Vapa (VAMP associated protein A) - Rat Genome Database

Name: Vapa
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Vapa (VAMP associated protein A) Rattus norvegicus

Analyze

Symbol:

Vapa

Name:

VAMP associated protein A

RGD ID:

61803

Description:

Enables identical protein binding activity. Involved in neuron projection development. Located in endoplasmic reticulum membrane and nuclear membrane. 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

Previously 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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	VAPA (VAMP associated protein A)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Vapa (vesicle-associated membrane protein, associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vapa (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VAPA (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VAPA (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vapa (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VAPA (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VAPA (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vapa (VAMP associated protein A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Vapa (vesicle-associated membrane protein, associated protein A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	VAPA (VAMP associated protein A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	vapal (VAMP (vesicle-associated membrane protein)-associated protein A, like)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	F42G2.5	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SCS22	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vap33	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ZC196.2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	vpr-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	vapa	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	105,177,904 - 105,208,400 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	105,177,907 - 105,207,847 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	9	113,588,500 - 113,618,316 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	9	118,698,807 - 118,728,640 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	9	117,054,450 - 117,084,266 (-)	NCBI	Rnor_WKY
Rnor_6.0	9	113,300,831 - 113,331,872 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	113,300,832 - 113,331,319 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	112,833,701 - 112,864,112 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	104,339,039 - 104,368,908 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	9	104,548,519 - 104,578,388 (-)	NCBI
Celera	9	102,564,697 - 102,594,412 (-)	NCBI		Celera
Cytogenetic Map	9	q37	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

chromosome 18p deletion syndrome (ISO)

dystonia (ISO)

genetic disease (ISO)

intellectual disability (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,6-tribromophenol (ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

3,3',5,5'-tetrabromobisphenol A (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

benzene (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

Brodifacoum (EXP)

cadmium dichloride (ISO)

caffeine (ISO)

cisplatin (ISO)

clozapine (ISO)

coumarin (ISO)

crocidolite asbestos (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP)

diuron (EXP)

dorsomorphin (ISO)

entinostat (ISO)

enzyme inhibitor (ISO)

epoxiconazole (ISO)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

fulvestrant (ISO)

fumonisin B1 (ISO)

gentamycin (EXP)

hexadecanoic acid (ISO)

hydroquinone (ISO)

indometacin (ISO)

ivermectin (ISO)

lead diacetate (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

ozone (ISO)

panobinostat (ISO)

paracetamol (ISO)

paraquat (EXP)

pirinixic acid (EXP)

resveratrol (ISO)

SB 431542 (ISO)

sunitinib (ISO)

tetrachloromethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

ceramide transport (ISO)

COPII-coated vesicle budding (ISO)

endoplasmic reticulum organization (ISO)

endoplasmic reticulum to Golgi vesicle-mediated transport (ISO)

negative regulation by host of viral genome replication (ISO)

neuron projection development (IBA,IMP,ISO)

phospholipid transport (ISO)

positive regulation by host of viral genome replication (ISO)

positive regulation of I-kappaB kinase/NF-kappaB signaling (ISO)

protein folding in endoplasmic reticulum (ISO)

protein localization to endoplasmic reticulum (ISO,ISS)

sphingomyelin biosynthetic process (ISO)

sterol transport (ISO)

viral release from host cell (ISO)

Cellular Component

bicellular tight junction (ISO)

endoplasmic reticulum (ISO,ISS)

endoplasmic reticulum exit site (ISO)

endoplasmic reticulum membrane (IBA,IDA,IEA,ISO)

Golgi membrane (ISO)

membrane (IDA)

microtubule cytoskeleton (ISO)

nuclear membrane (IDA)

perinuclear region of cytoplasm (ISO)

plasma membrane (IBA,ISO)

vesicle (ISO)

Molecular Function

FFAT motif binding (IBA,ISO)

identical protein binding (IPI)

microtubule binding (ISO)

protein binding (IPI,ISO)

protein domain specific binding (ISO)

protein heterodimerization activity (ISO)

protein-containing complex binding (IDA)

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.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Structural basis of FFAT motif-mediated ER targeting.	Kaiser SE, etal., Structure. 2005 Jul;13(7):1035-45.
4.	Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease.	Kikuchi M, etal., J Biol Chem. 2004 Jan 2;279(1):421-8. Epub 2003 Oct 15.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	Molecular cloning and characterization of mammalian homologues of vesicle-associated membrane protein-associated (VAMP-associated) proteins.	Nishimura Y, etal., Biochem Biophys Res Commun 1999 Jan 8;254(1):21-6.
8.	GOA pipeline	RGD automated data pipeline
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
10.	Promotion of neurite extension by protrudin requires its interaction with vesicle-associated membrane protein-associated protein.	Saita S, etal., J Biol Chem. 2009 May 15;284(20):13766-77. doi: 10.1074/jbc.M807938200. Epub 2009 Mar 16.
11.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
12.	Arl6IP1 has the ability to shape the mammalian ER membrane in a reticulon-like fashion.	Yamamoto Y, etal., Biochem J. 2014 Feb 15;458(1):69-79. doi: 10.1042/BJ20131186.

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	105,177,904 - 105,208,400 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	105,177,907 - 105,207,847 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	9	113,588,500 - 113,618,316 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	9	118,698,807 - 118,728,640 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	9	117,054,450 - 117,084,266 (-)	NCBI	Rnor_WKY
Rnor_6.0	9	113,300,831 - 113,331,872 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	113,300,832 - 113,331,319 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	112,833,701 - 112,864,112 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	104,339,039 - 104,368,908 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	9	104,548,519 - 104,578,388 (-)	NCBI
Celera	9	102,564,697 - 102,594,412 (-)	NCBI		Celera
Cytogenetic Map	9	q37	NCBI

VAPA
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	18	9,914,016 - 9,960,021 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	18	9,914,016 - 9,960,021 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	18	9,914,013 - 9,960,018 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	18	9,903,955 - 9,950,018 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	18	9,903,983 - 9,949,571	NCBI
Celera	18	9,797,515 - 9,843,493 (+)	NCBI		Celera
Cytogenetic Map	18	p11.22	NCBI
HuRef	18	9,893,891 - 9,921,843 (+)	NCBI		HuRef
CHM1_1	18	9,913,226 - 9,959,178 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	18	10,077,467 - 10,123,397 (+)	NCBI		T2T-CHM13v2.0

Vapa
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	65,887,048 - 65,925,441 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	65,885,322 - 65,920,550 (-)	Ensembl		GRCm39 Ensembl
GRCm38	17	65,580,053 - 65,616,462 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	65,578,327 - 65,613,555 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	65,929,393 - 65,962,895 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	65,479,598 - 65,513,084 (-)	NCBI		MGSCv36	mm8
Celera	17	69,883,322 - 69,916,704 (-)	NCBI		Celera
Cytogenetic Map	17	E1.1	NCBI

Vapa
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955402	2,270,850 - 2,298,227 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955402	2,274,248 - 2,309,461 (-)	NCBI	ChiLan1.0	ChiLan1.0

VAPA
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	18	14,188,987 - 14,230,079 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	18	4,329,479 - 4,373,047 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	18	6,613,042 - 6,642,425 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	18	6,612,105 - 6,637,829 (-)	Ensembl	panpan1.1		panPan2

VAPA
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	75,844,927 - 75,891,811 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	75,845,000 - 75,889,076 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	75,242,387 - 75,289,206 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	75,905,356 - 75,948,878 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	7	75,905,322 - 75,949,488 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	7	75,603,405 - 75,650,255 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	75,621,438 - 75,668,178 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	75,930,605 - 75,977,554 (+)	NCBI		UU_Cfam_GSD_1.0

Vapa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404944	2,321,989 - 2,357,518 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936626	1,548,139 - 1,568,656 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936626	1,550,305 - 1,585,783 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VAPA
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	98,210,053 - 98,254,226 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	98,212,335 - 98,254,272 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

VAPA
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	18	68,784,786 - 68,825,333 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	18	68,784,799 - 68,827,581 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666050	43,739,425 - 43,782,261 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vapa
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624770	18,411,789 - 18,447,009 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624770	18,411,921 - 18,447,004 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Vapa
54 total Variants

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.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
724544	Uae9	Urinary albumin excretion QTL 9	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	9	25268044	114175309	Rat
61385	Edpm9	Estrogen-dependent pituitary mass QTL 9	3.43	0.05	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	9	63869687	108869687	Rat
731171	Glom6	Glomerulus QTL 6	2.8	0.0003	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	9	64573531	109573531	Rat
1354626	Bvd1	Brain ventricular dilatation QTL 1	3.73	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	9	75712843	111552878	Rat
7794784	Mcs31	Mammary carcinoma susceptibility QTL 31	2.98		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	9	77813894	111552878	Rat

Markers in Region

RH76596

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	9	105,177,948 - 105,178,119 (+)	MAPPER	mRatBN7.2
Rnor_6.0	9	113,300,876 - 113,301,046	NCBI	Rnor6.0
Rnor_5.0	9	112,833,746 - 112,833,916	UniSTS	Rnor5.0
RGSC_v3.4	9	104,339,084 - 104,339,254	UniSTS	RGSC3.4
Celera	9	102,564,742 - 102,564,912	UniSTS
Cytogenetic Map	9	q37	UniSTS

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031631	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008767384	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084144	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084145	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF086630	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC061875	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473997	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220756	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228815	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000215	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000020681 ⟹ ENSRNOP00000020681

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	105,177,907 - 105,207,847 (-)	Ensembl
Rnor_6.0 Ensembl	9	113,300,832 - 113,331,319 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000086340 ⟹ ENSRNOP00000074577

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	105,177,907 - 105,191,458 (-)	Ensembl
Rnor_6.0 Ensembl	9	113,301,256 - 113,328,428 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000113264 ⟹ ENSRNOP00000083505

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	105,177,907 - 105,207,847 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000117261 ⟹ ENSRNOP00000089269

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	105,177,907 - 105,204,749 (-)	Ensembl

RefSeq Acc Id:

NM_031631 ⟹ NP_113819

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	105,177,904 - 105,207,847 (-)	NCBI
Rnor_6.0	9	113,300,831 - 113,331,319 (-)	NCBI
Rnor_5.0	9	112,833,701 - 112,864,112 (-)	NCBI
RGSC_v3.4	9	104,339,039 - 104,368,908 (-)	RGD
Celera	9	102,564,697 - 102,594,412 (-)	RGD

Sequence:

show sequence

CGCAGTGCGCGTGGCCGCGGCGACTGGTGTGGGGTTGAGTCAGTTGTGACACCCGGAGCTGCTG
ACCCGACAGGCAGCCCTCGGGACCCGCGGCCCGGCAGCAGGCGCGGAGCTTCGGGAATCGTGAG
CCTGGCCCCGTCCTAGAGCTCCGCGGAGCCGGCGCCGCCACCGTCCCCCGCCCCCGCCAGCGAA
CCGCCGCCGCGGGCGCGCCCCCGCTCTGCGCTGTCTCCTATGGCGTCCGCCTCCGGGGCCATGG
CGAAGCACGAGCAGATCCTGGTCCTCGACCCTCCTTCAGACCTCAAATTCAAAGGCCCCTTCAC
AGATGTAGTCACTACAAATCTTAAATTGCAGAATCCATCGGACAGAAAAGTGTGTTTCAAAGTG
AAGACCACAGCGCCCCGCCGGTACTGCGTGCGGCCCAACAGTGGGGTTATTGACCCAGGGTCAA
TCGTGACTGTCTCAGTAATGCTGCAGCCCTTTGACTATGATCCGAACGAAAAGAGTAAACATAA
GTTCATGGTACAGACAATTTTTGCTCCACCAAACATTTCAGATATGGAAGCTGTGTGGAAAGAG
GCAAAACCTGACGAACTAATGGATTCTAAACTGAGATGTGTATTTGAGATGCCGAATGAAAACG
ATAAGCTGAACGACATGGAACCTAGCAAAGCTGTCCCACTGAATGCATCCAAGCAAGATGGACC
CCTGCCAAAACCACATAGTGTTTCACTCAATGACACGGAGACAAGGAAACTGATGGAAGAGTGC
AAGCGACTTCAGGGAGAAATGATGAAGCTCTCAGAAGAAAACCGACACCTGAGAGATGAAGGCC
TACGGCTCAGAAAGGTAGCACATTCGGATAAACCTGGATCCACCTCAGCCGTGTCCTTCAGAGA
TAATGTCACCAGTCCTCTTCCTTCTCTTCTGGTTGTAATTGCAGCCATTTTCATTGGATTCTTT
CTAGGGAAATTCATCTTGTAGAGTGAAGCATGCAGAGTGCTGTTTCTTTTTTCTTTTCTCTCGA
CCAGAAAAAGATTTGTTTACCTACCATTTCATTGGTAGTATGGCCCACGGTGACCATGGCCCGT
GGTGACCATTTTTTTTTGTGTGTACAGCGTCATATAGGCTTTGCCTTTAATGATCTCTTACGGT
TAGAAAACACAATAAAAACAAACTGTTCGGCTACTGGACAAATTGTATATTACCAGATCATCAC
TAGCAGATGCCAGTCGCACATCCAGTCCTTTATGAAATTCATAATAAAGAATTGTTCTTTCTTT
GTGGTTTTAATAAGAGTTCAAGAATTGTTCAGTCTTGTAAATGTTATTTTAATAATCCCTTTAA
ATTTTATCTGTTGCTGTTACCTCTTGAAATATGATTTATTTAGATTGCTAATCCCACTCATTCA
GGAAATGCCAAGAGGTTTTCTGTGGGGGAAATGGTGCCTCTTACTGTGTAAATTTTCTCCTTTA
CCTTTGCTAATATCATGGCAGAATTTTCTTATCCCTTGTGAGGCAGTTTGTTGACTGAGTTTTT
CATCCTTACAATCCTGTCCCATGGTATTTAACATAAAAAATAAAACTGTTAACAGATTCTTGCT
CGACAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008767384 ⟹ XP_008765606

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	105,177,904 - 105,208,400 (-)	NCBI
Rnor_6.0	9	113,300,831 - 113,331,872 (-)	NCBI

Sequence:

