Human Gene SV2B (uc002bqv.3)
  Description: Homo sapiens synaptic vesicle glycoprotein 2B (SV2B), transcript variant 1, mRNA.
RefSeq Summary (NM_014848): This gene encodes a member of the synaptic vesicle proteins 2 (SV2) family and major facilitator superfamily of proteins. This protein and other members of the family are localized to synaptic vesicles and may function in the regulation of vesicle trafficking and exocytosis. Studies in mice suggest that the encoded protein may act as a protein receptor for botulinum neurotoxin E in neurons, and that this protein may be important for the integrity of the glomerular filtration barrier. This gene shows reduced expression in areas of synaptic loss in the hippocampus of human temporal lobe epilepsy patients. [provided by RefSeq, Sep 2016].
Transcript (Including UTRs)
   Position: hg19 chr15:91,643,182-91,844,539 Size: 201,358 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr15:91,769,494-91,835,782 Size: 66,289 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:91,643,182-91,844,539)mRNA (may differ from genome)Protein (683 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDHuman Cortex Gene ExpressionLynx
MalacardsMGIneXtProtOMIMPubMedReactome
TreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SV2B_HUMAN
DESCRIPTION: RecName: Full=Synaptic vesicle glycoprotein 2B;
FUNCTION: Probably plays a role in the control of regulated secretion in neural and endocrine cells (By similarity).
SUBUNIT: Interacts with SYT1 in a calcium-independent manner. Forms a complex with SYT1, syntaxin-1 and SNAP25 (By similarity).
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-pass membrane protein (By similarity). Cytoplasmic vesicle, secretory vesicle, acrosome (By similarity). Note=Associated with synaptic-like microvesicles but not with insulin-containing vesicles in insulin-secreting cells of the pancreas. Localizes to microvesicles in the pinealocytes. Localizes to the acrosome in spermatids (By similarity).
PTM: N-glycosylated (By similarity).
PTM: The N-terminal cytoplasmic domain is phosphorylated by CK1 (By similarity).
SIMILARITY: Belongs to the major facilitator superfamily.
SEQUENCE CAUTION: Sequence=BAA34455.2; Type=Erroneous initiation;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SV2B
CDC HuGE Published Literature: SV2B
Positive Disease Associations: Arthritis, Rheumatoid , Glucose , Heart Rate , serum metabolites , Sphingomyelins , Stroke
Related Studies:
  1. Arthritis, Rheumatoid
    J Wang et al. The pharmacogenomics journal 2012, Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis., The pharmacogenomics journal. [PubMed 22491018]
  2. Glucose
    , , . [PubMed 0]
  3. Heart Rate
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SV2B
Diseases sorted by gene-association score: prostate small cell carcinoma (17), temporal lobe epilepsy (16)

-  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: 29.59 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 145.37 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 -379.50891-0.426 Picture PostScript Text
3' UTR -2721.778757-0.311 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
IPR011701 - MFS
IPR020846 - MFS_dom
IPR016196 - MFS_dom_general_subst_transpt
IPR005828 - Sub_transporter
IPR005829 - Sugar_transporter_CS
IPR022308 - SV2_chordata

Pfam Domains:
PF00083 - Sugar (and other) transporter
PF07690 - Major Facilitator Superfamily
PF13599 - Pentapeptide repeats (9 copies)

SCOP Domains:
103473 - MFS general substrate transporter

ModBase Predicted Comparative 3D Structure on Q7L1I2
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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0005515 protein binding
GO:0022857 transmembrane transporter activity

Biological Process:
GO:0006836 neurotransmitter transport
GO:0007268 chemical synaptic transmission
GO:0055085 transmembrane transport

