Vps4a (vacuolar protein sorting 4 homolog A) - Rat Genome Database

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Gene: Vps4a (vacuolar protein sorting 4 homolog A) Rattus norvegicus
Analyze
Symbol: Vps4a
Name: vacuolar protein sorting 4 homolog A
RGD ID: 628810
Description: Enables small GTPase binding activity. Predicted to be involved in several processes, including positive regulation of viral life cycle; proteolysis involved in cellular protein catabolic process; and vesicle organization. Located in early endosome. Orthologous to human VPS4A (vacuolar protein sorting 4 homolog A); PARTICIPATES IN autophagy pathway; endocytosis pathway; INTERACTS WITH 2,6-dinitrotoluene; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: vacuolar protein sorting 4 homolog A (S. cerevisiae); vacuolar protein sorting 4a; vacuolar protein sorting 4a (yeast); vacuolar protein sorting protein 4a; vacuolar protein sorting-associated protein 4A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21934,934,999 - 34,948,267 (+)NCBI
Rnor_6.0 Ensembl1939,229,754 - 39,243,496 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01939,230,050 - 39,243,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01950,093,663 - 50,106,670 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,887,345 - 36,900,864 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11936,892,225 - 36,905,745 (+)NCBI
Celera1934,358,772 - 34,371,812 (+)NCBICelera
Cytogenetic Map19q12NCBI
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 Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10637304   PMID:11559748   PMID:11563910   PMID:11595185   PMID:12594041   PMID:15075231   PMID:16193069   PMID:16973552   PMID:17853893   PMID:17928862   PMID:17940959   PMID:18005716  
PMID:18606141   PMID:19129479   PMID:19199708   PMID:20616062   PMID:21238931   PMID:22547407   PMID:22660413   PMID:23533145   PMID:24107264   PMID:24814515   PMID:24878737   PMID:28064406  
PMID:29476059  


Genomics

Comparative Map Data
Vps4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21934,934,999 - 34,948,267 (+)NCBI
Rnor_6.0 Ensembl1939,229,754 - 39,243,496 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01939,230,050 - 39,243,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01950,093,663 - 50,106,670 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,887,345 - 36,900,864 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11936,892,225 - 36,905,745 (+)NCBI
Celera1934,358,772 - 34,371,812 (+)NCBICelera
Cytogenetic Map19q12NCBI
VPS4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1669,311,350 - 69,326,939 (+)EnsemblGRCh38hg38GRCh38
GRCh381669,311,350 - 69,326,939 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371669,345,253 - 69,360,842 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361667,902,788 - 67,916,447 (+)NCBINCBI36hg18NCBI36
Build 341667,902,787 - 67,916,446NCBI
Celera1653,859,828 - 53,873,486 (+)NCBI
Cytogenetic Map16q22.1NCBI
HuRef1655,223,517 - 55,237,174 (+)NCBIHuRef
CHM1_11670,753,291 - 70,766,948 (+)NCBICHM1_1
Vps4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398107,757,901 - 107,772,392 (+)NCBIGRCm39mm39
GRCm39 Ensembl8107,757,854 - 107,772,387 (+)Ensembl
GRCm388107,031,269 - 107,045,760 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8107,031,222 - 107,045,755 (+)EnsemblGRCm38mm10GRCm38
MGSCv378109,555,226 - 109,569,656 (+)NCBIGRCm37mm9NCBIm37
MGSCv368109,920,455 - 109,934,885 (+)NCBImm8
Celera8111,257,885 - 111,272,306 (+)NCBICelera
Cytogenetic Map8D3NCBI
Vps4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554847,368,938 - 7,375,964 (-)NCBIChiLan1.0ChiLan1.0
VPS4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11668,946,466 - 69,085,714 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01649,685,827 - 49,699,542 (+)NCBIMhudiblu_PPA_v0panPan3
VPS4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1580,327,059 - 80,340,380 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha580,311,739 - 80,330,670 (-)NCBI
ROS_Cfam_1.0580,755,360 - 80,774,301 (-)NCBI
UMICH_Zoey_3.1580,582,504 - 80,601,442 (-)NCBI
UNSW_CanFamBas_1.0580,265,344 - 80,284,280 (-)NCBI
UU_Cfam_GSD_1.0580,904,921 - 80,923,853 (-)NCBI
Vps4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934940,144,891 - 40,156,804 (-)NCBI
SpeTri2.0NW_00493647519,432,311 - 19,444,223 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1617,657,792 - 17,669,560 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2616,604,522 - 16,616,293 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VPS4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1558,081,800 - 58,095,115 (-)NCBI
Vero_WHO_p1.0NW_02366604720,811,652 - 20,825,117 (-)NCBI
Vps4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474617,044,173 - 17,059,295 (-)NCBI

