Vps13b (vacuolar protein sorting 13 homolog B) - Rat Genome Database

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Gene: Vps13b (vacuolar protein sorting 13 homolog B) Rattus norvegicus
Analyze
Symbol: Vps13b
Name: vacuolar protein sorting 13 homolog B
RGD ID: 1311183
Description: Human ortholog(s) of this gene implicated in Cohen syndrome. Orthologous to human VPS13B (vacuolar protein sorting 13 homolog B); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Coh1; Cohen syndrome homolog 1; Cohh1; LOC102555534; LOC315036; vacuolar protein sorting 13 homolog B (yeast); vacuolar protein sorting-associated protein 13B; vacuolar protein sorting-associated protein 13B-like
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
mRatBN7.2766,557,862 - 67,128,429 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl766,558,471 - 67,128,429 (+)Ensembl
Rnor_6.0774,118,834 - 74,722,341 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl775,852,610 - 75,858,812 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.0774,281,753 - 74,879,196 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4770,839,616 - 71,464,951 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1770,860,765 - 71,486,400 (+)NCBI
Celera763,647,181 - 64,211,271 (+)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:12730828   PMID:15632090  


Genomics

Comparative Map Data
Vps13b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2766,557,862 - 67,128,429 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl766,558,471 - 67,128,429 (+)Ensembl
Rnor_6.0774,118,834 - 74,722,341 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl775,852,610 - 75,858,812 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.0774,281,753 - 74,879,196 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4770,839,616 - 71,464,951 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1770,860,765 - 71,486,400 (+)NCBI
Celera763,647,181 - 64,211,271 (+)NCBICelera
Cytogenetic Map7q22NCBI
VPS13B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38899,013,274 - 99,877,580 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl899,013,266 - 99,877,580 (+)EnsemblGRCh38hg38GRCh38
GRCh378100,025,502 - 100,889,808 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368100,094,670 - 100,958,984 (+)NCBINCBI36hg18NCBI36
Build 348100,094,669 - 100,659,188NCBI
Celera896,211,225 - 97,075,608 (+)NCBI
Cytogenetic Map8q22.2NCBI
HuRef895,228,270 - 96,092,444 (+)NCBIHuRef
CHM1_18100,066,127 - 100,930,595 (+)NCBICHM1_1
Vps13b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391535,371,264 - 35,931,375 (+)NCBIGRCm39mm39
GRCm39 Ensembl1535,371,306 - 35,931,375 (+)Ensembl
GRCm381535,371,118 - 35,931,229 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1535,371,160 - 35,931,229 (+)EnsemblGRCm38mm10GRCm38
MGSCv371535,301,301 - 35,860,984 (+)NCBIGRCm37mm9NCBIm37
MGSCv361535,315,749 - 35,875,818 (+)NCBImm8
Celera1535,993,318 - 36,557,254 (+)NCBICelera
Cytogenetic Map15B3.1NCBI
Vps13b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541714,570,904 - 15,227,877 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541714,570,399 - 15,228,106 (+)NCBIChiLan1.0ChiLan1.0
VPS13B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1897,837,674 - 98,700,162 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl897,860,720 - 98,698,271 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0895,659,443 - 96,525,316 (+)NCBIMhudiblu_PPA_v0panPan3
VPS13B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1131,101,226 - 1,834,933 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl131,101,610 - 1,871,225 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha131,096,682 - 1,830,492 (+)NCBI
ROS_Cfam_1.0131,253,509 - 1,988,060 (+)NCBI
ROS_Cfam_1.0 Ensembl131,253,722 - 1,988,056 (+)Ensembl
UMICH_Zoey_3.1131,096,002 - 1,830,212 (+)NCBI
UNSW_CanFamBas_1.0131,203,819 - 1,943,474 (+)NCBI
UU_Cfam_GSD_1.0131,210,806 - 1,944,933 (+)NCBI
Vps13b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530335,855,538 - 36,526,292 (-)NCBI
SpeTri2.0NW_00493647043,281,905 - 43,952,523 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS13B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl437,090,935 - 37,820,419 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1437,085,929 - 37,821,159 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2440,006,383 - 40,389,291 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VPS13B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1893,899,666 - 94,737,123 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl893,901,284 - 94,735,262 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603945,953,328 - 46,821,705 (-)NCBIVero_WHO_p1.0
Vps13b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247636,101,943 - 6,866,457 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
DXRat132  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X116,926,119 - 116,926,150 (+)MAPPERmRatBN7.2
mRatBN7.21855,054,094 - 55,054,132 (-)MAPPERmRatBN7.2
Rnor_6.0774,457,911 - 74,458,114NCBIRnor6.0
Rnor_5.0774,623,381 - 74,623,584UniSTSRnor5.0
RGSC_v3.4X28,213,293 - 28,213,496UniSTSRGSC3.4
RGSC_v3.4X28,213,292 - 28,213,492RGDRGSC3.4
RGSC_v3.1X28,266,761 - 28,266,961RGD
CeleraX16,965,657 - 16,965,860UniSTS
SHRSP x BN MapX3.51RGD
SHRSP x BN MapX3.51UniSTS
Cytogenetic Map7q22UniSTS
D7Got258  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2766,951,413 - 66,951,646 (+)MAPPERmRatBN7.2
Rnor_6.0774,536,115 - 74,536,347NCBIRnor6.0
Rnor_5.0774,695,125 - 74,695,357UniSTSRnor5.0
RGSC_v3.4771,280,211 - 71,280,443UniSTSRGSC3.4
Celera764,035,468 - 64,035,700UniSTS
Cytogenetic Map7q22UniSTS
RH130106  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2767,127,249 - 67,127,438 (+)MAPPERmRatBN7.2
Rnor_6.0774,721,162 - 74,721,350NCBIRnor6.0
