Vps13d (vacuolar protein sorting 13 homolog D) - Rat Genome Database

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Gene: Vps13d (vacuolar protein sorting 13 homolog D) Rattus norvegicus
Analyze
Symbol: Vps13d
Name: vacuolar protein sorting 13 homolog D
RGD ID: 1308403
Description: Predicted to be involved in mitochondrion organization; positive regulation of mitophagy; and protein localization to organelle. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 4. Orthologous to human VPS13D (vacuolar protein sorting 13 homolog D); INTERACTS WITH 17beta-estradiol; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: intermembrane lipid transfer protein VPS13D; LOC313825; vacuolar protein sorting 13 homolog D (S. cerevisiae); vacuolar protein sorting 13D; vacuolar protein sorting 13D (yeast); vacuolar protein sorting-associated protein 13D
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
GRCr85162,113,732 - 162,339,121 (-)NCBIGRCr8
mRatBN7.25156,830,509 - 157,055,895 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,830,512 - 157,055,891 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5159,531,778 - 159,757,186 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05161,305,060 - 161,530,472 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05161,261,414 - 161,486,827 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05162,891,451 - 163,119,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,891,451 - 163,119,239 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05166,572,596 - 166,798,221 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45163,423,921 - 163,649,390 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15163,436,292 - 163,659,522 (-)NCBI
Celera5155,120,166 - 155,345,428 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19056867   PMID:29307555   PMID:29604224  


Genomics

Comparative Map Data
Vps13d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85162,113,732 - 162,339,121 (-)NCBIGRCr8
mRatBN7.25156,830,509 - 157,055,895 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,830,512 - 157,055,891 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5159,531,778 - 159,757,186 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05161,305,060 - 161,530,472 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05161,261,414 - 161,486,827 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05162,891,451 - 163,119,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,891,451 - 163,119,239 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05166,572,596 - 166,798,221 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45163,423,921 - 163,649,390 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15163,436,292 - 163,659,522 (-)NCBI
Celera5155,120,166 - 155,345,428 (-)NCBICelera
Cytogenetic Map5q36NCBI
VPS13D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38112,230,030 - 12,512,047 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl112,230,030 - 12,512,047 (+)EnsemblGRCh38hg38GRCh38
GRCh37112,290,087 - 12,572,099 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36112,212,700 - 12,494,686 (+)NCBINCBI36Build 36hg18NCBI36
Celera111,403,306 - 11,683,636 (+)NCBICelera
Cytogenetic Map1p36.22-p36.21NCBI
HuRef111,443,367 - 11,725,135 (+)NCBIHuRef
CHM1_1112,278,092 - 12,560,085 (+)NCBICHM1_1
T2T-CHM13v2.0111,774,166 - 12,056,190 (+)NCBIT2T-CHM13v2.0
Vps13d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394144,597,619 - 144,921,598 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4144,699,192 - 144,921,575 (-)EnsemblGRCm39 Ensembl
GRCm384144,871,045 - 145,195,037 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4144,972,622 - 145,195,005 (-)EnsemblGRCm38mm10GRCm38
MGSCv374144,565,040 - 144,780,495 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364144,562,525 - 144,784,898 (-)NCBIMGSCv36mm8
Celera4146,562,636 - 146,779,783 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map478.17NCBI
Vps13d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554861,513,712 - 1,767,956 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554861,515,630 - 1,772,107 (-)NCBIChiLan1.0ChiLan1.0
VPS13D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21215,723,507 - 216,007,469 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11214,370,442 - 214,654,430 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0110,978,555 - 11,260,839 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1112,197,389 - 12,476,612 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl112,197,389 - 12,476,612 (+)Ensemblpanpan1.1panPan2
VPS13D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1283,898,620 - 84,132,453 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl283,901,018 - 84,132,529 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha280,431,937 - 80,668,550 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0284,538,404 - 84,795,230 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1281,308,659 - 81,545,743 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0282,307,682 - 82,544,901 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0283,374,019 - 83,610,988 (-)NCBIUU_Cfam_GSD_1.0
Vps13d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505835,127,270 - 35,369,418 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936474955,040 - 1,195,859 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936474955,081 - 1,194,200 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS13D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl672,256,828 - 72,510,058 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1672,256,865 - 72,514,256 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2666,406,618 - 66,546,392 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS13D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120119,289,515 - 119,573,504 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20119,288,989 - 119,569,221 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605423,139,838 - 23,430,150 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps13d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624818632,278 - 885,445 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624818632,276 - 885,450 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vps13d
801 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:255
Count of miRNA genes:154
Interacting mature miRNAs:187
Transcripts:ENSRNOT00000022185
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
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

Markers in Region
D5Got104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25157,045,927 - 157,046,092 (+)MAPPERmRatBN7.2
Rnor_6.05163,109,276 - 163,109,440NCBIRnor6.0
Rnor_5.05166,788,258 - 166,788,422UniSTSRnor5.0
RGSC_v3.45163,639,427 - 163,639,591UniSTSRGSC3.4
RGSC_v3.45163,639,426 - 163,639,591RGDRGSC3.4
RGSC_v3.15163,649,615 - 163,649,779RGD
Celera5155,335,465 - 155,335,629UniSTS
RH 3.4 Map51071.2UniSTS
RH 3.4 Map51071.2RGD
RH 2.0 Map51082.0RGD
Cytogenetic Map5q36UniSTS
RH134805  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25156,830,675 - 156,830,864 (+)MAPPERmRatBN7.2
Rnor_6.05162,891,615 - 162,891,803NCBIRnor6.0
Rnor_5.05166,572,760 - 166,572,948UniSTSRnor5.0
RGSC_v3.45163,424,085 - 163,424,273UniSTSRGSC3.4
Celera5155,120,330 - 155,120,518UniSTS
RH 3.4 Map51060.7UniSTS
Cytogenetic Map5q36UniSTS
RH143390  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25156,832,895 - 156,833,002 (+)MAPPERmRatBN7.2
Rnor_6.05162,893,833 - 162,893,939NCBIRnor6.0
Rnor_5.05166,574,978 - 166,575,084UniSTSRnor5.0
RGSC_v3.45163,426,305 - 163,426,411UniSTSRGSC3.4
Celera5155,122,550 - 155,122,656UniSTS
RH 3.4 Map51060.7UniSTS
Cytogenetic Map5q36UniSTS
BG378368  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25157,030,890 - 157,030,980 (+)MAPPERmRatBN7.2
Rnor_6.05163,094,249 - 163,094,338NCBIRnor6.0
Rnor_5.05166,773,231 - 166,773,320UniSTSRnor5.0
RGSC_v3.45163,624,393 - 163,624,482UniSTSRGSC3.4
Celera5155,320,437 - 155,320,526UniSTS
RH 3.4 Map51060.7UniSTS
Cytogenetic Map5q36UniSTS
RH137459  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25156,952,278 - 156,952,497 (+)MAPPERmRatBN7.2
Rnor_6.05163,013,354 - 163,013,572NCBIRnor6.0
Rnor_5.05166,694,499 - 166,694,717UniSTSRnor5.0
RGSC_v3.45163,545,727 - 163,545,945UniSTSRGSC3.4
Celera5155,241,895 - 155,242,113UniSTS
Cytogenetic Map5q36UniSTS


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 32 24 8 19 8 8 8 62 31 25 10 8
Low 3 11 33 33 33 3 12 4 16 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022185   ⟹   ENSRNOP00000022185
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5156,830,512 - 157,055,891 (-)Ensembl
Rnor_6.0 Ensembl5162,891,451 - 163,119,239 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085291   ⟹   ENSRNOP00000070610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5156,830,512 - 157,055,891 (-)Ensembl
Rnor_6.0 Ensembl5162,893,828 - 163,119,208 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096625   ⟹   ENSRNOP00000089845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5156,830,512 - 157,055,891 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098901   ⟹   ENSRNOP00000079356
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5156,830,512 - 157,055,891 (-)Ensembl
RefSeq Acc Id: NM_001395589   ⟹   NP_001382518
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,113,732 - 162,339,099 (-)NCBI
mRatBN7.25156,830,509 - 157,055,891 (-)NCBI
RefSeq Acc Id: XM_006239351   ⟹   XP_006239413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,113,732 - 162,339,117 (-)NCBI
mRatBN7.25156,830,509 - 157,055,895 (-)NCBI
Rnor_6.05162,893,681 - 163,119,202 (-)NCBI
Rnor_5.05166,572,596 - 166,798,221 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239353   ⟹   XP_006239415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,113,732 - 162,339,116 (-)NCBI
mRatBN7.25156,830,509 - 157,055,895 (-)NCBI
Rnor_6.05162,893,681 - 163,119,202 (-)NCBI
Rnor_5.05166,572,596 - 166,798,221 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593444   ⟹   XP_017448933
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,113,732 - 162,305,194 (-)NCBI
mRatBN7.25156,830,509 - 157,021,977 (-)NCBI
Rnor_6.05162,893,681 - 163,085,284 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110137   ⟹   XP_038966065
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,226,869 - 162,339,120 (-)NCBI
mRatBN7.25156,943,654 - 157,055,891 (-)NCBI
RefSeq Acc Id: XM_039110138   ⟹   XP_038966066
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,253,355 - 162,339,120 (-)NCBI
mRatBN7.25156,970,138 - 157,055,895 (-)NCBI
RefSeq Acc Id: XM_063287847   ⟹   XP_063143917
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,113,732 - 162,339,116 (-)NCBI
RefSeq Acc Id: XM_063287848   ⟹   XP_063143918
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,113,732 - 162,339,116 (-)NCBI
RefSeq Acc Id: XR_005504466
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85162,263,062 - 162,339,121 (-)NCBI
mRatBN7.25156,979,845 - 157,055,895 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006239413   ⟸   XM_006239351
- Peptide Label: isoform X2
- UniProtKB: A6IU14 (UniProtKB/TrEMBL),   D3ZKC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239415   ⟸   XM_006239353
- Peptide Label: isoform X4
- UniProtKB: A6IU14 (UniProtKB/TrEMBL),   D3ZKC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448933   ⟸   XM_017593444
- Peptide Label: isoform X5
- UniProtKB: A6IU14 (UniProtKB/TrEMBL),   D3ZKC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070610   ⟸   ENSRNOT00000085291
RefSeq Acc Id: ENSRNOP00000022185   ⟸   ENSRNOT00000022185
RefSeq Acc Id: XP_038966065   ⟸   XM_039110137
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038966066   ⟸   XM_039110138
- Peptide Label: isoform X7
RefSeq Acc Id: ENSRNOP00000089845   ⟸   ENSRNOT00000096625
RefSeq Acc Id: ENSRNOP00000079356   ⟸   ENSRNOT00000098901
RefSeq Acc Id: NP_001382518   ⟸   NM_001395589
- UniProtKB: A0A8I6GHP9 (UniProtKB/TrEMBL),   A6IU14 (UniProtKB/TrEMBL),   D3ZKC6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143918   ⟸   XM_063287848
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JYD4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143917   ⟸   XM_063287847
- Peptide Label: isoform X1
Protein Domains
UBA

