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

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Gene: Vps26b (VPS26 retromer complex component B) Rattus norvegicus
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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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8833,675,025 - 33,696,132 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl833,675,025 - 33,696,132 (-)EnsemblGRCr8
mRatBN7.2825,415,877 - 25,436,985 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,415,261 - 25,436,985 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx829,457,840 - 29,478,947 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0827,752,138 - 27,773,245 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0825,632,133 - 25,653,240 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0828,054,407 - 28,075,514 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,054,407 - 28,075,514 (-)Ensemblrn6Rnor6.0
Rnor_5.0828,074,137 - 28,095,244 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera826,903,717 - 26,924,824 (-)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse:




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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl833,675,025 - 33,696,132 (-)EnsemblGRCr8
mRatBN7.2825,415,877 - 25,436,985 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,415,261 - 25,436,985 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx829,457,840 - 29,478,947 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0827,752,138 - 27,773,245 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0825,632,133 - 25,653,240 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0828,054,407 - 28,075,514 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,054,407 - 28,075,514 (-)Ensemblrn6Rnor6.0
Rnor_5.0828,074,137 - 28,095,244 (-)NCBIRnor_5.0Rnor_5.0rn5
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 Ensembl11134,224,613 - 134,247,794 (+)Ensemblhg38GRCh38
GRCh3711134,094,565 - 134,117,682 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611133,599,771 - 133,622,896 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38927,004,502 - 27,030,094 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl927,007,771 - 27,030,065 (-)Ensemblmm10GRCm38
MGSCv37926,812,087 - 26,837,679 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha51,119,865 - 1,140,152 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.05956,145 - 976,448 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248128,783,350 - 8,804,755 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vps26b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1822,902,804 - 22,923,726 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vps26b
179 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)83154366176543661Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000072851   ⟹   ENSRNOP00000064289
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl833,675,025 - 33,696,132 (-)Ensembl
mRatBN7.2 Ensembl825,415,877 - 25,436,985 (-)Ensembl
Rnor_6.0 Ensembl828,054,407 - 28,075,514 (-)Ensembl
Ensembl 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
RefSeq Acc Id: NP_001100279   ⟸   NM_001106809
- UniProtKB: B1WBS4 (UniProtKB/TrEMBL),   M0R4K2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000064289   ⟸   ENSRNOT00000072851
Ensembl 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
  ENSRNOT00000072851.3 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
Pfam Vps26 UniProtKB/TrEMBL
PhenoGen Vps26b PhenoGen
RatGTEx ENSRNOG00000047235 RatGTEx
UniProt 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