Vps50 (VPS50 subunit of EARP/GARPII complex) - Rat Genome Database

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Gene: Vps50 (VPS50 subunit of EARP/GARPII complex) Chinchilla lanigera
Analyze
Symbol: Vps50
Name: VPS50 subunit of EARP/GARPII complex
RGD ID: 8895337
Description: ENCODES a protein that exhibits SNARE binding (ortholog); INVOLVED IN endocytic recycling (ortholog); retrograde transport, endosome to Golgi (ortholog); ASSOCIATED WITH genetic disease (ortholog); NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND NEONATAL CHOLESTASIS (ortholog); pleomorphic xanthoastrocytoma (ortholog); FOUND IN EARP complex (ortholog); membrane (ortholog); perinuclear region of cytoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Ccdc132; coiled-coil domain containing 132; syndetin; VPS50 EARP/GARPII complex subunit; VPS50, EARP/GARPII complex subunit
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543210,134,141 - 10,245,895 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543210,134,280 - 10,244,390 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
Vps50
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543210,134,141 - 10,245,895 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543210,134,280 - 10,244,390 (+)NCBIChiLan1.0ChiLan1.0
VPS50
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38793,232,366 - 93,361,123 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl793,232,340 - 93,361,123 (+)EnsemblGRCh38hg38GRCh38
GRCh37792,861,679 - 92,990,435 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36792,699,589 - 92,826,274 (+)NCBINCBI36Build 36hg18NCBI36
Celera787,566,164 - 87,692,840 (+)NCBICelera
Cytogenetic Map7q21.2-q21.3NCBI
HuRef787,470,455 - 87,601,198 (+)NCBIHuRef
CHM1_1792,791,700 - 92,920,441 (+)NCBICHM1_1
T2T-CHM13v2.0794,474,420 - 94,603,577 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2792,190,974 - 92,319,745 (+)NCBI
Vps50
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3963,498,393 - 3,603,531 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl63,498,382 - 3,603,531 (+)EnsemblGRCm39 Ensembl
GRCm3863,498,393 - 3,603,531 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl63,498,382 - 3,603,531 (+)EnsemblGRCm38mm10GRCm38
MGSCv3763,448,393 - 3,553,531 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3663,448,405 - 3,553,307 (+)NCBIMGSCv36mm8
Celera63,656,648 - 3,761,558 (+)NCBICelera
Cytogenetic Map6A1NCBI
cM Map61.81NCBI
Vps50
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8432,439,101 - 32,540,299 (+)NCBIGRCr8
mRatBN7.2431,484,424 - 31,585,617 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl431,484,463 - 31,585,617 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx436,457,167 - 36,558,319 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0432,383,277 - 32,484,430 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0430,741,292 - 30,842,473 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0428,441,255 - 28,551,784 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl428,441,301 - 28,551,784 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0428,344,487 - 28,455,450 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4428,304,788 - 28,410,697 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1428,318,488 - 28,424,228 (+)NCBI
Celera426,870,657 - 26,971,611 (+)NCBICelera
Cytogenetic Map4q13NCBI
VPS50
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26111,074,309 - 111,202,358 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17159,340,873 - 159,467,006 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0785,188,960 - 85,315,452 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1798,783,520 - 98,909,208 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl798,786,809 - 98,908,113 (+)Ensemblpanpan1.1panPan2
VPS50
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11418,742,214 - 18,874,779 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1418,742,349 - 18,874,776 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1418,302,677 - 18,435,316 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01418,550,501 - 18,683,063 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1418,550,139 - 18,683,566 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11418,709,720 - 18,842,184 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01418,445,282 - 18,578,116 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01418,696,225 - 18,828,745 (+)NCBIUU_Cfam_GSD_1.0
Vps50
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511832,148,433 - 32,269,351 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936803530,402 - 651,502 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936803530,543 - 651,461 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS50
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl973,074,906 - 73,217,053 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1973,074,878 - 73,215,833 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2979,841,292 - 79,965,954 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS50
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12155,660,565 - 55,782,188 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2155,660,311 - 55,782,167 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604248,524,305 - 48,645,505 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps50
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462481359,528 - 189,169 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462481359,560 - 187,743 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


RefSeq Acc Id: ENSCLAT00000010920   ⟹   ENSCLAP00000010787
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495543210,134,141 - 10,245,895 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000010921   ⟹   ENSCLAP00000010788
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495543210,134,141 - 10,245,895 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000010922   ⟹   ENSCLAP00000010789
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495543210,139,046 - 10,241,266 (+)Ensembl
RefSeq Acc Id: XM_005388036   ⟹   XP_005388093
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495543210,134,280 - 10,244,390 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013516067   ⟹   XP_013371521
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495543210,134,280 - 10,244,390 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005388093 (Get FASTA)   NCBI Sequence Viewer  
  XP_013371521 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000010787.1
  ENSCLAP00000010788
  ENSCLAP00000010788.1
  ENSCLAP00000010789.1
RefSeq Acc Id: XP_005388093   ⟸   XM_005388036
- Peptide Label: isoform X1
- UniProtKB: A0A8C2YN36 (UniProtKB/TrEMBL),   A0A8C2V696 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013371521   ⟸   XM_013516067
- Peptide Label: isoform X2
- UniProtKB: A0A8C2V696 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000010787   ⟸   ENSCLAT00000010920
RefSeq Acc Id: ENSCLAP00000010788   ⟸   ENSCLAT00000010921
RefSeq Acc Id: ENSCLAP00000010789   ⟸   ENSCLAT00000010922

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000007444 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000010920.1 UniProtKB/TrEMBL
  ENSCLAT00000010921 ENTREZGENE
  ENSCLAT00000010921.1 UniProtKB/TrEMBL
  ENSCLAT00000010922.1 UniProtKB/TrEMBL
InterPro Syndetin_C UniProtKB/TrEMBL
  VPS50 UniProtKB/TrEMBL
  VPS54_N UniProtKB/TrEMBL
NCBI Gene Ccdc132 ENTREZGENE
PANTHER PTHR13258 UniProtKB/TrEMBL
  SYNDETIN UniProtKB/TrEMBL
Pfam DUF2451 UniProtKB/TrEMBL
  Vps54_N UniProtKB/TrEMBL
UniProt A0A8C2V696 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C2YN33_CHILA UniProtKB/TrEMBL
  A0A8C2YN36 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 Vps50  VPS50 subunit of EARP/GARPII complex    VPS50, EARP/GARPII complex subunit  Symbol and/or name change 5135510 APPROVED
2016-08-03 Vps50  VPS50, EARP/GARPII complex subunit    VPS50 EARP/GARPII complex subunit  Symbol and/or name change 5135510 APPROVED
2015-08-25 Vps50  VPS50 EARP/GARPII complex subunit  Ccdc132  coiled-coil domain containing 132  Symbol and/or name change 5135510 APPROVED