficking 1) - Rat Genome Database

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Gene: Vta1 (vesicle trafficking 1) Rattus norvegicus
Analyze
Symbol: Vta1
Name: vesicle trafficking 1
RGD ID: 1305031
Description: Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in multivesicular body. Orthologous to human VTA1 (vesicle trafficking 1); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Lip5; LOC292640; lysosomal trafficking regulator interacting protein-5; MGC112826; RGD1305031; similar to RIKEN cDNA 1110059P08; vacuolar protein sorting-associated protein VTA1 homolog; vesicle (multivesicular body) trafficking 1; Vps20-associated 1 homolog; Vps20-associated 1 homolog (S. cerevisiae)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8110,852,966 - 10,900,764 (-)NCBIGRCr8
mRatBN7.219,032,861 - 9,080,635 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19,032,335 - 9,080,635 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx18,752,160 - 8,799,898 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0114,754,070 - 14,801,806 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019,007,323 - 9,055,019 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.018,830,405 - 8,878,191 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl18,830,411 - 8,878,244 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0110,447,206 - 10,495,550 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419,512,291 - 9,560,020 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.119,512,290 - 9,560,020 (-)NCBI
Celera17,509,495 - 7,557,229 (-)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15173323   PMID:15644320   PMID:18385515   PMID:19056867   PMID:19199708   PMID:20358264   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
Vta1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8110,852,966 - 10,900,764 (-)NCBIGRCr8
mRatBN7.219,032,861 - 9,080,635 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19,032,335 - 9,080,635 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx18,752,160 - 8,799,898 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0114,754,070 - 14,801,806 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019,007,323 - 9,055,019 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.018,830,405 - 8,878,191 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl18,830,411 - 8,878,244 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0110,447,206 - 10,495,550 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419,512,291 - 9,560,020 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.119,512,290 - 9,560,020 (-)NCBI
Celera17,509,495 - 7,557,229 (-)NCBICelera
Cytogenetic Map1p13NCBI
VTA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386142,147,263 - 142,224,685 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6142,147,162 - 142,224,685 (+)EnsemblGRCh38hg38GRCh38
GRCh376142,468,400 - 142,545,822 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366142,510,103 - 142,583,778 (+)NCBINCBI36Build 36hg18NCBI36
Build 346142,510,102 - 142,583,776NCBI
Celera6143,208,886 - 143,282,564 (+)NCBICelera
Cytogenetic Map6q24.1-q24.2NCBI
HuRef6140,034,386 - 140,108,100 (+)NCBIHuRef
CHM1_16142,730,663 - 142,804,283 (+)NCBICHM1_1
T2T-CHM13v2.06143,339,355 - 143,416,853 (+)NCBIT2T-CHM13v2.0
Vta1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391014,531,077 - 14,581,233 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1014,530,499 - 14,581,304 (-)EnsemblGRCm39 Ensembl
GRCm381014,654,760 - 14,705,542 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1014,654,755 - 14,705,560 (-)EnsemblGRCm38mm10GRCm38
MGSCv371014,375,139 - 14,425,295 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361014,345,531 - 14,395,687 (-)NCBIMGSCv36mm8
Celera1014,558,320 - 14,607,904 (-)NCBICelera
Cytogenetic Map10A2NCBI
cM Map105.5NCBI
Vta1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543618,017,190 - 18,072,335 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543618,017,190 - 18,072,285 (-)NCBIChiLan1.0ChiLan1.0
VTA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25162,121,459 - 162,194,904 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16160,016,209 - 160,089,537 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06139,914,978 - 139,988,419 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16143,988,724 - 144,061,746 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6143,988,724 - 144,061,746 (+)Ensemblpanpan1.1panPan2
VTA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1133,830,300 - 33,895,865 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl133,830,313 - 33,895,073 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha134,728,526 - 34,794,046 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0134,004,743 - 34,070,405 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl134,004,746 - 34,070,565 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1133,875,224 - 33,940,792 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0133,757,084 - 33,822,600 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0134,067,989 - 34,133,582 (+)NCBIUU_Cfam_GSD_1.0
Vta1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946128,806,546 - 128,874,766 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366253,758,374 - 3,829,179 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366253,761,512 - 3,829,043 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VTA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl122,859,390 - 22,923,838 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1122,862,628 - 22,923,861 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2125,588,882 - 25,589,991 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VTA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11331,041,697 - 31,116,202 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1331,039,629 - 31,116,174 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660403,171,563 - 3,248,238 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vta1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475311,901,150 - 11,964,670 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475311,901,098 - 11,964,331 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vta1
173 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:233
Count of miRNA genes:160
Interacting mature miRNAs:178
Transcripts:ENSRNOT00000064836
Prediction methods:Microtar, 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
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1592587724697545Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1416280711481482Rat
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat

Markers in Region
RH133293  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219,033,146 - 9,033,326 (+)MAPPERmRatBN7.2
Rnor_6.018,830,688 - 8,830,867NCBIRnor6.0
Rnor_5.0110,448,052 - 10,448,231UniSTSRnor5.0
RGSC_v3.419,512,567 - 9,512,746UniSTSRGSC3.4
Celera17,509,771 - 7,509,950UniSTS
RH 3.4 Map1127.52UniSTS
Cytogenetic Map1p13UniSTS
AU049296  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219,074,411 - 9,074,635 (+)MAPPERmRatBN7.2
Rnor_6.018,871,948 - 8,872,171NCBIRnor6.0
Rnor_5.0110,489,312 - 10,489,535UniSTSRnor5.0
RGSC_v3.419,553,832 - 9,554,055UniSTSRGSC3.4
Celera17,551,041 - 7,551,264UniSTS
Cytogenetic Map1p13UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 39 57 41 19 41 8 11 74 35 41 11 8
Low 4
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000064836   ⟹   ENSRNOP00000061074
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19,032,868 - 9,080,633 (-)Ensembl
Rnor_6.0 Ensembl18,830,412 - 8,878,136 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075850   ⟹   ENSRNOP00000068514
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19,032,871 - 9,080,623 (-)Ensembl
Rnor_6.0 Ensembl18,830,411 - 8,878,244 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096797   ⟹   ENSRNOP00000088864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19,032,335 - 9,080,635 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098320   ⟹   ENSRNOP00000084084
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19,032,335 - 9,060,291 (-)Ensembl
RefSeq Acc Id: NM_001025640   ⟹   NP_001020811
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8110,852,966 - 10,900,735 (-)NCBI
mRatBN7.219,032,861 - 9,080,635 (-)NCBI
Rnor_6.018,830,412 - 8,878,136 (-)NCBI
Rnor_5.0110,447,206 - 10,495,550 (-)NCBI
RGSC_v3.419,512,291 - 9,560,020 (-)RGD
Celera17,509,495 - 7,557,229 (-)RGD
Sequence:
RefSeq Acc Id: NM_001398685   ⟹   NP_001385614
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8110,852,966 - 10,900,735 (-)NCBI
mRatBN7.219,032,861 - 9,080,635 (-)NCBI
RefSeq Acc Id: XR_010064556
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8110,852,973 - 10,900,764 (-)NCBI
RefSeq Acc Id: NP_001020811   ⟸   NM_001025640
- Peptide Label: isoform 2
- UniProtKB: Q4KM55 (UniProtKB/TrEMBL),   A0A8I5ZX91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068514   ⟸   ENSRNOT00000075850
RefSeq Acc Id: ENSRNOP00000061074   ⟸   ENSRNOT00000064836
RefSeq Acc Id: ENSRNOP00000088864   ⟸   ENSRNOT00000096797
RefSeq Acc Id: ENSRNOP00000084084   ⟸   ENSRNOT00000098320
RefSeq Acc Id: NP_001385614   ⟸   NM_001398685
- Peptide Label: isoform 1
- UniProtKB: A0A8I6A5Y0 (UniProtKB/TrEMBL),   A6JP73 (UniProtKB/TrEMBL),   A0A096MKH2 (UniProtKB/TrEMBL)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MKH2-F1-model_v2 AlphaFold A0A096MKH2 1-309 view protein structure

Transcriptome

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

Promoters
RGD ID:13689500
Promoter ID:EPDNEW_R25
Type:multiple initiation site
Name:Vta1_1
Description:vesicle trafficking 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_6.018,878,171 - 8,878,231EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305031 AgrOrtholog
BioCyc Gene G2FUF-62343 BioCyc
Ensembl Genes ENSRNOG00000011540 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064836 ENTREZGENE
  ENSRNOT00000064836.2 UniProtKB/TrEMBL
  ENSRNOT00000075850.3 UniProtKB/TrEMBL
  ENSRNOT00000096797 ENTREZGENE
  ENSRNOT00000096797.1 UniProtKB/TrEMBL
  ENSRNOT00000098320.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.270 UniProtKB/TrEMBL
  Immunoglobulin FC, subunit C UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7375248 IMAGE-MGC_LOAD
InterPro VPS_Vta1_N UniProtKB/TrEMBL
  Vta1-like UniProtKB/TrEMBL
  Vta1/CALS_N UniProtKB/TrEMBL
  Vta1_C UniProtKB/TrEMBL
KEGG Report rno:292640 UniProtKB/TrEMBL
MGC_CLONE MGC:112826 IMAGE-MGC_LOAD
NCBI Gene 292640 ENTREZGENE
PANTHER PTHR46009 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG UniProtKB/TrEMBL
Pfam Vta1 UniProtKB/TrEMBL
  Vta1_C UniProtKB/TrEMBL
PhenoGen Vta1 PhenoGen
RatGTEx ENSRNOG00000011540 RatGTEx
UniProt A0A096MKH2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZX91 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A5Y0 ENTREZGENE, UniProtKB/TrEMBL
  A6JP73 ENTREZGENE, UniProtKB/TrEMBL
  Q4KM55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Vta1  vesicle trafficking 1  Vta1  vesicle (multivesicular body) trafficking 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-09-17 Vta1  vesicle (multivesicular body) trafficking 1  Vta1  Vps20-associated 1 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Vta1  Vps20-associated 1 homolog (S. cerevisiae)  RGD1305031  similar to RIKEN cDNA 1110059P08  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1305031  similar to RIKEN cDNA 1110059P08  RGD1305031_predicted  similar to RIKEN cDNA 1110059P08 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305031_predicted  similar to RIKEN cDNA 1110059P08 (predicted)  LOC292640_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC292640_predicted  similar to RIKEN cDNA 1110059P08 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL