Vps4b (vacuolar protein sorting 4B) - Rat Genome Database

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Gene: Vps4b (vacuolar protein sorting 4B) Mus musculus
Analyze
Symbol: Vps4b
Name: vacuolar protein sorting 4B
RGD ID: 1314315
MGI Page MGI
Description: Predicted to enable ATP hydrolysis activity; protein C-terminus binding activity; and protein homodimerization activity. Involved in late endosomal microautophagy; multivesicular body assembly; and viral budding from plasma membrane. Acts upstream of or within cholesterol transport; endosome organization; and potassium ion transport. Located in cytosol. Orthologous to human VPS4B (vacuolar protein sorting 4 homolog B).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 8030489C12Rik; Skd; Skd1; suppressor of K(+) transport growth defect 1; suppressor of K+ transport defect 1; vacuolar protein sorting 4b (yeast); vacuolar protein sorting-associated protein 4B
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm4939  
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391106,698,518 - 106,724,455 (-)NCBIGRCm39mm39
GRCm39 Ensembl1106,691,801 - 106,724,458 (-)Ensembl
GRCm381106,770,788 - 106,796,725 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1106,764,071 - 106,796,728 (-)EnsemblGRCm38mm10GRCm38
MGSCv371108,667,365 - 108,693,302 (-)NCBIGRCm37mm9NCBIm37
MGSCv361108,598,705 - 108,624,223 (-)NCBImm8
Celera1109,620,154 - 109,646,158 (-)NCBICelera
Cytogenetic Map1E2.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8082782   PMID:10349636   PMID:10393249   PMID:10637304   PMID:10679028   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11563910   PMID:12477932   PMID:12520002  
PMID:12594041   PMID:15173323   PMID:15489334   PMID:16141072   PMID:16141073   PMID:16757520   PMID:17940959   PMID:18796009   PMID:21238931   PMID:21267068   PMID:21873635   PMID:22837474  
PMID:26496610   PMID:26720614   PMID:27103069   PMID:28835279   PMID:31218856   PMID:31218890   PMID:32325033   PMID:33682352   PMID:34041875  


Genomics

Comparative Map Data
Vps4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391106,698,518 - 106,724,455 (-)NCBIGRCm39mm39
GRCm39 Ensembl1106,691,801 - 106,724,458 (-)Ensembl
GRCm381106,770,788 - 106,796,725 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1106,764,071 - 106,796,728 (-)EnsemblGRCm38mm10GRCm38
MGSCv371108,667,365 - 108,693,302 (-)NCBIGRCm37mm9NCBIm37
MGSCv361108,598,705 - 108,624,223 (-)NCBImm8
Celera1109,620,154 - 109,646,158 (-)NCBICelera
Cytogenetic Map1E2.1NCBI
VPS4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1863,389,190 - 63,422,483 (-)EnsemblGRCh38hg38GRCh38
GRCh381863,389,190 - 63,422,495 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371861,056,423 - 61,089,709 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361859,207,403 - 59,240,732 (-)NCBINCBI36hg18NCBI36
Build 341859,207,406 - 59,240,673NCBI
Celera1857,776,059 - 57,809,388 (-)NCBI
Cytogenetic Map18q21.33NCBI
HuRef1857,754,990 - 57,788,280 (-)NCBIHuRef
CHM1_11861,052,390 - 61,085,722 (-)NCBICHM1_1
Vps4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21322,907,105 - 22,932,200 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1322,907,109 - 22,932,229 (-)Ensembl
Rnor_6.01326,825,261 - 26,850,460 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1326,825,261 - 26,850,460 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01331,975,737 - 32,000,936 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41312,959,843 - 12,984,933 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11312,959,842 - 12,984,933 (-)NCBI
Celera1322,765,509 - 22,790,596 (-)NCBICelera
Cytogenetic Map13p11NCBI
Vps4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540247,154,007 - 47,184,021 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540247,154,350 - 47,183,979 (-)NCBIChiLan1.0ChiLan1.0
VPS4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11860,062,080 - 60,095,109 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1860,060,285 - 60,095,109 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01856,749,439 - 56,782,660 (-)NCBIMhudiblu_PPA_v0panPan3
VPS4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1113,638,965 - 13,673,295 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl113,639,004 - 13,669,072 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha114,605,156 - 14,639,495 (+)NCBI
ROS_Cfam_1.0113,500,614 - 13,534,990 (+)NCBI
ROS_Cfam_1.0 Ensembl113,500,669 - 13,534,959 (+)Ensembl