Cellular Component:
GO:0001669 acrosomal vesicle
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AK294902 - Homo sapiens cDNA FLJ50759 complete cds, highly similar to Synaptic vesicle glycoprotein 2B.
BC030011 - Homo sapiens synaptic vesicle glycoprotein 2B, mRNA (cDNA clone MGC:26452 IMAGE:4826206), complete cds.
AF052188 - Homo sapiens clone 24673 mRNA sequence.
AB018278 - Homo sapiens KIAA0735 mRNA for KIAA0735 protein.
JD130079 - Sequence 111103 from Patent EP1572962.
JD182246 - Sequence 163270 from Patent EP1572962.
CR457086 - Homo sapiens full open reading frame cDNA clone RZPDo834E0814D for gene SV2B, synaptic vesicle glycoprotein 2B; complete cds, incl. stopcodon.
KJ898113 - Synthetic construct Homo sapiens clone ccsbBroadEn_07507 SV2B gene, encodes complete protein.
AB383969 - Synthetic construct DNA, clone: pF1KSDA0735, Homo sapiens SV2B gene for synaptic vesicle glycoprotein 2B, complete cds, without stop codon, in Flexi system.
DQ891614 - Synthetic construct clone IMAGE:100004244; FLH178639.01X; RZPDo839F05128D synaptic vesicle glycoprotein 2B (SV2B) gene, encodes complete protein.
EU176590 - Synthetic construct Homo sapiens clone IMAGE:100011421; FLH178638.01L; RZPDo839G02254D synaptic vesicle glycoprotein 2B (SV2B) gene, encodes complete protein.
JD495222 - Sequence 476246 from Patent EP1572962.
JD276666 - Sequence 257690 from Patent EP1572962.
JD265626 - Sequence 246650 from Patent EP1572962.
JD074967 - Sequence 55991 from Patent EP1572962.
JD496202 - Sequence 477226 from Patent EP1572962.
AL110287 - Homo sapiens EST from clone 361263, 5' end.
JD350617 - Sequence 331641 from Patent EP1572962.
JD448559 - Sequence 429583 from Patent EP1572962.
JD376564 - Sequence 357588 from Patent EP1572962.
JD146689 - Sequence 127713 from Patent EP1572962.
JD300805 - Sequence 281829 from Patent EP1572962.
JD260587 - Sequence 241611 from Patent EP1572962.
JD096635 - Sequence 77659 from Patent EP1572962.
JD085621 - Sequence 66645 from Patent EP1572962.
JD063033 - Sequence 44057 from Patent EP1572962.
JD171411 - Sequence 152435 from Patent EP1572962.
JD111936 - Sequence 92960 from Patent EP1572962.
JD215375 - Sequence 196399 from Patent EP1572962.
JD445541 - Sequence 426565 from Patent EP1572962.
JD471376 - Sequence 452400 from Patent EP1572962.
JD339969 - Sequence 320993 from Patent EP1572962.
JD450419 - Sequence 431443 from Patent EP1572962.
JD346067 - Sequence 327091 from Patent EP1572962.
JD491297 - Sequence 472321 from Patent EP1572962.
JD563326 - Sequence 544350 from Patent EP1572962.
JD134866 - Sequence 115890 from Patent EP1572962.
DQ587382 - Homo sapiens piRNA piR-54494, complete sequence.
JD154379 - Sequence 135403 from Patent EP1572962.
JD229538 - Sequence 210562 from Patent EP1572962.
JD258734 - Sequence 239758 from Patent EP1572962.
JD544248 - Sequence 525272 from Patent EP1572962.
JD251370 - Sequence 232394 from Patent EP1572962.
JD376671 - Sequence 357695 from Patent EP1572962.
AK124722 - Homo sapiens cDNA FLJ42732 fis, clone BRAWH2013294.
DQ575430 - Homo sapiens piRNA piR-43542, complete sequence.
DQ594719 - Homo sapiens piRNA piR-60831, complete sequence.
AK054975 - Homo sapiens cDNA FLJ30413 fis, clone BRACE2008655, weakly similar to Homo sapiens mRNA for GABAB receptor.
JD515074 - Sequence 496098 from Patent EP1572962.
JD473360 - Sequence 454384 from Patent EP1572962.
JD450575 - Sequence 431599 from Patent EP1572962.
DQ595053 - Homo sapiens piRNA piR-61165, complete sequence.
JD458170 - Sequence 439194 from Patent EP1572962.
JD471728 - Sequence 452752 from Patent EP1572962.
JD565177 - Sequence 546201 from Patent EP1572962.
JD316096 - Sequence 297120 from Patent EP1572962.
DQ575246 - Homo sapiens piRNA piR-43358, complete sequence.
JD545574 - Sequence 526598 from Patent EP1572962.
JD243536 - Sequence 224560 from Patent EP1572962.
JD515522 - Sequence 496546 from Patent EP1572962.
JD078695 - Sequence 59719 from Patent EP1572962.
JD446914 - Sequence 427938 from Patent EP1572962.
JD299064 - Sequence 280088 from Patent EP1572962.
JD565545 - Sequence 546569 from Patent EP1572962.
JD276044 - Sequence 257068 from Patent EP1572962.
DQ597308 - Homo sapiens piRNA piR-35374, complete sequence.
JD049168 - Sequence 30192 from Patent EP1572962.
JD082768 - Sequence 63792 from Patent EP1572962.
JD144121 - Sequence 125145 from Patent EP1572962.
JD537103 - Sequence 518127 from Patent EP1572962.
JD504805 - Sequence 485829 from Patent EP1572962.
JD393622 - Sequence 374646 from Patent EP1572962.
JD042536 - Sequence 23560 from Patent EP1572962.
JD108157 - Sequence 89181 from Patent EP1572962.
JD551052 - Sequence 532076 from Patent EP1572962.
JD282726 - Sequence 263750 from Patent EP1572962.
DQ592467 - Homo sapiens piRNA piR-59579, complete sequence.
AL109781 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 30103.
DQ579610 - Homo sapiens piRNA piR-47722, complete sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04512 - ECM-receptor interaction

Reactome (by CSHL, EBI, and GO)

Protein Q7L1I2 (Reactome details) participates in the following event(s):

R-HSA-5244415 BoNT/A HC:LC binds SV2A, B, or C and GT1b on the target cell surface
R-HSA-5250607 BoNT/D HC:LC binds SV2A or B or C and GD2 on the target cell surface
R-HSA-5250880 BoNT/F HC:LC binds SV2A or B or C and GT1b on the target cell surface
R-HSA-5244503 BoNT/E HC:LC binds SV2A or B and GT1b on the target cell surface
R-HSA-5250968 Toxicity of botulinum toxin type A (BoNT/A)
R-HSA-5250955 Toxicity of botulinum toxin type D (BoNT/D)
R-HSA-5250981 Toxicity of botulinum toxin type F (BoNT/F)
R-HSA-5250992 Toxicity of botulinum toxin type E (BoNT/E)
R-HSA-168799 Neurotoxicity of clostridium toxins
R-HSA-5339562 Uptake and actions of bacterial toxins
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: C6G489, KIAA0735, NM_014848, NP_055663, O94840, Q6IAR8, Q7L1I2, SV2B_HUMAN
UCSC ID: uc002bqv.3
RefSeq Accession: NM_014848
Protein: Q7L1I2 (aka SV2B_HUMAN)
CCDS: CCDS10370.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014848.4
exon count: 14CDS single in 3' UTR: no RNA size: 11361
ORF size: 2052CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4166.50frame shift in genome: no % Coverage: 99.84
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 8138# 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.