Vat1l (vesicle amine transport 1-like) - Rat Genome Database

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Gene: Vat1l (vesicle amine transport 1-like) Rattus norvegicus
Analyze
Symbol: Vat1l
Name: vesicle amine transport 1-like
RGD ID: 1598315
Description: Predicted to enable oxidoreductase activity and zinc ion binding activity. Orthologous to human VAT1L (vesicle amine transport 1 like); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361414; similar to Synaptic vesicle membrane protein VAT-1 homolog; synaptic vesicle membrane protein VAT-1 homolog-like; vesicle amine transport protein 1 homolog (T. californica)-like
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
GRCr81959,103,636 - 59,272,950 (+)NCBIGRCr8
mRatBN7.21942,194,511 - 42,363,835 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1942,194,533 - 42,363,831 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1949,018,744 - 49,188,061 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01949,672,018 - 49,841,343 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01951,920,674 - 52,084,000 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01946,525,895 - 46,693,838 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1946,525,919 - 46,693,838 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01957,347,948 - 57,515,080 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41944,247,738 - 44,443,163 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1941,505,009 - 41,671,974 (+)NCBICelera
Cytogenetic Map19q12NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Vat1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81959,103,636 - 59,272,950 (+)NCBIGRCr8
mRatBN7.21942,194,511 - 42,363,835 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1942,194,533 - 42,363,831 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1949,018,744 - 49,188,061 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01949,672,018 - 49,841,343 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01951,920,674 - 52,084,000 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01946,525,895 - 46,693,838 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1946,525,919 - 46,693,838 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01957,347,948 - 57,515,080 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41944,247,738 - 44,443,163 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1941,505,009 - 41,671,974 (+)NCBICelera
Cytogenetic Map19q12NCBI
VAT1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381677,788,564 - 77,980,107 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1677,788,564 - 77,980,107 (+)EnsemblGRCh38hg38GRCh38
GRCh371677,822,461 - 78,014,004 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361676,379,984 - 76,571,505 (+)NCBINCBI36Build 36hg18NCBI36
Celera1662,120,178 - 62,312,112 (+)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1663,578,661 - 63,770,626 (+)NCBIHuRef
CHM1_11679,234,021 - 79,425,469 (+)NCBICHM1_1
T2T-CHM13v2.01683,844,682 - 84,036,081 (+)NCBIT2T-CHM13v2.0
Vat1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398114,932,307 - 115,100,814 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8114,932,352 - 115,100,811 (+)EnsemblGRCm39 Ensembl
GRCm388114,205,281 - 114,374,074 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8114,205,612 - 114,374,071 (+)EnsemblGRCm38mm10GRCm38
MGSCv378116,729,540 - 116,897,970 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368117,091,617 - 117,260,047 (+)NCBIMGSCv36mm8
Celera8118,413,837 - 118,583,874 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map860.62NCBI
Vat1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555221,001,451 - 1,163,000 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555221,001,814 - 1,162,948 (+)NCBIChiLan1.0ChiLan1.0
VAT1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21887,523,819 - 87,715,390 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11693,443,143 - 93,634,649 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01658,379,548 - 58,571,129 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11677,813,568 - 78,006,297 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1677,813,309 - 78,006,446 (+)Ensemblpanpan1.1panPan2
VAT1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1573,330,322 - 73,476,928 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl573,332,809 - 73,477,833 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha573,277,814 - 73,424,709 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0573,637,050 - 73,783,574 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl573,637,057 - 73,783,588 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1573,576,869 - 73,723,477 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0573,412,353 - 73,559,455 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0573,896,511 - 74,043,666 (-)NCBIUU_Cfam_GSD_1.0
Vat1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934933,317,927 - 33,458,432 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647526,130,611 - 26,271,539 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647526,130,693 - 26,271,187 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VAT1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl69,957,771 - 10,120,510 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.169,957,498 - 10,120,543 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.269,899,133 - 10,062,116 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VAT1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1563,276,259 - 63,463,206 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl563,276,314 - 63,463,233 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604712,585,744 - 12,772,654 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vat1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247469,032,786 - 9,189,595 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247469,033,604 - 9,189,588 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vat1l
1586 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:500
Count of miRNA genes:173
Interacting mature miRNAs:199
Transcripts:ENSRNOT00000015993, ENSRNOT00000075628
Prediction methods:Miranda, Targetscan
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
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat

Markers in Region
D19Rat89  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21942,248,839 - 42,248,951 (+)MAPPERmRatBN7.2
Rnor_6.01946,580,407 - 46,580,518NCBIRnor6.0
Rnor_5.01957,402,460 - 57,402,571UniSTSRnor5.0
RGSC_v3.41944,306,625 - 44,306,737RGDRGSC3.4
RGSC_v3.41944,306,626 - 44,306,737UniSTSRGSC3.4
RGSC_v3.11944,311,506 - 44,311,618RGD
Celera1941,559,305 - 41,559,418UniSTS
RH 3.4 Map19558.5RGD
RH 3.4 Map19558.5UniSTS
RH 2.0 Map19586.6RGD
FHH x ACI Map1933.4299RGD
Cytogenetic Map19q12UniSTS
RH137640  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21942,299,941 - 42,300,061 (+)MAPPERmRatBN7.2
Rnor_6.01946,631,709 - 46,631,828NCBIRnor6.0
Rnor_5.01957,453,075 - 57,453,194UniSTSRnor5.0
RGSC_v3.41944,364,661 - 44,364,780UniSTSRGSC3.4
Celera1941,609,884 - 41,610,003UniSTS
RH 3.4 Map19557.5UniSTS
Cytogenetic Map19q12UniSTS


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 74 6 3
Low 3 13 19 6 13 6 6 6 22 34 6 6
Below cutoff 26 11 8 6 8 2 4 7 4 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075628   ⟹   ENSRNOP00000063952
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1942,194,533 - 42,363,831 (+)Ensembl
Rnor_6.0 Ensembl1946,525,919 - 46,693,838 (+)Ensembl
RefSeq Acc Id: NM_001400980   ⟹   NP_001387909
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81959,103,636 - 59,272,950 (+)NCBI
mRatBN7.21942,194,511 - 42,363,835 (+)NCBI
RefSeq Acc Id: XM_039098305   ⟹   XP_038954233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81959,104,641 - 59,272,950 (+)NCBI
mRatBN7.21942,195,482 - 42,363,835 (+)NCBI
RefSeq Acc Id: XM_039098306   ⟹   XP_038954234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81959,120,966 - 59,272,950 (+)NCBI
mRatBN7.21942,211,863 - 42,363,835 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001387909 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954233 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954234 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000063952
  ENSRNOP00000063952.3
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000063952   ⟸   ENSRNOT00000075628
RefSeq Acc Id: XP_038954233   ⟸   XM_039098305
- Peptide Label: isoform X1
- UniProtKB: A6IZE1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954234   ⟸   XM_039098306
- Peptide Label: isoform X1
- UniProtKB: A6IZE1 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001387909   ⟸   NM_001400980
- UniProtKB: M0R3N4 (UniProtKB/TrEMBL)
Protein Domains
Enoyl reductase (ER)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R3N4-F1-model_v2 AlphaFold M0R3N4 1-378 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598315 AgrOrtholog
BioCyc Gene G2FUF-5598 BioCyc
Ensembl Genes ENSRNOG00000011989 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075628 ENTREZGENE
  ENSRNOT00000075628.5 UniProtKB/TrEMBL
Gene3D-CATH Medium-chain alcohol dehydrogenases, catalytic domain UniProtKB/TrEMBL
  NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro ADH_GroES-like UniProtKB/TrEMBL
  GroES-like UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
  PKS_ER UniProtKB/TrEMBL
  Quin_OxRdtase/zeta-crystal_CS UniProtKB/TrEMBL
NCBI Gene 361414 ENTREZGENE
PANTHER SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE UniProtKB/TrEMBL
  SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE UniProtKB/TrEMBL
Pfam ADH_N UniProtKB/TrEMBL
  ADH_zinc_N_2 UniProtKB/TrEMBL
PhenoGen Vat1l PhenoGen
PROSITE QOR_ZETA_CRYSTAL UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011989 RatGTEx
SMART PKS_ER UniProtKB/TrEMBL
Superfamily-SCOP GroES_like UniProtKB/TrEMBL
  SSF51735 UniProtKB/TrEMBL
UniProt A6IZE1 ENTREZGENE, UniProtKB/TrEMBL
  M0R3N4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-09-17 Vat1l  vesicle amine transport 1-like  Vat1l  vesicle amine transport protein 1 homolog (T. californica)-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-09 Vat1l  vesicle amine transport protein 1 homolog (T. californica)-like  LOC361414  similar to Synaptic vesicle membrane protein VAT-1 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC361414  similar to Synaptic vesicle membrane protein VAT-1 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL