Human Gene SORBS3 (ENST00000240123.12_4) from GENCODE V47lift37
  Description: sorbin and SH3 domain containing 3, transcript variant 1 (from RefSeq NM_005775.5)
Gencode Transcript: ENST00000240123.12_4
Gencode Gene: ENSG00000120896.14_9
Transcript (Including UTRs)
   Position: hg19 chr8:22,409,440-22,433,301 Size: 23,862 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr8:22,412,020-22,432,241 Size: 20,222 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:22,409,440-22,433,301)mRNA (may differ from genome)Protein (671 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VINEX_HUMAN
DESCRIPTION: RecName: Full=Vinexin; AltName: Full=SH3-containing adapter molecule 1; Short=SCAM-1; AltName: Full=Sorbin and SH3 domain-containing protein 3;
FUNCTION: Vinexin alpha isoform promotes up-regulation of actin stress fiber formation. Vinexin beta isoform plays a role in cell spreading and enhances the activation of JNK/SAPK in response to EGF stimulation by using its third SH3 domain.
SUBUNIT: Interacts with DLG5 through its third SH3 domain (By similarity). Interacts with vinculin by the first two SH3 domains and the proline rich region of vinculin. Binds to SOS (guanine nucleotide exchange factor of RAS and RAC), through its third SH3 domain. The formation of this complex is down-regulated by phosphorylation of SOS. Interacts with INPPL1/SHIP2, SAFB2, SOCS7 and SRCIN1. Interacts with FASLG. Interacts with MAPK1/ERK2 (By similarity).
INTERACTION: Q14151:SAFB2; NbExp=3; IntAct=EBI-1222956, EBI-352869; Q9QWI6-2:Srcin1 (xeno); NbExp=4; IntAct=EBI-1222956, EBI-775607; O00401:WASL; NbExp=2; IntAct=EBI-1222956, EBI-957615;
SUBCELLULAR LOCATION: Isoform Alpha: Cell junction (By similarity). Cytoplasm, cytoskeleton (By similarity). Note=Localized at cell-extracellular matrix junctions (By similarity). Both isoforms were localized at focal adhesion and cell-cell adhesion sites.
SUBCELLULAR LOCATION: Isoform Beta: Cell junction (By similarity). Nucleus. Cytoplasm, cytoskeleton (By similarity). Note=Localized at cell-extracellular matrix junctions (By similarity). Both isoforms were localized at focal adhesion and cell-cell adhesion sites, vinexin beta was also found in the nucleus.
TISSUE SPECIFICITY: Both isoforms are expressed in different tissues like heart, placenta, brain, skeletal muscle and pancreas. Isoform beta is especially found in liver.
PTM: Phosphorylated at Ser-530 by MAPK1/ERK2 during cell spreading (By similarity).
SIMILARITY: Contains 3 SH3 domains.
SIMILARITY: Contains 1 SoHo 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


-  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: 89.49 RPKM in Artery - Tibial
Total median expression: 1800.35 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 -63.90151-0.423 Picture PostScript Text
3' UTR -436.201060-0.412 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
IPR000108 - p67phox
IPR011511 - SH3_2
IPR001452 - SH3_domain
IPR003127 - Sorb

Pfam Domains:
PF00018 - SH3 domain
PF02208 - Sorbin homologous domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
50044 - SH3-domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2CT3 - NMR MuPIT 2DLM - NMR MuPIT 2NWM - NMR MuPIT 2YUP - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O60504
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0017166 vinculin binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006936 muscle contraction
GO:0007015 actin filament organization
GO:0007155 cell adhesion
GO:0031589 cell-substrate adhesion
GO:0043410 positive regulation of MAPK cascade
GO:0051495 positive regulation of cytoskeleton organization
GO:0051496 positive regulation of stress fiber assembly

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005925 focal adhesion
GO:0030054 cell junction


-  Descriptions from all associated GenBank mRNAs
  BC091514 - Homo sapiens sorbin and SH3 domain containing 3, mRNA (cDNA clone MGC:111432 IMAGE:6201273), complete cds.
AK303950 - Homo sapiens cDNA FLJ59267 complete cds, highly similar to Vinexin.
AF037261 - Homo sapiens SH3-containing adaptor molecule-1 mRNA, complete cds.
BC067260 - Homo sapiens sorbin and SH3 domain containing 3, mRNA (cDNA clone MGC:74729 IMAGE:6186182), complete cds.
AK301196 - Homo sapiens cDNA FLJ60912 complete cds, highly similar to Vinexin.
AB527718 - Synthetic construct DNA, clone: pF1KB6225, Homo sapiens SORBS3 gene for sorbin and SH3 domain containing 3, without stop codon, in Flexi system.
AF064807 - Homo sapiens vinexin beta mRNA, complete cds.
BC010146 - Homo sapiens sorbin and SH3 domain containing 3, mRNA (cDNA clone IMAGE:4328970), complete cds.
CU679639 - Synthetic construct Homo sapiens gateway clone IMAGE:100018116 5' read SORBS3 mRNA.
KJ892946 - Synthetic construct Homo sapiens clone ccsbBroadEn_02340 SORBS3 gene, encodes complete protein.
BC004314 - Homo sapiens sorbin and SH3 domain containing 3, mRNA (cDNA clone IMAGE:3628014), partial cds.
JD560163 - Sequence 541187 from Patent EP1572962.
JD103339 - Sequence 84363 from Patent EP1572962.
JD357918 - Sequence 338942 from Patent EP1572962.
JD324200 - Sequence 305224 from Patent EP1572962.
JD457883 - Sequence 438907 from Patent EP1572962.
JD297838 - Sequence 278862 from Patent EP1572962.
JD123437 - Sequence 104461 from Patent EP1572962.
JD557673 - Sequence 538697 from Patent EP1572962.
JD439519 - Sequence 420543 from Patent EP1572962.
JD219049 - Sequence 200073 from Patent EP1572962.
JD438799 - Sequence 419823 from Patent EP1572962.
JD123778 - Sequence 104802 from Patent EP1572962.
JD201646 - Sequence 182670 from Patent EP1572962.
JD485293 - Sequence 466317 from Patent EP1572962.
JD460386 - Sequence 441410 from Patent EP1572962.
JD163546 - Sequence 144570 from Patent EP1572962.
JD269324 - Sequence 250348 from Patent EP1572962.
JD079907 - Sequence 60931 from Patent EP1572962.
JD467463 - Sequence 448487 from Patent EP1572962.
JD157401 - Sequence 138425 from Patent EP1572962.
JD406418 - Sequence 387442 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O60504 (Reactome details) participates in the following event(s):

R-HSA-445705 Release Of ADP From Myosin
R-HSA-445699 ATP Hydrolysis By Myosin
R-HSA-445700 Myosin Binds ATP
R-HSA-445704 Calcium Binds Caldesmon
R-HSA-445355 Smooth Muscle Contraction
R-HSA-397014 Muscle contraction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000240123.1, ENST00000240123.10, ENST00000240123.11, ENST00000240123.2, ENST00000240123.3, ENST00000240123.4, ENST00000240123.5, ENST00000240123.6, ENST00000240123.7, ENST00000240123.8, ENST00000240123.9, NM_005775, O60504, Q5BJE4, Q6NX54, Q96FY4, Q9UQE4, SCAM1, uc317egv.1, uc317egv.2, VINEX_HUMAN
UCSC ID: ENST00000240123.12_4
RefSeq Accession: NM_005775.5
Protein: O60504 (aka VINEX_HUMAN)

-  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.