Human Gene VAT1 (uc010whk.1)
  Description: Homo sapiens vesicle amine transport protein 1 homolog (T. californica) (VAT1), mRNA.
RefSeq Summary (NM_006373): Synaptic vesicles are responsible for regulating the storage and release of neurotransmitters in the nerve terminal. The protein encoded by this gene is an abundant integral membrane protein of cholinergic synaptic vesicles and is thought to be involved in vesicular transport. It belongs to the quinone oxidoreductase subfamily of zinc-containing alcohol dehydrogenase proteins. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:41,166,622-41,174,373 Size: 7,752 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr17:41,168,078-41,174,339 Size: 6,262 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:41,166,622-41,174,373)mRNA (may differ from genome)Protein (325 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VAT1
Diseases sorted by gene-association score: immature cataract (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 152.26 RPKM in Adrenal Gland
Total median expression: 2564.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.2034-0.359 Picture PostScript Text
3' UTR -578.781456-0.398 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013149 - ADH_C
IPR002085 - ADH_SF_Zn-type
IPR011032 - GroES-like
IPR016040 - NAD(P)-bd_dom
IPR002364 - Quin_OxRdtase/zeta-crystal_CS

Pfam Domains:
PF00107 - Zinc-binding dehydrogenase
PF13602 - Zinc-binding dehydrogenase

SCOP Domains:
50129 - GroES-like
51735 - NAD(P)-binding Rossmann-fold domains

ModBase Predicted Comparative 3D Structure on B4DPX4
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  LF209355 - JP 2014500723-A/16858: Polycomb-Associated Non-Coding RNAs.
LF327928 - JP 2014500723-A/135431: Polycomb-Associated Non-Coding RNAs.
BC008725 - Homo sapiens vesicle amine transport protein 1 homolog (T. californica), mRNA (cDNA clone MGC:3015 IMAGE:3162543), complete cds.
BC015041 - Homo sapiens vesicle amine transport protein 1 homolog (T. californica), mRNA (cDNA clone MGC:9483 IMAGE:3919901), complete cds.
U18009 - Human chromosome 17q21 mRNA clone LF113.
BC001913 - Homo sapiens vesicle amine transport protein 1 homolog (T. californica), mRNA (cDNA clone IMAGE:3547155), partial cds.
BC014279 - Homo sapiens vesicle amine transport protein 1 homolog (T. californica), mRNA (cDNA clone MGC:11123 IMAGE:3834206), complete cds.
AK097072 - Homo sapiens cDNA FLJ39753 fis, clone SMINT2018343, highly similar to Synaptic vesicle membrane protein VAT-1homolog (EC 1.-.-.-).
BC068489 - Homo sapiens cDNA clone IMAGE:5299207, containing frame-shift errors.
BC090858 - Homo sapiens vesicle amine transport protein 1 homolog (T. californica), mRNA (cDNA clone MGC:102756 IMAGE:6528247), complete cds.
AK000237 - Homo sapiens cDNA FLJ20230 fis, clone COLF5378, highly similar to VATH_HUMAN SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG.
JD113078 - Sequence 94102 from Patent EP1572962.
JD214944 - Sequence 195968 from Patent EP1572962.
JD078152 - Sequence 59176 from Patent EP1572962.
JD553596 - Sequence 534620 from Patent EP1572962.
JD255928 - Sequence 236952 from Patent EP1572962.
JD278010 - Sequence 259034 from Patent EP1572962.
JD173112 - Sequence 154136 from Patent EP1572962.
LF327929 - JP 2014500723-A/135432: Polycomb-Associated Non-Coding RNAs.
JD481328 - Sequence 462352 from Patent EP1572962.
JD514302 - Sequence 495326 from Patent EP1572962.
JD076540 - Sequence 57564 from Patent EP1572962.
JD279660 - Sequence 260684 from Patent EP1572962.
JD374185 - Sequence 355209 from Patent EP1572962.
JD220607 - Sequence 201631 from Patent EP1572962.
JD545075 - Sequence 526099 from Patent EP1572962.
JD279014 - Sequence 260038 from Patent EP1572962.
U25779 - Human chromosome 17q21 mRNA clone 694:2.
LF327930 - JP 2014500723-A/135433: Polycomb-Associated Non-Coding RNAs.
JD316945 - Sequence 297969 from Patent EP1572962.
JD253505 - Sequence 234529 from Patent EP1572962.
JD094836 - Sequence 75860 from Patent EP1572962.
JD291362 - Sequence 272386 from Patent EP1572962.
JD353215 - Sequence 334239 from Patent EP1572962.
LF327931 - JP 2014500723-A/135434: Polycomb-Associated Non-Coding RNAs.
JD264266 - Sequence 245290 from Patent EP1572962.
JD226782 - Sequence 207806 from Patent EP1572962.
JD519279 - Sequence 500303 from Patent EP1572962.
JD416521 - Sequence 397545 from Patent EP1572962.
JD418457 - Sequence 399481 from Patent EP1572962.
JD259252 - Sequence 240276 from Patent EP1572962.
JD090489 - Sequence 71513 from Patent EP1572962.
JD428579 - Sequence 409603 from Patent EP1572962.
JD124438 - Sequence 105462 from Patent EP1572962.
JD318358 - Sequence 299382 from Patent EP1572962.
JD460593 - Sequence 441617 from Patent EP1572962.
JD076200 - Sequence 57224 from Patent EP1572962.
AK290460 - Homo sapiens cDNA FLJ75120 complete cds, highly similar to Homo sapiens vesicle amine transport protein 1 homolog (T californica) (VAT1), mRNA.
JD495406 - Sequence 476430 from Patent EP1572962.
JD565495 - Sequence 546519 from Patent EP1572962.
JD066350 - Sequence 47374 from Patent EP1572962.
AK298536 - Homo sapiens cDNA FLJ54106 complete cds, moderately similar to Synaptic vesicle membrane protein VAT-1 homolog (EC 1.-.-.-).
JD348359 - Sequence 329383 from Patent EP1572962.
AK315838 - Homo sapiens cDNA, FLJ79487 complete cds, highly similar to Synaptic vesicle membrane protein VAT-1homolog (EC 1.-.-.-).
JD105235 - Sequence 86259 from Patent EP1572962.
JD209128 - Sequence 190152 from Patent EP1572962.
LF327932 - JP 2014500723-A/135435: Polycomb-Associated Non-Coding RNAs.
JD554230 - Sequence 535254 from Patent EP1572962.
BT007369 - Homo sapiens vesicle amine transport protein 1 homolog (T californica) mRNA, complete cds.
HQ258013 - Synthetic construct Homo sapiens clone IMAGE:100072322 vesicle amine transport protein 1 homolog (T. californica) (VAT1) gene, encodes complete protein.
DL492336 - Novel nucleic acids.
DL490825 - Novel nucleic acids.
JD020743 - Sequence 1767 from Patent EP1572962.
MA563505 - JP 2018138019-A/135431: Polycomb-Associated Non-Coding RNAs.
MA563506 - JP 2018138019-A/135432: Polycomb-Associated Non-Coding RNAs.
MA563507 - JP 2018138019-A/135433: Polycomb-Associated Non-Coding RNAs.
MA563508 - JP 2018138019-A/135434: Polycomb-Associated Non-Coding RNAs.
MA563509 - JP 2018138019-A/135435: Polycomb-Associated Non-Coding RNAs.
MA444932 - JP 2018138019-A/16858: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK298536, B4DPX4, B4DPX4_HUMAN, NM_006373, NP_006364
UCSC ID: uc010whk.1
RefSeq Accession: NM_006373
Protein: B4DPX4

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK298536.1
exon count: 6CDS single in 3' UTR: no RNA size: 1174
ORF size: 978CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2153.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.