Vti1a (vesicle transport through interaction with t-SNAREs 1A) - Rat Genome Database

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Gene: Vti1a (vesicle transport through interaction with t-SNAREs 1A) Rattus norvegicus
Analyze
Symbol: Vti1a
Name: vesicle transport through interaction with t-SNAREs 1A
RGD ID: 621490
Description: Predicted to enable SNAP receptor activity and SNARE binding activity. Involved in endoplasmic reticulum to Golgi vesicle-mediated transport; synaptic vesicle to endosome fusion; and vesicle fusion with Golgi apparatus. Located in several cellular components, including cytoplasmic vesicle; neuronal cell body; and perinuclear region of cytoplasm. Part of SNARE complex. Orthologous to human VTI1A (vesicle transport through interaction with t-SNAREs 1A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DD6A4-2(1); SNARE Vti1a-beta protein; vesicle transport through interaction with t-SNAREs homolog 1A; vesicle transport through interaction with t-SNAREs homolog 1A (yeast); vesicle transport v-SNARE protein Vti1-like 2; Vti1; Vti1-pending; vti1-rp2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Vti1a_v1   Vti1a_v2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21254,356,343 - 254,661,854 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1254,356,429 - 254,661,852 (+)Ensembl
Rnor_6.01276,310,072 - 276,508,635 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1276,309,927 - 276,490,602 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01283,705,427 - 283,902,980 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41261,664,003 - 261,905,744 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11261,875,047 - 262,116,789 (+)NCBI
Celera1250,063,252 - 250,364,895 (+)NCBICelera
Cytogenetic Map1q55NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:11101518   PMID:11786915   PMID:15215310   PMID:18195106   PMID:19132534   PMID:19224922   PMID:21803295   PMID:22243751   PMID:22958904   PMID:23677696   PMID:24095276  


Genomics

Comparative Map Data
Vti1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21254,356,343 - 254,661,854 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1254,356,429 - 254,661,852 (+)Ensembl
Rnor_6.01276,310,072 - 276,508,635 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1276,309,927 - 276,490,602 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01283,705,427 - 283,902,980 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41261,664,003 - 261,905,744 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11261,875,047 - 262,116,789 (+)NCBI
Celera1250,063,252 - 250,364,895 (+)NCBICelera
Cytogenetic Map1q55NCBI
VTI1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10112,446,998 - 112,818,744 (+)EnsemblGRCh38hg38GRCh38
GRCh3810112,446,988 - 112,855,368 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710114,206,746 - 114,615,127 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610114,196,746 - 114,568,493 (+)NCBINCBI36hg18NCBI36
Build 3410114,197,005 - 114,487,522NCBI
Celera10107,934,279 - 108,306,193 (+)NCBI
Cytogenetic Map10q25.2NCBI
HuRef10107,834,405 - 108,205,925 (+)NCBIHuRef
CHM1_110114,488,406 - 114,860,295 (+)NCBICHM1_1
Vti1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391955,304,489 - 55,615,893 (+)NCBIGRCm39mm39
GRCm39 Ensembl1955,304,727 - 55,615,741 (+)Ensembl
GRCm381955,316,030 - 55,627,461 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1955,316,295 - 55,627,309 (+)EnsemblGRCm38mm10GRCm38
MGSCv371955,390,841 - 55,701,051 (+)NCBIGRCm37mm9NCBIm37
MGSCv361955,369,601 - 55,679,811 (+)NCBImm8
Celera1957,507,484 - 57,817,205 (+)NCBICelera
Cytogenetic Map19D2NCBI
Vti1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543117,542,979 - 17,919,191 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543117,542,605 - 17,910,809 (+)NCBIChiLan1.0ChiLan1.0
VTI1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110112,476,478 - 112,857,949 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10112,476,859 - 112,845,615 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v010109,037,834 - 109,539,019 (+)NCBIMhudiblu_PPA_v0panPan3
VTI1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12823,496,553 - 23,854,609 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2823,496,593 - 23,842,369 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2823,648,320 - 24,006,512 (+)NCBI
ROS_Cfam_1.02824,029,018 - 24,386,280 (+)NCBI
UMICH_Zoey_3.12823,586,067 - 23,944,129 (+)NCBI
UNSW_CanFamBas_1.02823,597,236 - 23,951,876 (+)NCBI
UU_Cfam_GSD_1.02823,793,699 - 24,150,727 (+)NCBI
Vti1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721322,089,354 - 22,551,182 (-)NCBI
SpeTri2.0NW_0049364863,010,169 - 3,353,512 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VTI1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14122,849,004 - 123,215,942 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114122,848,727 - 123,217,568 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214133,772,147 - 133,859,216 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VTI1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19105,330,089 - 105,828,029 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl9105,330,143 - 105,695,049 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604866,533,145 - 67,038,520 (+)NCBIVero_WHO_p1.0
Vti1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473733,601,794 - 34,020,779 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Rat87  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21254,527,799 - 254,527,966 (+)MAPPERmRatBN7.2
Rnor_6.01276,479,854 - 276,480,020NCBIRnor6.0
Rnor_5.01283,874,199 - 283,874,365UniSTSRnor5.0
RGSC_v3.41261,771,754 - 261,772,403UniSTSRGSC3.4
RGSC_v3.41261,771,753 - 261,771,920RGDRGSC3.4
RGSC_v3.41261,771,754 - 261,771,920UniSTSRGSC3.4
RGSC_v3.11261,982,799 - 261,982,965RGD
Celera1250,232,535 - 250,232,681UniSTS
RH 3.4 Map11683.4RGD
RH 3.4 Map11683.4UniSTS
RH 2.0 Map11270.2RGD
SHRSP x BN Map1143.63RGD
Cytogenetic Map1q55UniSTS
RH128782  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21254,627,635 - 254,627,833 (+)MAPPERmRatBN7.2
Rnor_6.01276,578,740 - 276,578,937NCBIRnor6.0
Rnor_5.01283,972,264 - 283,972,461UniSTSRnor5.0
RGSC_v3.41261,872,624 - 261,872,821UniSTSRGSC3.4
Celera1250,332,557 - 250,332,754UniSTS
Celera1250,323,104 - 250,323,301UniSTS
RH 3.4 Map11649.6UniSTS
Cytogenetic Map1q55UniSTS
RH143954  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21254,432,108 - 254,432,217 (+)MAPPERmRatBN7.2
Rnor_6.01276,385,553 - 276,385,661NCBIRnor6.0
Rnor_5.01283,779,898 - 283,780,006UniSTSRnor5.0
RGSC_v3.41261,676,174 - 261,676,282UniSTSRGSC3.4
Celera1250,138,912 - 250,139,020UniSTS
RH 3.4 Map11683.9UniSTS
Cytogenetic Map1q55UniSTS
AA891586  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21254,369,124 - 254,369,259 (+)MAPPERmRatBN7.2
Rnor_6.01276,322,689 - 276,322,823NCBIRnor6.0
Rnor_5.01283,717,521 - 283,717,655UniSTSRnor5.0
Celera1250,075,820 - 250,075,954UniSTS
RH 3.4 Map11652.5UniSTS
Cytogenetic Map1q55UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1245907761257976495Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:298
Count of miRNA genes:121
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000066236, ENSRNOT00000067460
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.


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 8 25 9 19 9 8 8 40 11 10 11 8
Low 35 32 32 32 3 34 24 31
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_023101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF034238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF262221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF262222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066236   ⟹   ENSRNOP00000061050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1254,356,429 - 254,612,102 (+)Ensembl
Rnor_6.0 Ensembl1276,310,072 - 276,487,667 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067460   ⟹   ENSRNOP00000058953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1254,356,429 - 254,536,747 (+)Ensembl
Rnor_6.0 Ensembl1276,309,927 - 276,490,602 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108016   ⟹   ENSRNOP00000083070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1254,356,429 - 254,661,852 (+)Ensembl
RefSeq Acc Id: NM_023101   ⟹   NP_075589
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,540 - 254,660,041 (+)NCBI
Rnor_6.01276,310,072 - 276,508,635 (+)NCBI
Rnor_5.01283,705,427 - 283,902,980 (+)NCBI
RGSC_v3.41261,664,003 - 261,905,744 (+)RGD
Celera1250,063,252 - 250,364,895 (+)RGD
Sequence:
RefSeq Acc Id: XM_039090066   ⟹   XP_038945994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,661,854 (+)NCBI
RefSeq Acc Id: XM_039090071   ⟹   XP_038945999
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,661,854 (+)NCBI
RefSeq Acc Id: XM_039090073   ⟹   XP_038946001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,661,854 (+)NCBI
RefSeq Acc Id: XM_039090076   ⟹   XP_038946004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,573,027 (+)NCBI
RefSeq Acc Id: XM_039090081   ⟹   XP_038946009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,536,834 (+)NCBI
RefSeq Acc Id: XM_039090083   ⟹   XP_038946011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,573,027 (+)NCBI
RefSeq Acc Id: XM_039090086   ⟹   XP_038946014
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,559,452 (+)NCBI
RefSeq Acc Id: XM_039090088   ⟹   XP_038946016
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,660,023 (+)NCBI
RefSeq Acc Id: XM_039090089   ⟹   XP_038946017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,536,834 (+)NCBI
RefSeq Acc Id: XM_039090093   ⟹   XP_038946021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,660,023 (+)NCBI
RefSeq Acc Id: XM_039090097   ⟹   XP_038946025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,660,023 (+)NCBI
RefSeq Acc Id: XM_039090100   ⟹   XP_038946028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,453,202 (+)NCBI
RefSeq Acc Id: XM_039090101   ⟹   XP_038946029
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,432,251 (+)NCBI
RefSeq Acc Id: XM_039090105   ⟹   XP_038946033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,450,586 (+)NCBI
RefSeq Acc Id: XM_039090108   ⟹   XP_038946036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,453,202 (+)NCBI
RefSeq Acc Id: XM_039090109   ⟹   XP_038946037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,431,823 (+)NCBI
RefSeq Acc Id: XM_039090113   ⟹   XP_038946041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,432,251 (+)NCBI
RefSeq Acc Id: XM_039090117   ⟹   XP_038946045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,450,586 (+)NCBI
RefSeq Acc Id: XM_039090118   ⟹   XP_038946046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,431,823 (+)NCBI
RefSeq Acc Id: XM_039090121   ⟹   XP_038946049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,534,949 (+)NCBI
RefSeq Acc Id: XM_039090126   ⟹   XP_038946054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21254,356,343 - 254,377,734 (+)NCBI
Protein Sequences
Protein RefSeqs NP_075589 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945994 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945999 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946001 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946004 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946009 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946011 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946014 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946016 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946017 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946021 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946025 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946028 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946029 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946033 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946036 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946037 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946041 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946045 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946046 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946049 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946054 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF97790 (Get FASTA)   NCBI Sequence Viewer  
  AAF97791 (Get FASTA)   NCBI Sequence Viewer  
  EDL94471 (Get FASTA)   NCBI Sequence Viewer  
  EDL94472 (Get FASTA)   NCBI Sequence Viewer  
  Q9JI51 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_075589   ⟸   NM_023101
- UniProtKB: Q9JI51 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058953   ⟸   ENSRNOT00000067460
RefSeq Acc Id: ENSRNOP00000061050   ⟸   ENSRNOT00000066236
RefSeq Acc Id: XP_038945994   ⟸   XM_039090066
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945999   ⟸   XM_039090071
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946001   ⟸   XM_039090073
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038946016   ⟸   XM_039090088
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038946021   ⟸   XM_039090093
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038946025   ⟸   XM_039090097
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038946004   ⟸   XM_039090076
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038946011   ⟸   XM_039090083
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038946014   ⟸   XM_039090086
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038946017   ⟸   XM_039090089
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038946009   ⟸   XM_039090081
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946049   ⟸   XM_039090121
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038946028   ⟸   XM_039090100
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038946036   ⟸   XM_039090108
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038946033   ⟸   XM_039090105
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038946045   ⟸   XM_039090117
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038946029   ⟸   XM_039090101
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038946041   ⟸   XM_039090113
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038946037   ⟸   XM_039090109
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038946046   ⟸   XM_039090118
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038946054   ⟸   XM_039090126
- Peptide Label: isoform X20
RefSeq Acc Id: ENSRNOP00000083070   ⟸   ENSRNOT00000108016
Transcriptome