Transcriptome

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

Promoters
RGD ID:13694256
Promoter ID:EPDNEW_R4772
Type:initiation region
Name:Vps13d_1
Description:vacuolar protein sorting 13 homolog D
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_6.05163,119,197 - 163,119,257EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308403 AgrOrtholog
BioCyc Gene G2FUF-39253 BioCyc
Ensembl Genes ENSRNOG00000016443 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022185.7 UniProtKB/TrEMBL
  ENSRNOT00000085291.2 UniProtKB/TrEMBL
  ENSRNOT00000096625 ENTREZGENE
  ENSRNOT00000096625.1 UniProtKB/TrEMBL
  ENSRNOT00000098901.1 UniProtKB/TrEMBL
Gene3D-CATH DNA helicase RuvA subunit, C-terminal domain UniProtKB/TrEMBL
InterPro UBA-like UniProtKB/TrEMBL
  UBA/transl_elong_EF1B_N_euk UniProtKB/TrEMBL
  VP13D_UBA UniProtKB/TrEMBL
  VPS13 UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_mid_rpt UniProtKB/TrEMBL
  VPS13_N2 UniProtKB/TrEMBL
  VPS13A_N UniProtKB/TrEMBL
  VPSAP UniProtKB/TrEMBL
KEGG Report rno:313825 UniProtKB/TrEMBL
NCBI Gene 313825 ENTREZGENE
PANTHER PTHR16166 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 13D UniProtKB/TrEMBL
Pfam Chorein_N UniProtKB/TrEMBL
  DUF1162 UniProtKB/TrEMBL
  UBA UniProtKB/TrEMBL
  VPS13 UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_mid_rpt UniProtKB/TrEMBL
PhenoGen Vps13d PhenoGen
PROSITE UBA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016443 RatGTEx
SMART UBA UniProtKB/TrEMBL
Superfamily-SCOP UBA_like UniProtKB/TrEMBL
UniProt A0A0G2JYD4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G572_RAT UniProtKB/TrEMBL
  A0A8I6GHP9 ENTREZGENE, UniProtKB/TrEMBL
  A6IU14 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKC6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-19 Vps13d  vacuolar protein sorting 13 homolog D  Vps13d  vacuolar protein sorting 13D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-13 Vps13d  vacuolar protein sorting 13D  Vps13d  vacuolar protein sorting 13 homolog D (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-25 Vps13d  vacuolar protein sorting 13 homolog D (S. cerevisiae)  Vps13d  vacuolar protein sorting 13D (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Vps13d  vacuolar protein sorting 13D (yeast)   Vps13d_predicted  vacuolar protein sorting 13D (yeast) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Vps13d_predicted  vacuolar protein sorting 13D (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED