Vma21 (vacuolar ATPase assembly factor VMA21) - Rat Genome Database

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Gene: Vma21 (vacuolar ATPase assembly factor VMA21) Rattus norvegicus
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Symbol: Vma21
Name: vacuolar ATPase assembly factor VMA21
RGD ID: 1566155
Description: Predicted to be involved in lysosomal lumen acidification and vacuolar proton-transporting V-type ATPase complex assembly. Predicted to be located in ER to Golgi transport vesicle membrane; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment membrane. Predicted to be active in endoplasmic reticulum membrane. Human ortholog(s) of this gene implicated in X-linked myopathy with excessive autophagy. Orthologous to human VMA21 (vacuolar ATPase assembly factor VMA21); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100912478; LOC501658; RGD1566155; similar to 2610030H06Rik protein; vacuolar ATPase assembly integral membrane protein VMA21; vacuolar ATPase assembly integral membrane protein VMA21-like; VMA21 vacuolar H+-ATPase homolog; VMA21 vacuolar H+-ATPase homolog (S. cerevisiae); VMA21, vacuolar ATPase assembly factor
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
GRCr8X154,536,493 - 154,545,794 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX154,536,493 - 154,545,794 (+)EnsemblGRCr8
mRatBN7.2X149,491,709 - 149,501,010 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX149,491,738 - 149,499,272 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX151,685,889 - 151,695,190 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X155,220,078 - 155,229,379 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X152,761,648 - 152,770,949 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01670,142,561 - 70,151,833 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1670,142,761 - 70,242,979 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1734,939,517 - 34,945,317 (-)Ensemblrn6Rnor6.0
Rnor_5.01669,812,633 - 69,821,254 (-)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.01738,458,277 - 38,463,846 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X157,237,405 - 157,244,955 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Cytogenetic MapXq37NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Vma21
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X154,536,493 - 154,545,794 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX154,536,493 - 154,545,794 (+)EnsemblGRCr8
mRatBN7.2X149,491,709 - 149,501,010 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX149,491,738 - 149,499,272 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX151,685,889 - 151,695,190 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X155,220,078 - 155,229,379 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X152,761,648 - 152,770,949 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01670,142,561 - 70,151,833 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1670,142,761 - 70,242,979 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1734,939,517 - 34,945,317 (-)Ensemblrn6Rnor6.0
Rnor_5.01669,812,633 - 69,821,254 (-)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.01738,458,277 - 38,463,846 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X157,237,405 - 157,244,955 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Cytogenetic MapXq37NCBI
VMA21
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X151,396,595 - 151,409,364 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX151,396,515 - 151,409,364 (+)Ensemblhg38GRCh38
GRCh37X150,565,067 - 150,577,836 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X150,316,363 - 150,328,494 (+)NCBIBuild 36Build 36hg18NCBI36
CeleraX150,814,162 - 150,826,340 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX139,424,159 - 139,436,336 (+)NCBIHuRef
CHM1_1X150,440,375 - 150,452,556 (+)NCBICHM1_1
T2T-CHM13v2.0X149,664,671 - 149,677,438 (+)NCBIT2T-CHM13v2.0
Vma21
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X70,856,368 - 70,868,312 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX70,859,530 - 70,883,363 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X71,812,752 - 71,824,706 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX71,815,924 - 71,839,757 (+)Ensemblmm10GRCm38
MGSCv37X69,062,118 - 69,070,045 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X68,065,529 - 68,077,421 (+)NCBIMGSCv36mm8
CeleraX62,796,922 - 62,804,890 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.07NCBI
Vma21
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554986,874,776 - 6,887,658 (+)Ensembl
ChiLan1.0NW_0049554986,874,980 - 6,887,561 (+)NCBIChiLan1.0ChiLan1.0
VMA21
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X151,483,269 - 151,573,061 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X151,487,209 - 151,499,726 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X140,995,525 - 141,008,351 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X150,954,069 - 150,966,109 (+)NCBIPanPan1.1PanPan1.1panPan2
VMA21
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X119,429,680 - 119,502,007 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX119,429,931 - 119,435,756 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX104,810,848 - 104,816,673 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X121,647,624 - 121,723,089 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX121,648,347 - 121,657,626 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X118,368,631 - 118,374,456 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X120,851,851 - 120,857,676 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X120,734,452 - 120,740,277 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vma21
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X116,975,135 - 116,986,976 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367141,272,565 - 1,281,287 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367141,273,528 - 1,281,266 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VMA21
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X122,872,141 - 122,882,976 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X140,500,076 - 140,510,866 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VMA21
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X125,939,537 - 125,951,819 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX125,939,913 - 125,947,561 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606563,703,654 - 63,716,583 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vma21
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249231,542,308 - 1,546,083 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vma21
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v113402,287 - 408,984 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:859
Count of miRNA genes:313
Interacting mature miRNAs:408
Transcripts:ENSRNOT00000071269, ENSRNOT00000073245
Prediction methods:Microtar, Miranda, Rnahybrid
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
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
10 12 61 134 57 60 41 86 41 298 168 11 125 71 73 19 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000071269   ⟹   ENSRNOP00000064271
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX154,537,171 - 154,545,794 (+)Ensembl
mRatBN7.2 EnsemblX149,492,417 - 149,499,272 (+)Ensembl
Rnor_6.0 Ensembl1670,142,761 - 70,242,979 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000090457   ⟹   ENSRNOP00000069673
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1734,939,517 - 34,945,317 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120047   ⟹   ENSRNOP00000088143
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX149,491,738 - 149,497,562 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000151409   ⟹   ENSRNOP00000112507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX154,536,493 - 154,545,794 (+)Ensembl
RefSeq Acc Id: NM_001402260   ⟹   NP_001389189
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X154,536,493 - 154,545,794 (+)NCBI
mRatBN7.2X149,491,709 - 149,501,010 (+)NCBI
RefSeq Acc Id: NM_001402261   ⟹   NP_001389190
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X154,537,171 - 154,545,794 (+)NCBI
mRatBN7.2X149,492,387 - 149,501,010 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001389189 (Get FASTA)   NCBI Sequence Viewer  
  NP_001389190 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82822 (Get FASTA)   NCBI Sequence Viewer  
  EDL82823 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064271
  ENSRNOP00000064271.1
  ENSRNOP00000112507
  ENSRNOP00000112507.1
Ensembl Acc Id: ENSRNOP00000064271   ⟸   ENSRNOT00000071269
Ensembl Acc Id: ENSRNOP00000088143   ⟸   ENSRNOT00000120047
Ensembl Acc Id: ENSRNOP00000069673   ⟸   ENSRNOT00000090457
RefSeq Acc Id: NP_001389189   ⟸   NM_001402260
- Peptide Label: isoform 1
- UniProtKB: A0A8I6A8R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001389190   ⟸   NM_001402261
- Peptide Label: isoform 2
- UniProtKB: D3ZM03 (UniProtKB/TrEMBL),   A6KUL7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000112507   ⟸   ENSRNOT00000151409

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZM03-F1-model_v2 AlphaFold D3ZM03 1-101 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566155 AgrOrtholog
BioCyc Gene G2FUF-720 BioCyc
Ensembl Genes ENSRNOG00000048606 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000058793 Ensembl
Ensembl Transcript ENSRNOT00000071269 ENTREZGENE
  ENSRNOT00000071269.4 UniProtKB/TrEMBL
  ENSRNOT00000151409 ENTREZGENE
  ENSRNOT00000151409.1 UniProtKB/TrEMBL
InterPro VMA21-like_domain UniProtKB/TrEMBL
NCBI Gene 501658 ENTREZGENE
PANTHER PTHR31792 UniProtKB/TrEMBL
  VACUOLAR ATPASE ASSEMBLY INTEGRAL MEMBRANE PROTEIN VMA21 UniProtKB/TrEMBL
Pfam VMA21 UniProtKB/TrEMBL
PhenoGen Vma21 PhenoGen
RatGTEx ENSRNOG00000048606 RatGTEx
  ENSRNOG00000058793 RatGTEx
UniProt A0A8I6A8R1 ENTREZGENE
  A0ABK0M2Z8_RAT UniProtKB/TrEMBL
  A6KUL7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZM03 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Vma21  vacuolar ATPase assembly factor VMA21  LOC100912478  vacuolar ATPase assembly integral membrane protein VMA21-like  Data merged from RGD:6486572 737654 PROVISIONAL
2019-04-02 Vma21  vacuolar ATPase assembly factor VMA21  Vma21  VMA21, vacuolar ATPase assembly factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2018-09-17 Vma21  VMA21, vacuolar ATPase assembly factor  Vma21  VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100912478  vacuolar ATPase assembly integral membrane protein VMA21-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-25 Vma21  VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)  RGD1566155  similar to 2610030H06Rik protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566155  similar to 2610030H06Rik protein   RGD1566155_predicted  similar to 2610030H06Rik protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566155_predicted  similar to 2610030H06Rik protein (predicted)  LOC501658  similar to 2610030H06Rik protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501658  similar to 2610030H06Rik protein      Symbol and Name status set to provisional 70820 PROVISIONAL