Position Markers
AW553189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,948,535 - 34,948,650 (+)MAPPER
Rnor_6.01939,243,567 - 39,243,681NCBIRnor6.0
Rnor_5.01950,106,939 - 50,107,053UniSTSRnor5.0
RGSC_v3.41936,901,133 - 36,901,247UniSTSRGSC3.4
Celera1934,372,081 - 34,372,195UniSTS
Cytogenetic Map19q12UniSTS
AI325971  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,948,630 - 34,948,806 (+)MAPPER
Rnor_6.01939,243,662 - 39,243,837NCBIRnor6.0
Rnor_5.01950,107,034 - 50,107,209UniSTSRnor5.0
RGSC_v3.41936,901,228 - 36,901,403UniSTSRGSC3.4
Celera1934,372,176 - 34,372,351UniSTS
Cytogenetic Map19q12UniSTS
RH129713  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,948,652 - 34,948,834 (+)MAPPER
Rnor_6.01939,243,684 - 39,243,865NCBIRnor6.0
Rnor_5.01950,107,056 - 50,107,237UniSTSRnor5.0
RGSC_v3.41936,901,250 - 36,901,431UniSTSRGSC3.4
Celera1934,372,198 - 34,372,379UniSTS
RH 3.4 Map19315.1UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)193119430141686140Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)193119430141686140Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)193119430141686140Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:114
Count of miRNA genes:91
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000027607, ENSRNOT00000050612
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.


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 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050612   ⟹   ENSRNOP00000046690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1939,229,754 - 39,243,496 (+)Ensembl
RefSeq Acc Id: NM_145678   ⟹   NP_663711
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21934,935,210 - 34,948,267 (+)NCBI
Rnor_6.01939,230,243 - 39,243,298 (+)NCBI
Rnor_5.01950,093,663 - 50,106,670 (+)NCBI
RGSC_v3.41936,887,345 - 36,900,864 (+)RGD
Celera1934,358,772 - 34,371,812 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255560   ⟹   XP_006255622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21934,934,999 - 34,947,824 (+)NCBI
Rnor_6.01939,230,050 - 39,242,855 (+)NCBI
Rnor_5.01950,093,663 - 50,106,670 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_663711 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255622 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH70931 (Get FASTA)   NCBI Sequence Viewer  
  BAC00961 (Get FASTA)   NCBI Sequence Viewer  
  EDL92462 (Get FASTA)   NCBI Sequence Viewer  
  Q793F9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_663711   ⟸   NM_145678
- UniProtKB: Q793F9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255622   ⟸   XM_006255560
- Peptide Label: isoform X1
- UniProtKB: Q6IRG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046690   ⟸   ENSRNOT00000050612
Protein Domains
AAA   MIT

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628810 AgrOrtholog
Ensembl Genes ENSRNOG00000020351 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046690 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050612 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7096867 IMAGE-MGC_LOAD
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 rno:246772 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91460 IMAGE-MGC_LOAD
NCBI Gene 246772 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 Vps4a 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 F7F1Y3_RAT UniProtKB/TrEMBL
  Q6IRG3 ENTREZGENE, UniProtKB/TrEMBL
  Q793F9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Vps4a  vacuolar protein sorting 4 homolog A  Vps4a  vacuolar protein sorting 4 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vps4a  vacuolar protein sorting 4 homolog A (S. cerevisiae)  Vps4a  vacuolar protein sorting 4a (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Vps4a  vacuolar protein sorting 4a (yeast)    vacuolar protein sorting protein 4a  Name updated 1299863 APPROVED
2003-02-27 Vps4a  vacuolar protein sorting protein 4a      Symbol and Name status set to provisional 70820 PROVISIONAL