Vapa (VAMP associated protein A) - Rat Genome Database

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Gene: Vapa (VAMP associated protein A) Rattus norvegicus
Analyze
Symbol: Vapa
Name: VAMP associated protein A
RGD ID: 61803
Description: Exhibits identical protein binding activity. Involved in cell death and neuron projection development. Localizes to endoplasmic reticulum membrane and nuclear membrane. Predicted to colocalize with bicellular tight junction and perinuclear region of cytoplasm. Orthologous to human VAPA (VAMP associated protein A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 33 kDa Vamp-associated protein; VAMP (vesicle-associated membrane protein)-associated protein A; VAMP-A; VAMP-associated protein A; VAP-33; VAP-A; vesicle-associated membrane protein associated protein A (33 kDa); vesicle-associated membrane protein, associated protein a; vesicle-associated membrane protein, associated protein A (33 kDa); vesicle-associated membrane protein-associated protein A
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
mRatBN7.29105,177,904 - 105,208,400 (-)NCBI
Rnor_6.0 Ensembl9113,300,832 - 113,331,319 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09113,300,831 - 113,331,872 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09112,833,701 - 112,864,112 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49104,339,039 - 104,368,908 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19104,548,519 - 104,578,388 (-)NCBI
Celera9102,564,697 - 102,594,412 (-)NCBICelera
Cytogenetic Map9q37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:10523508   PMID:10655491   PMID:12477932   PMID:12761501   PMID:15489334   PMID:16025302   PMID:16227268   PMID:16791210   PMID:16895911   PMID:18504258   PMID:18713837   PMID:19515777  
PMID:20178991   PMID:21700703   PMID:24105263   PMID:25468996   PMID:29476059   PMID:29941597   PMID:30741634   PMID:31594761  


Genomics

Comparative Map Data
Vapa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29105,177,904 - 105,208,400 (-)NCBI
Rnor_6.0 Ensembl9113,300,832 - 113,331,319 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09113,300,831 - 113,331,872 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09112,833,701 - 112,864,112 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49104,339,039 - 104,368,908 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19104,548,519 - 104,578,388 (-)NCBI
Celera9102,564,697 - 102,594,412 (-)NCBICelera
Cytogenetic Map9q37NCBI
VAPA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl189,914,016 - 9,960,021 (+)EnsemblGRCh38hg38GRCh38
GRCh38189,914,016 - 9,960,021 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37189,914,013 - 9,960,018 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36189,903,955 - 9,950,018 (+)NCBINCBI36hg18NCBI36
Build 34189,903,983 - 9,949,571NCBI
Celera189,797,515 - 9,843,493 (+)NCBI
Cytogenetic Map18p11.22NCBI
HuRef189,893,891 - 9,921,843 (+)NCBIHuRef
CHM1_1189,913,226 - 9,959,178 (+)NCBICHM1_1
Vapa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391765,887,048 - 65,925,441 (-)NCBIGRCm39mm39
GRCm39 Ensembl1765,885,322 - 65,920,550 (-)Ensembl
GRCm381765,580,053 - 65,616,462 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1765,578,327 - 65,613,555 (-)EnsemblGRCm38mm10GRCm38
MGSCv371765,929,393 - 65,962,895 (-)NCBIGRCm37mm9NCBIm37
MGSCv361765,479,598 - 65,513,084 (-)NCBImm8
Celera1769,883,322 - 69,916,704 (-)NCBICelera
Cytogenetic Map17E1.1NCBI
Vapa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554022,270,850 - 2,298,227 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554022,274,248 - 2,309,461 (-)NCBIChiLan1.0ChiLan1.0
VAPA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1186,613,042 - 6,642,425 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl186,612,105 - 6,637,829 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0184,329,479 - 4,373,047 (-)NCBIMhudiblu_PPA_v0panPan3
VAPA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1775,844,927 - 75,891,811 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl775,845,000 - 75,889,076 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha775,242,387 - 75,289,206 (+)NCBI
ROS_Cfam_1.0775,905,356 - 75,948,878 (+)NCBI
UMICH_Zoey_3.1775,603,405 - 75,650,255 (+)NCBI
UNSW_CanFamBas_1.0775,621,438 - 75,668,178 (+)NCBI
UU_Cfam_GSD_1.0775,930,605 - 75,977,554 (+)NCBI
Vapa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049442,321,989 - 2,357,518 (-)NCBI
SpeTri2.0NW_0049366261,550,305 - 1,585,783 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VAPA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl698,207,580 - 98,254,288 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1698,212,335 - 98,254,272 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
VAPA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11868,784,786 - 68,825,333 (+)NCBI
ChlSab1.1 Ensembl1868,784,799 - 68,827,581 (+)Ensembl
Vero_WHO_p1.0NW_02366605043,739,425 - 43,782,261 (+)NCBI
Vapa
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477018,411,921 - 18,447,004 (+)NCBI

Position Markers
RH76596  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29105,177,948 - 105,178,119 (+)MAPPER
Rnor_6.09113,300,876 - 113,301,046NCBIRnor6.0
Rnor_5.09112,833,746 - 112,833,916UniSTSRnor5.0
RGSC_v3.49104,339,084 - 104,339,254UniSTSRGSC3.4
Celera9102,564,742 - 102,564,912UniSTS
Cytogenetic Map9q37UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:526
Count of miRNA genes:251
Interacting mature miRNAs:307
Transcripts:ENSRNOT00000020681
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: ENSRNOT00000020681   ⟹   ENSRNOP00000020681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9113,300,832 - 113,331,319 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086340   ⟹   ENSRNOP00000074577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9113,301,256 - 113,328,428 (-)Ensembl
RefSeq Acc Id: NM_031631   ⟹   NP_113819
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29105,177,904 - 105,207,847 (-)NCBI
Rnor_6.09113,300,831 - 113,331,319 (-)NCBI
Rnor_5.09112,833,701 - 112,864,112 (-)NCBI
RGSC_v3.49104,339,039 - 104,368,908 (-)RGD
Celera9102,564,697 - 102,594,412 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767384   ⟹   XP_008765606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29105,177,904 - 105,208,400 (-)NCBI
Rnor_6.09113,300,831 - 113,331,872 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039084144   ⟹   XP_038940072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29105,177,904 - 105,207,808 (-)NCBI
RefSeq Acc Id: XM_039084145   ⟹   XP_038940073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29105,177,904 - 105,204,764 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113819   ⟸   NM_031631
- UniProtKB: Q9Z270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008765606   ⟸   XM_008767384
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000020681   ⟸   ENSRNOT00000020681
RefSeq Acc Id: ENSRNOP00000074577   ⟸   ENSRNOT00000086340
RefSeq Acc Id: XP_038940072   ⟸   XM_039084144
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038940073   ⟸   XM_039084145
- Peptide Label: isoform X3
Protein Domains
MSP

Transcriptome

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

Promoters
RGD ID:13696902
Promoter ID:EPDNEW_R7426
Type:initiation region
Name:Vapa_1
Description:VAMP associated protein A
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_6.09113,331,278 - 113,331,338EPDNEW

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)
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: SBN/Ygl sequenced by MCW
SBN/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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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:61803 AgrOrtholog
Ensembl Genes ENSRNOG00000014765 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020681 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074577 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020681 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000086340 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598274 IMAGE-MGC_LOAD
InterPro Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MSP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PapD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:58857 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72396 IMAGE-MGC_LOAD
NCBI Gene 58857 ENTREZGENE
PANTHER PTHR10809 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Motile_Sperm UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vapa PhenoGen
PIRSF VAMP-associated UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE MSP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49354 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217149
UniProt A0A0G2K8E6_RAT UniProtKB/TrEMBL
  Q9Z270 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6P723 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-11 Vapa  VAMP associated protein A  Vapa  VAMP (vesicle-associated membrane protein)-associated protein A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Vapa  VAMP (vesicle-associated membrane protein)-associated protein A  Vapa  vesicle-associated membrane protein, associated protein a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Vapa  vesicle-associated membrane protein, associated protein a      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains coiled-coil, t-SNARE homology domain near the carboxyl-terminal 61779
gene_expression ubiquitously expressed 61779