Vps26b (VPS26 retromer complex component B) - Rat Genome Database

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Gene: Vps26b (VPS26 retromer complex component B) Rattus norvegicus
Analyze
Symbol: Vps26b
Name: VPS26 retromer complex component B
RGD ID: 1597170
Description: Predicted to be involved in intracellular protein transport; regulation of neurotransmitter receptor localization to postsynaptic specialization membrane; and retrograde transport, endosome to Golgi. Predicted to act upstream of or within cellular response to type II interferon. Predicted to be located in early endosome; late endosome; and phagocytic vesicle. Predicted to be part of retromer complex. Predicted to be active in glutamatergic synapse; postsynaptic early endosome; and postsynaptic recycling endosome. Orthologous to human VPS26B (VPS26 retromer complex component B); PARTICIPATES IN retromer-mediated pathway; INTERACTS WITH bisphenol A; cocaine; finasteride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC300472; similar to Vacuolar protein sorting 26 homolog (VPS26 protein homolog); vacuolar protein sorting 26 homolog B; vacuolar protein sorting 26 homolog B (S. pombe); vacuolar protein sorting-associated protein 26B
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
GRCr8833,675,025 - 33,696,132 (-)NCBIGRCr8
mRatBN7.2825,415,877 - 25,436,985 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,415,261 - 25,436,985 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx829,457,840 - 29,478,947 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0827,752,138 - 27,773,245 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0825,632,133 - 25,653,240 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0828,054,407 - 28,075,514 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,054,407 - 28,075,514 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0828,074,137 - 28,095,244 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera826,903,717 - 26,924,824 (-)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Retromer and sorting nexins in endosomal sorting. Gallon M and Cullen PJ, Biochem Soc Trans. 2015 Feb;43(1):33-47. doi: 10.1042/BST20140290.
2. 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.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:12947022   PMID:19144319   PMID:21040701   PMID:21920005  


Genomics

Comparative Map Data
Vps26b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8833,675,025 - 33,696,132 (-)NCBIGRCr8
mRatBN7.2825,415,877 - 25,436,985 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,415,261 - 25,436,985 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx829,457,840 - 29,478,947 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0827,752,138 - 27,773,245 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0825,632,133 - 25,653,240 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0828,054,407 - 28,075,514 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,054,407 - 28,075,514 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0828,074,137 - 28,095,244 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera826,903,717 - 26,924,824 (-)NCBICelera
Cytogenetic Map8q13NCBI
VPS26B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811134,224,671 - 134,247,788 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11134,224,671 - 134,247,788 (+)EnsemblGRCh38hg38GRCh38
GRCh3711134,094,565 - 134,117,682 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611133,599,771 - 133,622,896 (+)NCBINCBI36Build 36hg18NCBI36
Celera11131,267,426 - 131,290,549 (+)NCBICelera
Cytogenetic Map11q25NCBI
HuRef11130,049,435 - 130,072,447 (+)NCBIHuRef
CHM1_111133,981,297 - 134,004,422 (+)NCBICHM1_1
T2T-CHM13v2.011134,266,510 - 134,289,633 (+)NCBIT2T-CHM13v2.0
Vps26b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39926,915,798 - 26,941,390 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl926,919,067 - 26,941,361 (-)EnsemblGRCm39 Ensembl
GRCm38927,004,502 - 27,030,094 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl927,007,771 - 27,030,065 (-)EnsemblGRCm38mm10GRCm38
MGSCv37926,812,087 - 26,837,679 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36926,757,217 - 26,779,503 (-)NCBIMGSCv36mm8
Celera924,262,683 - 24,288,269 (-)NCBICelera
Cytogenetic Map9A4NCBI
cM Map912.07NCBI
Vps26b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541235,035,208 - 35,061,441 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541235,035,730 - 35,061,441 (+)NCBIChiLan1.0ChiLan1.0
VPS26B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29134,949,546 - 134,972,529 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111136,049,438 - 136,071,711 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v011129,077,964 - 129,100,936 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111132,936,077 - 132,958,364 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11132,936,077 - 132,958,364 (+)Ensemblpanpan1.1panPan2
VPS26B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.151,000,035 - 1,020,195 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl5999,392 - 1,020,196 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha51,119,865 - 1,140,152 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.05956,145 - 976,448 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl5956,219 - 976,410 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.15989,347 - 1,009,658 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.05989,525 - 1,009,829 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.051,027,461 - 1,047,763 (-)NCBIUU_Cfam_GSD_1.0
Vps26b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947115,985,248 - 116,005,237 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366841,599,754 - 1,617,662 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366841,597,706 - 1,617,689 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS26B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl960,785,998 - 60,805,193 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1960,786,192 - 60,802,507 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2967,482,521 - 67,487,024 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS26B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11125,284,997 - 125,307,748 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1125,285,056 - 125,305,549 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666043736,937 - 759,728 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps26b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248128,783,378 - 8,804,753 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248128,783,350 - 8,804,755 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vps26b
88 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:606
Count of miRNA genes:276
Interacting mature miRNAs:356
Transcripts:ENSRNOT00000072851
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat

Markers in Region
A004P16  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8q13UniSTS
RH142645  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2825,419,217 - 25,419,332 (+)MAPPERmRatBN7.2
Rnor_6.0828,057,748 - 28,057,862NCBIRnor6.0
Rnor_5.0828,077,478 - 28,077,592UniSTSRnor5.0
Celera826,907,058 - 26,907,172UniSTS
RH 3.4 Map8220.2UniSTS
Cytogenetic Map8q13UniSTS
AW535173  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2825,417,063 - 25,417,219 (+)MAPPERmRatBN7.2
Rnor_6.0828,055,594 - 28,055,749NCBIRnor6.0
Rnor_5.0828,075,324 - 28,075,479UniSTSRnor5.0
Celera826,904,904 - 26,905,059UniSTS
RH 3.4 Map8219.9UniSTS
Cytogenetic Map8q13UniSTS


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 43 51 35 19 35 8 11 74 35 34 11 8
Low 6 6 6 7
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000072851   ⟹   ENSRNOP00000064289
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl825,415,877 - 25,436,985 (-)Ensembl
Rnor_6.0 Ensembl828,054,407 - 28,075,514 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106733   ⟹   ENSRNOP00000089779
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl825,415,261 - 25,436,985 (-)Ensembl
RefSeq Acc Id: NM_001106809   ⟹   NP_001100279
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8833,675,025 - 33,696,132 (-)NCBI
mRatBN7.2825,415,877 - 25,436,985 (-)NCBI
Rnor_6.0828,054,407 - 28,075,514 (-)NCBI
Rnor_5.0828,074,137 - 28,095,244 (-)NCBI
Celera826,903,717 - 26,924,824 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100279 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61865 (Get FASTA)   NCBI Sequence Viewer  
  EDL83337 (Get FASTA)   NCBI Sequence Viewer  
  EDL83338 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064289
  ENSRNOP00000064289.1
  ENSRNOP00000089779.1
RefSeq Acc Id: NP_001100279   ⟸   NM_001106809
- UniProtKB: B1WBS4 (UniProtKB/TrEMBL),   M0R4K2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064289   ⟸   ENSRNOT00000072851
RefSeq Acc Id: ENSRNOP00000089779   ⟸   ENSRNOT00000106733

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WBS4-F1-model_v2 AlphaFold B1WBS4 1-336 view protein structure

Transcriptome

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

Promoters
RGD ID:13695818
Promoter ID:EPDNEW_R6343
Type:initiation region
Name:Vps26b_1
Description:VPS26 retromer complex component B
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_6.0828,075,509 - 28,075,569EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597170 AgrOrtholog
BioCyc Gene G2FUF-31306 BioCyc
Ensembl Genes ENSRNOG00000047235 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072851 ENTREZGENE
  ENSRNOT00000072851.2 UniProtKB/TrEMBL
  ENSRNOT00000106733.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.640 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7105156 IMAGE-MGC_LOAD
InterPro Arrestin_C UniProtKB/TrEMBL
  Vps26-related UniProtKB/TrEMBL
KEGG Report rno:300472 UniProtKB/TrEMBL
MGC_CLONE MGC:187418 IMAGE-MGC_LOAD
NCBI Gene 300472 ENTREZGENE
PANTHER PTHR12233 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26B UniProtKB/TrEMBL
Pfam Vps26 UniProtKB/TrEMBL
PhenoGen Vps26b PhenoGen
RatGTEx ENSRNOG00000047235 RatGTEx
UniProt A0A8I6ACK7_RAT UniProtKB/TrEMBL
  B1WBS4 ENTREZGENE, UniProtKB/TrEMBL
  M0R4K2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-01 Vps26b  VPS26 retromer complex component B  Vps26b  vacuolar protein sorting 26 homolog B (S. pombe)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Vps26b  vacuolar protein sorting 26 homolog B (S. pombe)  LOC300472  similar to Vacuolar protein sorting 26 homolog (VPS26 protein homolog)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC300472  similar to Vacuolar protein sorting 26 homolog (VPS26 protein homolog)      Symbol and Name status set to provisional 70820 PROVISIONAL