Vta1 (vesicle trafficking 1) - Rat Genome Database

Name: Vta1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Vta1 (vesicle trafficking 1) Rattus norvegicus

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Symbol:

Vta1

Name:

vesicle trafficking 1

RGD ID:

1305031

Description:

Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in multivesicular body. Orthologous to human VTA1 (vesicle trafficking 1); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

Lip5; LOC292640; lysosomal trafficking regulator interacting protein-5; MGC112826; RGD1305031; similar to RIKEN cDNA 1110059P08; vacuolar protein sorting-associated protein VTA1 homolog; vesicle (multivesicular body) trafficking 1; Vps20-associated 1 homolog; Vps20-associated 1 homolog (S. cerevisiae)

RGD Orthologs

Alliance Orthologs

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):	VTA1 (vesicle trafficking 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB
Mus musculus (house mouse):	Vta1 (vesicle (multivesicular body) trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vta1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VTA1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VTA1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vta1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VTA1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VTA1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vta1 (vesicle trafficking 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	VTA1 (vesicle trafficking 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Vta1 (vesicle (multivesicular body) trafficking 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	vta1 (vesicle (multivesicular body) trafficking 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vta1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	VTA1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	vta1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

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
GRCr8	1	10,852,966 - 10,900,764 (-)	NCBI		GRCr8
mRatBN7.2	1	9,032,861 - 9,080,635 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	9,032,335 - 9,080,635 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	8,752,160 - 8,799,898 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	14,754,070 - 14,801,806 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	9,007,323 - 9,055,019 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	8,830,405 - 8,878,191 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	8,830,411 - 8,878,244 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	10,447,206 - 10,495,550 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	9,512,291 - 9,560,020 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	9,512,290 - 9,560,020 (-)	NCBI
Celera	1	7,509,495 - 7,557,229 (-)	NCBI		Celera
Cytogenetic Map	1	p13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Familial Behcet-Like Autoinflammatory Syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

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

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

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

4,4'-sulfonyldiphenol (EXP,ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

amitrole (EXP)

arsenite(3-) (ISO)

atrazine (ISO)

bisphenol A (EXP,ISO)

bisphenol F (EXP,ISO)

cadmium dichloride (EXP)

carbon nanotube (ISO)

clofibrate (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

cylindrospermopsin (ISO)

decabromodiphenyl ether (ISO)

dexamethasone (ISO)

Dibutyl phosphate (ISO)

dicrotophos (ISO)

doxorubicin (ISO)

flutamide (EXP)

folic acid (ISO)

fulvestrant (ISO)

indometacin (ISO)

ivermectin (ISO)

methimazole (EXP)

pregnenolone 16alpha-carbonitrile (EXP)

sodium dodecyl sulfate (ISO)

sulfadimethoxine (EXP)

temozolomide (ISO)

thiram (ISO)

titanium dioxide (ISO)

uranium atom (ISO)

valproic acid (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

late endosome to vacuole transport via multivesicular body sorting pathway (IBA)

multivesicular body sorting pathway (ISO)

protein transport (IEA)

Cellular Component

cytoplasm (ISO)

cytosol (ISO)

endosome membrane (IEA)

intracellular membrane-bounded organelle (ISO)

multivesicular body (IBA)

nucleoplasm (IEA,ISO)

Molecular Function

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

endocytosis pathway (IEA)

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.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:15173323	PMID:15644320	PMID:18385515	PMID:19056867	PMID:19199708	PMID:20358264	PMID:23376485	PMID:23533145

Genomics

Comparative Map Data

Vta1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	10,852,966 - 10,900,764 (-)	NCBI		GRCr8
mRatBN7.2	1	9,032,861 - 9,080,635 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	9,032,335 - 9,080,635 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	8,752,160 - 8,799,898 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	14,754,070 - 14,801,806 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	9,007,323 - 9,055,019 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	8,830,405 - 8,878,191 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	8,830,411 - 8,878,244 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	10,447,206 - 10,495,550 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	9,512,291 - 9,560,020 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	9,512,290 - 9,560,020 (-)	NCBI
Celera	1	7,509,495 - 7,557,229 (-)	NCBI		Celera
Cytogenetic Map	1	p13	NCBI

VTA1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	142,147,263 - 142,224,685 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	142,147,162 - 142,224,685 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	142,468,400 - 142,545,822 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	142,510,103 - 142,583,778 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	142,510,102 - 142,583,776	NCBI
Celera	6	143,208,886 - 143,282,564 (+)	NCBI		Celera
Cytogenetic Map	6	q24.1-q24.2	NCBI
HuRef	6	140,034,386 - 140,108,100 (+)	NCBI		HuRef
CHM1_1	6	142,730,663 - 142,804,283 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	6	143,339,355 - 143,416,853 (+)	NCBI		T2T-CHM13v2.0

Vta1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	14,531,077 - 14,581,233 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	14,530,499 - 14,581,304 (-)	Ensembl		GRCm39 Ensembl
GRCm38	10	14,654,760 - 14,705,542 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	14,654,755 - 14,705,560 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	14,375,139 - 14,425,295 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	14,345,531 - 14,395,687 (-)	NCBI		MGSCv36	mm8
Celera	10	14,558,320 - 14,607,904 (-)	NCBI		Celera
Cytogenetic Map	10	A2	NCBI
cM Map	10	5.5	NCBI

Vta1
(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_004955436	18,017,190 - 18,072,335 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955436	18,017,190 - 18,072,285 (-)	NCBI	ChiLan1.0	ChiLan1.0

VTA1
(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-v2	5	162,121,459 - 162,194,904 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	160,016,209 - 160,089,537 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	139,914,978 - 139,988,419 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	143,988,724 - 144,061,746 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	143,988,724 - 144,061,746 (+)	Ensembl	panpan1.1		panPan2

VTA1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	33,830,300 - 33,895,865 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	33,830,313 - 33,895,073 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	34,728,526 - 34,794,046 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	34,004,743 - 34,070,405 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	34,004,746 - 34,070,565 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	33,875,224 - 33,940,792 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	33,757,084 - 33,822,600 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	34,067,989 - 34,133,582 (+)	NCBI		UU_Cfam_GSD_1.0

Vta1
(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_024404946	128,806,546 - 128,874,766 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936625	3,758,374 - 3,829,179 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936625	3,761,512 - 3,829,043 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VTA1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	22,859,390 - 22,923,838 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	22,862,628 - 22,923,861 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	25,588,882 - 25,589,991 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

VTA1
(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	13	31,041,697 - 31,116,202 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	13	31,039,629 - 31,116,174 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666040	3,171,563 - 3,248,238 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vta1
(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_004624753	11,901,150 - 11,964,670 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624753	11,901,098 - 11,964,331 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Vta1
178 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	233
Count of miRNA genes:	160
Interacting mature miRNAs:	178
Transcripts:	ENSRNOT00000064836
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2313090	Bmd69	Bone mineral density QTL 69	4.4	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	1	32356093	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	5925877	24697545	Rat
1578650	Bmd6	Bone mineral density QTL 6	12.2		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	1	509108	43284926	Rat
1354647	Despr8	Despair related QTL 8		0.0000341	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	1	24744506	Rat
1578651	Bmd7	Bone mineral density QTL 7	14.2		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	1	509108	43284926	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
7421626	Bp360	Blood pressure QTL 360		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	4393289	49393289	Rat
2313070	Bss52	Bone structure and strength QTL 52	4.4	0.0001	body length (VT:0001256)	body length (CMO:0000013)	1	1	32356093	Rat
738020	Pia8	Pristane induced arthritis QTL 8	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	1	65833076	Rat
1600360	Mcs16	Mammary carcinoma susceptibility QTL 16	2.4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	2244390	43433040	Rat
2298546	Neuinf4	Neuroinflammation QTL 4	5.1		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	1	1	28736750	Rat
1578669	Bss9	Bone structure and strength QTL 9	6.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	1	509108	43284926	Rat
1300170	Rf6	Renal function QTL 6	3.14		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	1	4162807	11481482	Rat
2313053	Bss51	Bone structure and strength QTL 51	3.8	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	1	32356093	Rat

Markers in Region

RH133293

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	9,033,146 - 9,033,326 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	8,830,688 - 8,830,867	NCBI	Rnor6.0
Rnor_5.0	1	10,448,052 - 10,448,231	UniSTS	Rnor5.0
RGSC_v3.4	1	9,512,567 - 9,512,746	UniSTS	RGSC3.4
Celera	1	7,509,771 - 7,509,950	UniSTS
RH 3.4 Map	1	127.52	UniSTS
Cytogenetic Map	1	p13	UniSTS