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

Promoters
RGD ID:13691003
Promoter ID:EPDNEW_R1524
Type:initiation region
Name:Vti1a_1
Description:vesicle transport through interaction with t-SNAREs 1A
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_6.01276,309,974 - 276,310,034EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621490 AgrOrtholog
Ensembl Genes ENSRNOG00000042786 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000058953 UniProtKB/TrEMBL
  ENSRNOP00000061050 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066236 UniProtKB/TrEMBL
  ENSRNOT00000067460 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.400 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GOSR2/Membrin/Bos1 UniProtKB/Swiss-Prot
  SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  T_SNARE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  v-SNARE_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vesicle_trsprt_v-SNARE_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:65277 UniProtKB/Swiss-Prot
NCBI Gene 65277 ENTREZGENE
Pfam V-SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vti1a PhenoGen
PIRSF Membrin-2 UniProtKB/Swiss-Prot
SMART t_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47661 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LT41_RAT UniProtKB/TrEMBL
  F1M938_RAT UniProtKB/TrEMBL
  Q9JI51 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9JI52 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-12-18 Vti1a  vesicle transport through interaction with t-SNAREs 1A  Vti1a  vesicle transport through interaction with t-SNAREs homolog 1A (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Vti1a  vesicle transport through interaction with t-SNAREs homolog 1A (yeast)      Symbol and Name status set to approved 625702 APPROVED
2003-11-10 Vti1a  vesicle transport through interaction with t-SNAREs homolog 1A (yeast)  Vti1-pending  SNARE Vti1a-beta protein  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 PROVISIONAL
2002-08-07 Vti1-pending  SNARE Vti1a-beta protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization splice variant Vti1a_v2, in contrast to Vti1a_v1, is enriched in synaptic vesicles and colocalizes with synaptobrevin 634537
gene_cellular_localization in neurons found in cell body and nerve terminals 634537