UMICH_Zoey_3.1113,538,762 - 13,573,109 (+)NCBI
UNSW_CanFamBas_1.0113,468,029 - 13,502,377 (+)NCBI
UU_Cfam_GSD_1.0113,716,838 - 13,751,163 (+)NCBI
Vps4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494426,887,096 - 26,922,486 (+)NCBI
SpeTri2.0NW_0049364972,126,064 - 2,161,451 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1158,233,051 - 158,270,679 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11158,233,039 - 158,273,533 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21175,754,073 - 175,760,220 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11816,336,959 - 16,370,208 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1816,336,921 - 16,370,291 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660609,317,729 - 9,350,925 (-)NCBIVero_WHO_p1.0
Vps4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247929,098,291 - 9,128,931 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13824984Twq5_mtestis weight QTL 5 (mouse)13000000185000000Mouse
1357753Kidq2_mkidney weight QTL 2 (mouse)Not determined134721057150318120Mouse
1357488Splq3_mspleen weight QTL 3 (mouse)Not determined134721057150318120Mouse
1558860W10q7_mweight 10 weeks QTL 7 (mouse)Not determined134721057150318120Mouse
1357721Sle17_msystematic lupus erythematosus susceptibility 17 (mouse)Not determined139093727126517573Mouse
1301722Cia9_mcollagen induced arthritis QTL 9 (mouse)Not determined145744740189571420Mouse
4142291Aec2_mautoimmune exocrinopathy 2 (mouse)Not determined52418578182423027Mouse
1301748Abbp1_mA/J and C57BL/6 blood pressure 1 (mouse)Not determined162907596120601949Mouse
10412185Hcs9_mhepatocarcinogenesis susceptibility 9 (mouse)Not determined163815531189571420Mouse
1300841Ssial1_msusceptibility to sialadenitis 1 (mouse)Not determined163880843153681816Mouse
27095918Ulnl1_mulna length 1, 5 week (mouse)167300000129800000Mouse
1300976Bmd19_mbone mineral density 19 (mouse)Not determined173227055108910684Mouse
4142394Mssq1_mmandible size and shape QTL 1 (mouse)Not determined73687970107688108Mouse
1301304Hrq3_mheart rate quantitative locus 3 (mouse)Not determined173687970107688108Mouse
1300989Lrdg1_mlight induced retinal degeneration 1 (mouse)Not determined173716016147249632Mouse
4141914Gcsfis_mG-CSF induced splenomegaly (mouse)Not determined74477076148839837Mouse
1357847Jckm2_mjuvenile cystic kidney modifier 2 (mouse)Not determined174952818133363199Mouse
27095931Pglq1_mpelvic girdle length QTL 1, 5 week (mouse)176000000128600000Mouse
27095928Pglq6_mpelvic girdle length QTL 6, 10 week (mouse)176000000148900000Mouse
26884448Sklq1_mskull length QTL 1, 5 week (mouse)176000000181500000Mouse
1558928Mord2_mmodifier of retinal degeneration 2 (mouse)Not determined177146478110608345Mouse
4141725Wbcq4_mwhite blood cell quantitative locus 4 (mouse)Not determined179930958113931066Mouse
12050069Nabq1_mnasal bone morphology QTL 1 (mouse)179930958113931066Mouse
13452395Leusq2_mleucocytosis susceptibility QTL 2 (mouse)180267876126458780Mouse
1301350Nidd4k_mNidd4 on KK-A (mouse)Not determined782314261147249632Mouse
1357439Popoa_mpremature ovulation and primary oocyte arrest (mouse)Not determined182665468135687641Mouse
10412238Alpq5_malcohol preference QTL 5 (mouse)Not determined182904910116904910Mouse
12791004Aath7_maortic arch atherosclerosis 7 (mouse)182904910116904910Mouse
11667074Led2_mlate embryonic death 2 (mouse)185768306117267351Mouse
12790991Aath1_maortic arch atherosclerosis 1 (mouse)186556204120556204Mouse
4141329Mleu1_mmyeloid leukemia survival 1 (mouse)Not determined89858782123858782Mouse
15039333Nmrs1_mNAFLD-associated magnetic resonance shift 1 (mouse)189858782123858782Mouse
1357760Synch3_msynechia 3 (mouse)Not determined192973712126973820Mouse
4141627Bwq7_mbody weight, QTL 7 (mouse)Not determined193013187124570059Mouse
12879491Hfnq1_mhair follicle number QTL 1 (mouse)193382588123709030Mouse
10045976Tir6_mtrypanosome infection response 6 (mouse)Not determined193609133120601949Mouse
27095913Scvln2_msacral vertebrae length 2, 5 week (mouse)194200000148900000Mouse
27095901Scvln8_msacral vertebrae length 2, 10 week (mouse)194200000172200000Mouse
27226779Tibl1_mtibia length 1, 5 week (mouse)195600000162200000Mouse
1301123Cd8mts2_mCD8 memory T cell subset 2 (mouse)Not determined196690656130690827Mouse
1301753Tir3a_mtrypansomiasis infection response 3a (mouse)Not determined197126256131126460Mouse
13452398Leusq5_mleucocytosis susceptibility QTL 5 (mouse)198547060126458780Mouse
1301536Pbbcp1_mperipheral blood B cell percentage 1 (mouse)Not determined199579930133580115Mouse
1301193Lxw3_mlupus BXSB x NZW 3 (mouse)Not determined1103040804137040937Mouse
12879492Ecgnq1_meccrine gland number QTL 1 (mouse)1103350337120607496Mouse
10412162Nobq3_mNew Zealand obese QTL 3 (mouse)Not determined1104005680191493284Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2024
Count of miRNA genes:848
Interacting mature miRNAs:1100
Transcripts:ENSMUST00000094646, ENSMUST00000112736, ENSMUST00000126057, ENSMUST00000127606, ENSMUST00000147705
Prediction methods: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: ENSMUST00000094646   ⟹   ENSMUSP00000092230
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1106,697,160 - 106,724,458 (-)Ensembl
GRCm38.p6 Ensembl1106,769,430 - 106,796,728 (-)Ensembl
RefSeq Acc Id: ENSMUST00000112736   ⟹   ENSMUSP00000108356
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1106,691,801 - 106,724,397 (-)Ensembl
GRCm38.p6 Ensembl1106,764,071 - 106,796,667 (-)Ensembl
RefSeq Acc Id: ENSMUST00000126057
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1106,718,830 - 106,724,307 (-)Ensembl
GRCm38.p6 Ensembl1106,791,100 - 106,796,577 (-)Ensembl
RefSeq Acc Id: ENSMUST00000127606
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1106,713,534 - 106,717,679 (-)Ensembl
GRCm38.p6 Ensembl1106,785,804 - 106,789,949 (-)Ensembl
RefSeq Acc Id: ENSMUST00000147705
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1106,705,028 - 106,710,524 (-)Ensembl
GRCm38.p6 Ensembl1106,777,298 - 106,782,794 (-)Ensembl
RefSeq Acc Id: ENSMUST00000190531
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1106,707,171 - 106,708,354 (-)Ensembl
GRCm38.p6 Ensembl1106,779,441 - 106,780,624 (-)Ensembl
RefSeq Acc Id: NM_009190   ⟹   NP_033216
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391106,698,518 - 106,724,455 (-)NCBI
GRCm381106,770,788 - 106,796,725 (-)ENTREZGENE
MGSCv371108,667,365 - 108,693,302 (-)RGD
Celera1109,620,154 - 109,646,158 (-)RGD
cM Map1 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_033216   ⟸   NM_009190
- UniProtKB: P46467 (UniProtKB/Swiss-Prot),   Q3TN07 (UniProtKB/TrEMBL),   Q8BM73 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000108356   ⟸   ENSMUST00000112736
RefSeq Acc Id: ENSMUSP00000092230   ⟸   ENSMUST00000094646
Protein Domains
AAA   MIT   Vps4_C

Promoters
RGD ID:6874652
Promoter ID:EPDNEW_M777
Type:initiation region
Name:Vps4b_1
Description:Mus musculus vacuolar protein sorting 4B , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381106,796,644 - 106,796,704EPDNEW
RGD ID:6818709
Promoter ID:MM_KWN:1811
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000112736,   OTTMUST00000051389,   OTTMUST00000051391
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361108,693,036 - 108,693,536 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1100499 AgrOrtholog
Ensembl Genes ENSMUSG00000009907 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000092230 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000108356 UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000094646 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000112736 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AAA_lid_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_AAA_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MIT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MIT_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VPS4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps4_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20479 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1100499 ENTREZGENE
NCBI Gene 20479 ENTREZGENE
PANTHER PTHR23074:SF72 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AAA_lid_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MIT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps4_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vps4b PhenoGen
PROSITE AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MIT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF116846 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P46467 ENTREZGENE
  Q3TN07 ENTREZGENE, UniProtKB/TrEMBL
  Q3U8P5_MOUSE UniProtKB/TrEMBL
  Q8BM73 ENTREZGENE, UniProtKB/TrEMBL
  VPS4B_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q91W22 UniProtKB/Swiss-Prot
  Q9R1C9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-21 Vps4b  vacuolar protein sorting 4B    vacuolar protein sorting 4b (yeast)  Symbol and/or name change 5135510 APPROVED