AU049296

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	9,074,411 - 9,074,635 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	8,871,948 - 8,872,171	NCBI	Rnor6.0
Rnor_5.0	1	10,489,312 - 10,489,535	UniSTS	Rnor5.0
RGSC_v3.4	1	9,553,832 - 9,554,055	UniSTS	RGSC3.4
Celera	1	7,551,041 - 7,551,264	UniSTS
Cytogenetic Map	1	p13	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025640	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001398685	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_010064556	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC098787	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473994	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000064836 ⟹ ENSRNOP00000061074

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	9,032,868 - 9,080,633 (-)	Ensembl
Rnor_6.0 Ensembl	1	8,830,412 - 8,878,136 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000075850 ⟹ ENSRNOP00000068514

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	9,032,871 - 9,080,623 (-)	Ensembl
Rnor_6.0 Ensembl	1	8,830,411 - 8,878,244 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000096797 ⟹ ENSRNOP00000088864

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	9,032,335 - 9,080,635 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000098320 ⟹ ENSRNOP00000084084

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	9,032,335 - 9,060,291 (-)	Ensembl

RefSeq Acc Id:

NM_001025640 ⟹ NP_001020811

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	10,852,966 - 10,900,735 (-)	NCBI
mRatBN7.2	1	9,032,861 - 9,080,635 (-)	NCBI
Rnor_6.0	1	8,830,412 - 8,878,136 (-)	NCBI
Rnor_5.0	1	10,447,206 - 10,495,550 (-)	NCBI
RGSC_v3.4	1	9,512,291 - 9,560,020 (-)	RGD
Celera	1	7,509,495 - 7,557,229 (-)	RGD

Sequence:

show sequence

CTGGCCCCGCTGCCGCCGCTGCCCGCGCAGTTTAAGAGCATACAGCACCATTTGAGAACGGCGC
AGGAGCATGACAAGCGAGATCCTGTGGTGGCCTACTACTCTTAAGAAACAGTTGGGGGATAATG
AAGCTGTTACTCAAGAAATCGTTGGTTGTGCCCATTTGGAAAATTATGCTTTGAAAATGTTCCT
GTACGCGGACAACGAAGACCGAGCTGGACGATTTCACAAAAACATGATCAAGTCCTTCTACACT
GCCAGCCTTTTAATAGATGTCATCACAGTGTTTGGCGAGCTCACAGATGAAAATGTGAAACATA
GAAAGTACGCAAGGTGGAAGGCAACATATATTCATAACTGCTTAAAGAATGGGGAGACTCCTCA
AGCAGGCCCTGTTGGAATAGAGGAAGATAACGATGTTGAGGAAAATGAAGATGTTGGTGCAACC
TCTCTGCCCACTCAGCCACCTCAGCCATCATCATCCTCAACGTACGACCCAAGCAACTTGGCAG
CAGGCAGCTACAGTGGGATACAGATCCCTCCGGGTGCACATGCTCCAGCCAATACCCCTGCAGA
AGTGCCGCACAGCACAGGTGTAACAAGTAATGCTGTCCAGCCTAGTCCACAGACTGTCCCAGCC
ATTCCCGCCATTGATCCTGACCTGTACACAGCTTCCCAGGGGGATGTCCGCCTGACCCCAGAGG
ACTTTGCTCGGGCTCAGAAGTACTGCAAGTACGCTGGCAGTGCCCTGCAGTATGAAGACGTGAG
CACCGCGGTGCAGAACCTGCAGAAGGCCCTCAGGCTGCTGACAACGGGCAGGGAATGAAGCTCT
GCTCACGGACCCCATGCGTTTTCTGCATAGAGAACTAACATTCAGTACACTTTCCTCAGCCTTT
CAGGAGCATGGTTTTACAGAAGACCTCAGTTCCCCGAGTAAGACAGTGGCTCCTGTTGTCGTCA
GCTGCCTCAGCCAGTTGTCATTGAGCGTGTAGAGCTGATGTTAGCATCAAACCCCGCTATGGAA
TGTCCCTGTAGAAAATCCTGGTGGGTATAGTATGCTTTCTTAATGTATACACACTAAAGGACGT
TTTTGAAAAGTCGGTAATATTTGGACAAACCATATTATGTTGCTTTAATATTCTAAATTAAACT
TTTAATAAAGATTACCAGAATGTTAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

NM_001398685 ⟹ NP_001385614

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	10,852,966 - 10,900,735 (-)	NCBI
mRatBN7.2	1	9,032,861 - 9,080,635 (-)	NCBI

RefSeq Acc Id:

XR_010064556

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	10,852,973 - 10,900,764 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001020811	(Get FASTA)	NCBI Sequence Viewer
	NP_001385614	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH98787	(Get FASTA)	NCBI Sequence Viewer
	EDL93745	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000061074.1
	ENSRNOP00000068514.2
	ENSRNOP00000084084.1
	ENSRNOP00000088864.1

RefSeq Acc Id:	NP_001020811 ⟸ NM_001025640
- Peptide Label:	isoform 2
- UniProtKB:	Q4KM55 (UniProtKB/TrEMBL), A0A8I5ZX91 (UniProtKB/TrEMBL)
- Sequence:	show sequence MTSEILWWPTTLKKQLGDNEAVTQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTAS LLIDVITVFGELTDENVKHRKYARWKATYIHNCLKNGETPQAGPVGIEEDNDVEENEDVGATSL PTQPPQPSSSSTYDPSNLAAGSYSGIQIPPGAHAPANTPAEVPHSTGVTSNAVQPSPQTVPAIP AIDPDLYTASQGDVRLTPEDFARAQKYCKYAGSALQYEDVSTAVQNLQKALRLLTTGRE hide sequence

Ensembl Acc Id:

ENSRNOP00000068514 ⟸ ENSRNOT00000075850

Ensembl Acc Id:

ENSRNOP00000061074 ⟸ ENSRNOT00000064836

Ensembl Acc Id:

ENSRNOP00000088864 ⟸ ENSRNOT00000096797

Ensembl Acc Id:

ENSRNOP00000084084 ⟸ ENSRNOT00000098320

RefSeq Acc Id:	NP_001385614 ⟸ NM_001398685
- Peptide Label:	isoform 1
- UniProtKB:	A0A8I6A5Y0 (UniProtKB/TrEMBL), A6JP73 (UniProtKB/TrEMBL)

Protein Domains

Vta1 C-terminal Vta1/callose synthase N-terminal

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-A0A096MKH2-F1-model_v2	AlphaFold	A0A096MKH2	1-309	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689500

Promoter ID:

EPDNEW_R25

Type:

multiple initiation site

Name:

Vta1_1

Description:

vesicle trafficking 1

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	1	8,878,171 - 8,878,231	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305031	AgrOrtholog
BioCyc Gene	G2FUF-62343	BioCyc
Ensembl Genes	ENSRNOG00000011540	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000064836.2	UniProtKB/TrEMBL
	ENSRNOT00000075850.3	UniProtKB/TrEMBL
	ENSRNOT00000096797.1	UniProtKB/TrEMBL
	ENSRNOT00000098320.1	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.270	UniProtKB/TrEMBL
	Immunoglobulin FC, subunit C	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7375248	IMAGE-MGC_LOAD
InterPro	VPS_Vta1_N	UniProtKB/TrEMBL
	Vta1-like	UniProtKB/TrEMBL
	Vta1/CALS_N	UniProtKB/TrEMBL
	Vta1_C	UniProtKB/TrEMBL
KEGG Report	rno:292640	UniProtKB/TrEMBL
MGC_CLONE	MGC:112826	IMAGE-MGC_LOAD
NCBI Gene	292640	ENTREZGENE
PANTHER	PTHR46009	UniProtKB/TrEMBL
	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG	UniProtKB/TrEMBL
Pfam	Vta1	UniProtKB/TrEMBL
	Vta1_C	UniProtKB/TrEMBL
PhenoGen	Vta1	PhenoGen
RatGTEx	ENSRNOG00000011540	RatGTEx
UniProt	A0A096MKH2_RAT	UniProtKB/TrEMBL
	A0A8I5ZX91	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6A5Y0	ENTREZGENE, UniProtKB/TrEMBL
	A6JP73	ENTREZGENE, UniProtKB/TrEMBL
	Q4KM55	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-04-13	Vta1	vesicle trafficking 1	Vta1	vesicle (multivesicular body) trafficking 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-09-17	Vta1	vesicle (multivesicular body) trafficking 1	Vta1	Vps20-associated 1 homolog (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-06	Vta1	Vps20-associated 1 homolog (S. cerevisiae)	RGD1305031	similar to RIKEN cDNA 1110059P08	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1305031	similar to RIKEN cDNA 1110059P08	RGD1305031_predicted	similar to RIKEN cDNA 1110059P08 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1305031_predicted	similar to RIKEN cDNA 1110059P08 (predicted)	LOC292640_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC292640_predicted	similar to RIKEN cDNA 1110059P08 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)