Rnor_5.0774,878,017 - 74,878,205UniSTSRnor5.0
RGSC_v3.4771,463,775 - 71,463,963UniSTSRGSC3.4
Celera764,210,092 - 64,210,280UniSTS
RH 3.4 Map7639.8UniSTS
Cytogenetic Map7q22UniSTS
28.MHAa64g4.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2766,995,869 - 66,996,007 (+)MAPPERmRatBN7.2
Rnor_6.0774,582,552 - 74,582,689NCBIRnor6.0
Rnor_5.0774,742,186 - 74,742,323UniSTSRnor5.0
RGSC_v3.4771,331,251 - 71,331,388UniSTSRGSC3.4
Celera764,078,535 - 64,078,672UniSTS
Cytogenetic Map7q22UniSTS
D15Mit56  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2767,007,877 - 67,007,973 (+)MAPPERmRatBN7.2
Rnor_6.0774,595,159 - 74,595,254NCBIRnor6.0
Rnor_5.0774,753,832 - 74,753,927UniSTSRnor5.0
RGSC_v3.4771,344,190 - 71,344,285UniSTSRGSC3.4
Celera764,090,973 - 64,091,068UniSTS
Cytogenetic Map7q22UniSTS
BI302144  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2766,569,796 - 66,569,977 (+)MAPPERmRatBN7.2
Rnor_6.0774,130,157 - 74,130,337NCBIRnor6.0
Rnor_5.0774,295,361 - 74,295,541UniSTSRnor5.0
RGSC_v3.4770,851,096 - 70,851,276UniSTSRGSC3.4
Celera763,658,504 - 63,658,684UniSTS
RH 3.4 Map7640.18UniSTS
Cytogenetic Map7q22UniSTS
AU048643  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0774,457,925 - 74,458,050NCBIRnor6.0
Rnor_5.0774,623,395 - 74,623,520UniSTSRnor5.0
RGSC_v3.4X28,213,357 - 28,213,482UniSTSRGSC3.4
CeleraX16,965,671 - 16,965,796UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)753612714103945643Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)759238038104238038Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)761074194106074194Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)762004452101773158Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)762004452101773158Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:329
Count of miRNA genes:218
Interacting mature miRNAs:252
Transcripts:ENSRNOT00000033021
Prediction methods:Microtar, Miranda, Rnahybrid, 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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl775,852,610 - 75,856,798 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081524
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl775,852,610 - 75,858,812 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094539   ⟹   ENSRNOP00000093776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl766,558,471 - 67,127,314 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105415   ⟹   ENSRNOP00000077378
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl766,558,471 - 67,128,429 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114232   ⟹   ENSRNOP00000094909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl766,558,471 - 67,128,429 (+)Ensembl
RefSeq Acc Id: NM_001134886   ⟹   NP_001128358
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,558,471 - 67,128,429 (+)NCBI
Rnor_6.0774,118,834 - 74,722,341 (+)NCBI
Rnor_5.0774,281,753 - 74,879,196 (+)NCBI
RGSC_v3.4770,839,616 - 71,464,951 (+)RGD
Celera763,647,181 - 64,211,271 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039079215   ⟹   XP_038935143
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,557,862 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079216   ⟹   XP_038935144
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,583,796 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079217   ⟹   XP_038935145
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,557,862 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079218   ⟹   XP_038935146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,557,862 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079219   ⟹   XP_038935147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,557,862 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079220   ⟹   XP_038935148
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,598,884 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079221   ⟹   XP_038935149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,557,862 - 67,111,055 (+)NCBI
RefSeq Acc Id: XM_039079222   ⟹   XP_038935150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,873,780 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079223   ⟹   XP_038935151
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,878,527 - 67,128,427 (+)NCBI
RefSeq Acc Id: XM_039079224   ⟹   XP_038935152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2766,557,863 - 66,952,996 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128358   ⟸   NM_001134886
- Sequence:
RefSeq Acc Id: XP_038935143   ⟸   XM_039079215
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935145   ⟸   XM_039079217
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935146   ⟸   XM_039079218
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038935147   ⟸   XM_039079219
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038935149   ⟸   XM_039079221
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935152   ⟸   XM_039079224
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038935144   ⟸   XM_039079216
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038935148   ⟸   XM_039079220
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038935150   ⟸   XM_039079222
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038935151   ⟸   XM_039079223
- Peptide Label: isoform X9
RefSeq Acc Id: ENSRNOP00000077378   ⟸   ENSRNOT00000105415
RefSeq Acc Id: ENSRNOP00000093776   ⟸   ENSRNOT00000094539
RefSeq Acc Id: ENSRNOP00000094909   ⟸   ENSRNOT00000114232

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
BUF/N (2020)
Visual CSV TAB Printer
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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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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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