show sequence

CCGTCTCTCCTGGGATGCCTGGCTCCCAGGCAGCCTGCAAAAACCCTTTTCTTTTTCCAATGCA
GACGAGACAACCTCGGCGAGCCAAAAGCAGAGTCAGCGGCCCCACCCACTCGCCTCCAACGGAC
CCGGGTTGCCTTCCCGGTTCCCAGCAGCCCCCGCGGAGACGCCGCCCGCACGGGGCATGCTGGG
AGTCGAGGTACCCGGCACTTCTTGACTGTCTTCCGTTCGGAATTCCACTTGGAACGCTGTGAGG
TAGCATCGTAGTCGGCGCTACAGCCCCGCATTCGCAGCTCCAGGGCGCCAAGAACGACGCCCCT
CGCCCGGCGCCGCGCACCCCGTCTCCCACAAACAGCCCTACTACGCCCCCTGCACGCTCTACAG
AGATTGACAGCAGCGCGGCGCAGGGAGCTGCGGCCAAGTCGGAGGTGCGCAGGCGCACTAGCTC
AGCGCCGAGCCCAGTTAGGCCCGGAGGGCGGGGCCAACACGAGGGCTCTGGGCCGCGGGGGCGC
GCACGGAGACACGTAAGGCCGTCACGTGGGGAGCCGAGGATCGCAGTGCGCGTGGCCGCGGCGA
CTGGTGTGGGGTTGAGTCAGTTGTGACACCCGGAGCTGCTGACCCGACAGGCAGCCCTCGGGAC
CCGCGGCCCGGCAGCAGGCGCGGAGCTTCGGGAATCGTGAGCCTGGCCCCGTCCTAGAGCTCCG
CGGAGCCGGCGCCGCCACCGTCCCCCGCCCCCGCCAGCGAACCGCCGCCGCGGGCGCGCCCCCG
CTCTGCGCTGTCTCCTATGGCGTCCGCCTCCGGGGCCATGGCGAAGCACGAGCAGATCCTGGTC
CTCGACCCTCCTTCAGACCTCAAATTCAAAGGCCCCTTCACAGATGTAGTCACTACAAATCTTA
AATTGCAGAATCCATCGGACAGAAAAGTGTGTTTCAAAGTGAAGACCACAGCGCCCCGCCGGTA
CTGCGTGCGGCCCAACAGTGGGGTTATTGACCCAGGGTCAATCGTGACTGTCTCAGTAATGCTG
CAGCCCTTTGACTATGATCCGAACGAAAAGAGTAAACATAAGTTCATGGTACAGACAATTTTTG
CTCCACCAAACATTTCAGATATGGAAGCTGTGTGGAAAGAGGCAAAACCTGACGAACTAATGGA
TTCTAAACTGAGATGTGTATTTGAGATGCCGAATGAAAACGATAAGCTGGGTAAAACTCTACCA
GGGATCGCGTCAGCTGTCACCTCAGTGAGCAGCATCAGCAGTACAGTTGCAACACCTGCCAGTT
ATCACATGAAGAGTGATCCCAGGGAGCTAAAAGAGGTGAAGCAGAACGACATGGAACCTAGCAA
AGCTGTCCCACTGAATGCATCCAAGCAAGATGGACCCCTGCCAAAACCACATAGTGTTTCACTC
AATGACACGGAGACAAGGAAACTGATGGAAGAGTGCAAGCGACTTCAGGGAGAAATGATGAAGC
TCTCAGAAGAAAACCGACACCTGAGAGATGAAGGCCTACGGCTCAGAAAGGTAGCACATTCGGA
TAAACCTGGATCCACCTCAGCCGTGTCCTTCAGAGATAATGTCACCAGTCCTCTTCCTTCTCTT
CTGGTTGTAATTGCAGCCATTTTCATTGGATTCTTTCTAGGGAAATTCATCTTGTAGAGTGAAG
CATGCAGAGTGCTGTTTCTTTTTTCTTTTCTCTCGACCAGAAAAAGATTTGTTTACCTACCATT
TCATTGGTAGTATGGCCCGCGGTGACCATGGCCCGTGGTGACCATTTTTTTTTGTGTGTACAGC
GTCATATAGGCTTTGCCTTTAATGATCTCTTACGGTTAGAAAACACAATAAAAACAAACTGTTC
GGCTACTGGACAAATTGTATATTACCAGATCATCACTAGCAGATGCCAGTCGCACATCCAGTCC
TTTATGAAATTCATAATAAAGAATTGTTCTTTCTTTGTGGTTTTAATAAGAGTTCAAGAATTGT
TCAGTCTTGTAAATGTTATTTTAATAATCCCTTTAAATTTTATCTGTTGCTGTTACCTCTTGAA
ATATGATTTATTTAGATTGCTAATCCCACTCATTCAGGAAATGCCAAGAGGTTTTCTGTGGGGG
AAATGGTGCCTCTTACTGTGTAAATTTTCTCCTTTACCTTTGCTAATATCATGGCAGAATTTTC
TTATCCCTTGTGAGGCAGTTTGTTGACTGAGTTTTTCATCCTTACAATCCTGTCCCATGGTATT
TAACATAAAAAATAAAACTGTTAACAGATTCTTGCTCGACA

hide sequence

RefSeq Acc Id:

XM_039084144 ⟹ XP_038940072

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	105,177,904 - 105,207,808 (-)	NCBI

RefSeq Acc Id:

XM_039084145 ⟹ XP_038940073

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	105,177,904 - 105,204,764 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_113819	(Get FASTA)	NCBI Sequence Viewer
	XP_008765606	(Get FASTA)	NCBI Sequence Viewer
	XP_038940072	(Get FASTA)	NCBI Sequence Viewer
	XP_038940073	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD13579	(Get FASTA)	NCBI Sequence Viewer
	AAH61875	(Get FASTA)	NCBI Sequence Viewer
	EDL91818	(Get FASTA)	NCBI Sequence Viewer
	EDL91819	(Get FASTA)	NCBI Sequence Viewer
	EDL91820	(Get FASTA)	NCBI Sequence Viewer
	Q9Z270	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_113819 ⟸ NM_031631

- UniProtKB:

Q6P723 (UniProtKB/Swiss-Prot), Q9Z270 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MASASGAMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPN
SGVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRC
VFEMPNENDKLNDMEPSKAVPLNASKQDGPLPKPHSVSLNDTETRKLMEECKRLQGEMMKLSEE
NRHLRDEGLRLRKVAHSDKPGSTSAVSFRDNVTSPLPSLLVVIAAIFIGFFLGKFIL

hide sequence

RefSeq Acc Id:	XP_008765606 ⟸ XM_008767384
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5ZVH7 (UniProtKB/TrEMBL)
- Sequence:	show sequence MASASGAMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPN SGVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRC VFEMPNENDKLGKTLPGIASAVTSVSSISSTVATPASYHMKSDPRELKEVKQNDMEPSKAVPLN ASKQDGPLPKPHSVSLNDTETRKLMEECKRLQGEMMKLSEENRHLRDEGLRLRKVAHSDKPGST SAVSFRDNVTSPLPSLLVVIAAIFIGFFLGKFIL hide 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
- UniProtKB:	A0A8I6GHY4 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSRNOP00000083505 ⟸ ENSRNOT00000113264

RefSeq Acc Id:

ENSRNOP00000089269 ⟸ ENSRNOT00000117261

Protein Domains

MSP

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9Z270-F1-model_v2	AlphaFold	Q9Z270	1-249	view protein structure

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	9	113,331,278 - 113,331,338	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:61803	AgrOrtholog
BioCyc Gene	G2FUF-26488	BioCyc
Ensembl Genes	ENSRNOG00000014765	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000020681	ENTREZGENE
	ENSRNOP00000020681.3	UniProtKB/Swiss-Prot
	ENSRNOP00000074577.2	UniProtKB/TrEMBL
	ENSRNOP00000083505	ENTREZGENE
	ENSRNOP00000083505.1	UniProtKB/TrEMBL
	ENSRNOP00000089269	ENTREZGENE
	ENSRNOP00000089269.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000020681	ENTREZGENE
	ENSRNOT00000020681.7	UniProtKB/Swiss-Prot
	ENSRNOT00000086340.2	UniProtKB/TrEMBL
	ENSRNOT00000113264	ENTREZGENE
	ENSRNOT00000113264.1	UniProtKB/TrEMBL
	ENSRNOT00000117261	ENTREZGENE
	ENSRNOT00000117261.1	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
	VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A	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
	A0A8I5ZVH7	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6GHY4	ENTREZGENE, UniProtKB/TrEMBL
	Q6P723	ENTREZGENE
	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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