Human Gene VAMP4 (ENST00000236192.12_9) from GENCODE V47lift37
  Description: vesicle associated membrane protein 4, transcript variant 1 (from RefSeq NM_003762.5)
Gencode Transcript: ENST00000236192.12_9
Gencode Gene: ENSG00000117533.15_11
Transcript (Including UTRs)
   Position: hg19 chr1:171,669,300-171,711,205 Size: 41,906 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:171,673,646-171,707,554 Size: 33,909 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:171,669,300-171,711,205)mRNA (may differ from genome)Protein (141 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q6IAZ3_HUMAN
DESCRIPTION: SubName: Full=VAMP4 protein; SubName: Full=Vesicle-associated membrane protein 4; SubName: Full=Vesicle-associated membrane protein 4, isoform CRA_b; SubName: Full=cDNA FLJ76098, highly similar to Homo sapiens vesicle-associated membrane protein 4 (VAMP4), transcript variant 2, mRNA;
SIMILARITY: Contains 1 v-SNARE coiled-coil homology domain.

-  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: VAMP4
Diseases sorted by gene-association score: mednik syndrome (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: 15.30 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 374.54 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 -71.70205-0.350 Picture PostScript Text
3' UTR -990.404346-0.228 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
IPR001388 - Synaptobrevin
IPR016444 - Synaptobrevin_met/fun

Pfam Domains:
PF00957 - Synaptobrevin

SCOP Domains:
58038 - SNARE fusion complex
111479 - Fzo-like conserved region

ModBase Predicted Comparative 3D Structure on Q6IAZ3
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0016192 vesicle-mediated transport

Cellular Component:
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030285 integral component of synaptic vesicle membrane


-  Descriptions from all associated GenBank mRNAs
  BC031264 - Homo sapiens vesicle-associated membrane protein 4, mRNA (cDNA clone MGC:39731 IMAGE:5275603), complete cds.
AK290441 - Homo sapiens cDNA FLJ76098 complete cds, highly similar to Homo sapiens vesicle-associated membrane protein 4 (VAMP4), transcript variant 2, mRNA.
AL035296 - H.sapiens gene from PAC 560B9.
BC005974 - Homo sapiens vesicle-associated membrane protein 4, mRNA (cDNA clone MGC:14658 IMAGE:4102457), complete cds.
BC007019 - Homo sapiens vesicle-associated membrane protein 4, mRNA (cDNA clone MGC:12355 IMAGE:3961237), complete cds.
AF044310 - Homo sapiens VAMP 4 (VAMP4) mRNA, complete cds.
KJ892593 - Synthetic construct Homo sapiens clone ccsbBroadEn_01987 VAMP4 gene, encodes complete protein.
CR457011 - Homo sapiens full open reading frame cDNA clone RZPDo834G085D for gene VAMP4, vesicle-associated membrane protein 4; complete cds, incl. stopcodon.
KJ905971 - Synthetic construct Homo sapiens clone ccsbBroadEn_15641 VAMP4 gene, encodes complete protein.
KY966300 - Homo sapiens cell line 94T778 VAMP4/TAF3 fusion mRNA, partial sequence.
KY966279 - Homo sapiens cell line 93T449 VAMP4/TAF3 fusion mRNA, partial sequence.
AF052100 - Homo sapiens clone 23645 mRNA sequence.
AK123624 - Homo sapiens cDNA FLJ41630 fis, clone DFNES2011245, weakly similar to Homo sapiens VAMP 4 (VAMP4) mRNA.
AK056124 - Homo sapiens cDNA FLJ31562 fis, clone NT2RI2001422.
JD147778 - Sequence 128802 from Patent EP1572962.
JD488115 - Sequence 469139 from Patent EP1572962.
JD053576 - Sequence 34600 from Patent EP1572962.
JD538163 - Sequence 519187 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A024R8Z6, ENST00000236192.1, ENST00000236192.10, ENST00000236192.11, ENST00000236192.2, ENST00000236192.3, ENST00000236192.4, ENST00000236192.5, ENST00000236192.6, ENST00000236192.7, ENST00000236192.8, ENST00000236192.9, hCG_37824 , NM_003762, Q6IAZ3, Q6IAZ3_HUMAN, uc317eaz.1, uc317eaz.2, VAMP4
UCSC ID: ENST00000236192.12_9
RefSeq Accession: NM_003762.5
Protein: Q6IAZ3

-  Gene Model Information
  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.