DA/OlaHsd (2019)
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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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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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/Stm (2019)
Visual CSV TAB Printer
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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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
FXLE16/Stm (2020)
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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)
Visual CSV TAB Printer
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
GK/FarMcwi (2019)
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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
HXB10/IpcvMcwi (2019)
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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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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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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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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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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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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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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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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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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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
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/NRrrcMcwi (2019)
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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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SHR/OlalpcvMcwi (2019)
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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)
Visual CSV TAB Printer
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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 74541362 74541363 C G snv IS/Kyo (KyushuU), WKY/NHsd (KNAW), GK/Ox (KNAW), ACI/EurMcwi (KNAW), ACI/N (KNAW), BUF/MNa (KyushuU), WKY/N (KNAW), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), IS-Tlk/Kyo (KyushuU), ACI/EurMcwi (MCW)
7 74541408 74541409 A C snv IS/Kyo (KyushuU), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW), ACI/N (KNAW), ACI/EurMcwi (KNAW), GK/Ox (KNAW), WKY/N (KNAW), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), HWY/Slc (KyushuU), WKY/NHsd (KNAW), BBDP/WorN (KNAW), MR/N (KNAW)
7 74541498 74541499 G C snv DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), IS-Tlk/Kyo (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), WKY/NHsd (KNAW), WKY/N (KNAW), GK/Ox (KNAW), ACI/EurMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (MCW)
7 74541500 74541501 A G snv ACI/EurMcwi (MCW), ACI/N (KNAW), ACI/EurMcwi (KNAW), WKY/NHsd (KNAW), BUF/MNa (KyushuU), IS/Kyo (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), GK/Ox (KNAW), WKY/N (KNAW), IS-Tlk/Kyo (KyushuU)
7 74541541 74541542 G C snv ACI/EurMcwi (MCW), ACI/EurMcwi (KNAW), GK/Ox (KNAW), WKY/NHsd (KNAW), IS/Kyo (KyushuU), BUF/MNa (KyushuU), IS-Tlk/Kyo (KyushuU), LEC/Tj (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU)
7 74656926 74656927 C T snv MR/N (KNAW), GH/OmrMcwi (MCW), BBDP/WorN (KNAW), HTX/Kyo (KyushuU), HWY/Slc (KyushuU)
7 74854163 74854164 C T snv WKY/NHsd (KNAW), WKY/N (KNAW), GK/Ox (KNAW), ACI/EurMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (MCW), BUF/MNa (KyushuU)
7 74858583 74858584 C A snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 66813995 66813996 C G snv GK/FarMcwi (2019), WKY/N (2020), ACI/N (2020), ACI/EurMcwi (2019)
7 66814041 66814042 A C snv GK/FarMcwi (2019), ACI/N (2020), WKY/N (2020), ACI/EurMcwi (2019), PVG/Seac (2019)
7 66814131 66814132 G C snv WKY/N (2020), GK/FarMcwi (2019), ACI/N (2020), ACI/EurMcwi (2019)
7 66814133 66814134 A G snv WKY/N (2020), GK/FarMcwi (2019), ACI/EurMcwi (2019), ACI/N (2020)
7 66814174 66814175 G C snv ACI/EurMcwi (2019), ACI/N (2020), GK/FarMcwi (2019), WKY/N (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311183 AgrOrtholog
BioCyc Gene G2FUF-33662 BioCyc
Ensembl Genes ENSRNOG00000055234 Ensembl
  ENSRNOG00000066252 Ensembl, ENTREZGENE
Ensembl Protein ENSRNOP00000077378 ENTREZGENE
  ENSRNOP00000093776 ENTREZGENE
  ENSRNOP00000094909 ENTREZGENE
Ensembl Transcript ENSRNOT00000094539 ENTREZGENE
  ENSRNOT00000105415 ENTREZGENE
  ENSRNOT00000114232 ENTREZGENE
NCBI Gene 315036 ENTREZGENE
PhenoGen Vps13b PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Vps13b  vacuolar protein sorting 13 homolog B  LOC102555534  vacuolar protein sorting-associated protein 13B-like  Data Merged 737654 PROVISIONAL
2016-05-11 Vps13b  vacuolar protein sorting 13 homolog B  Vps13b  vacuolar protein sorting 13 homolog B (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102555534  vacuolar protein sorting-associated protein 13B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-04-20 Vps13b  vacuolar protein sorting 13 homolog B (yeast)  Cohh1  Cohen syndrome homolog 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cohh1  Cohen syndrome homolog 1   Cohh1_predicted  Cohen syndrome homolog 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cohh1_predicted  Cohen syndrome homolog 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED