Human Gene SH3PXD2A (ENST00000369774.9_11) from GENCODE V47lift37
  Description: SH3 and PX domains 2A, transcript variant 8 (from RefSeq NM_001394020.1)
Gencode Transcript: ENST00000369774.9_11
Gencode Gene: ENSG00000107957.17_17
Transcript (Including UTRs)
   Position: hg19 chr10:105,353,784-105,615,334 Size: 261,551 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr10:105,361,573-105,615,024 Size: 253,452 Coding Exon Count: 15 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:105,353,784-105,615,334)mRNA (may differ from genome)Protein (1133 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SPD2A_HUMAN
DESCRIPTION: RecName: Full=SH3 and PX domain-containing protein 2A; AltName: Full=Adapter protein TKS5; AltName: Full=Five SH3 domain-containing protein; AltName: Full=SH3 multiple domains protein 1; AltName: Full=Tyrosine kinase substrate with five SH3 domains;
FUNCTION: Adapter protein involved in invadopodia and podosome formation, extracellular matrix degradation and invasiveness of some cancer cells. Binds matrix metalloproteinases (ADAMs), NADPH oxidases (NOXs) and phosphoinositides. Acts as an organizer protein that allows NOX1- or NOX3-dependent reactive oxygen species (ROS) generation and ROS localization. In association with ADAM12, mediates the neurotoxic effect of beta-amyloid peptide.
SUBUNIT: Interacts (via N-terminus) with CYBA (By similarity). Interacts with ADAM12, ADAM15 and ADAM19. Interacts with NOXO1. Interacts (via SH3 domains) with NOXA1. Interacts with FASLG.
SUBCELLULAR LOCATION: Cytoplasm. Cell projection, podosome. Note=Cytoplasmic in normal cells and localizes to podosomes in SRC-transformed cells.
TISSUE SPECIFICITY: Found in several cancer cell lines, particularly invasive breast carcinomas and melanomas.
DOMAIN: The PX domain is required for podosome localization because of its ability to bind phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) and, to a lesser extent, phosphatidylinositol 4- phosphate (PtdIns(4)P), phosphatidylinositol 5-phosphate (PtdIns(5)P), and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). Binds to the third intramolecular SH3 domain (By similarity).
DOMAIN: The fifth SH3 domain mediates binding with ADAM12, ADAM15 and ADAM19.
PTM: Tyrosine phosphorylated by SRC. Phosphorylation plays a regulatory role in the protein localization. The intramolecular interaction of the PX domain with the third SH3 domain maintains the protein in the cytoplasm and phosphorylation disrupts this interaction, resulting in the redistribution of the protein from cytoplasm to the perimembrane region. Phosphorylated on serine upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the SH3PXD2 family.
SIMILARITY: Contains 1 PX (phox homology) domain.
SIMILARITY: Contains 5 SH3 domains.
SEQUENCE CAUTION: Sequence=BAA24848.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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: SH3PXD2A
Diseases sorted by gene-association score: malignant peripheral nerve sheath tumor* (247)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 40.28 RPKM in Nerve - Tibial
Total median expression: 716.16 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 -183.50310-0.592 Picture PostScript Text
3' UTR -2757.107789-0.354 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
IPR001683 - Phox
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00787 - PX domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
50044 - SH3-domain
64268 - PX domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DNU - NMR MuPIT 2EGA - NMR MuPIT 2EGC - NMR MuPIT 2EKH - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q5TCZ1
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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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016176 superoxide-generating NADPH oxidase activator activity
GO:0035091 phosphatidylinositol binding

Biological Process:
GO:0006801 superoxide metabolic process
GO:0030198 extracellular matrix organization
GO:0043085 positive regulation of catalytic activity
GO:0055114 oxidation-reduction process
GO:0071800 podosome assembly
GO:0072593 reactive oxygen species metabolic process
GO:0072675 osteoclast fusion

Cellular Component:
GO:0002102 podosome
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030054 cell junction
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK295314 - Homo sapiens cDNA FLJ59690 complete cds, highly similar to Mus musculus SH3 and PX domains 2A (Sh3pxd2a), mRNA.
AB007878 - Homo sapiens KIAA0418 mRNA, partial cds.
AK302015 - Homo sapiens cDNA FLJ58079 complete cds, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
AK295660 - Homo sapiens cDNA FLJ56087 complete cds, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
AK294736 - Homo sapiens cDNA FLJ56896 complete cds, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
AK304828 - Homo sapiens cDNA FLJ57808 complete cds, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
AK315983 - Homo sapiens cDNA, FLJ78882 complete cds, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
AK056469 - Homo sapiens cDNA FLJ31907 fis, clone NT2RP7004396, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
AK294454 - Homo sapiens cDNA FLJ53508 complete cds, highly similar to Homo sapiens SH3 multiple domains 1 (SH3MD1), mRNA.
BC156572 - Synthetic construct Homo sapiens clone IMAGE:100062077, MGC:190164 SH3 and PX domains 2A (SH3PXD2A) mRNA, encodes complete protein.
BC146309 - Synthetic construct Homo sapiens clone IMAGE:100015244, MGC:180262 SH3 and PX domains 2A (SH3PXD2A) mRNA, encodes complete protein.
AB385330 - Synthetic construct DNA, clone: pF1KA0418, Homo sapiens SH3PXD2A gene for SH3 and PX domain-containing protein 2A, complete cds, without stop codon, in Flexi system.
MP202722 - Sequence 33 from Patent WO2019090263.
LF211366 - JP 2014500723-A/18869: Polycomb-Associated Non-Coding RNAs.
AK025783 - Homo sapiens cDNA: FLJ22130 fis, clone HEP19632.
BX647371 - Homo sapiens mRNA; cDNA DKFZp686B16111 (from clone DKFZp686B16111).
AK096575 - Homo sapiens cDNA FLJ39256 fis, clone OCBBF2008822.
AL833070 - Homo sapiens mRNA; cDNA DKFZp451A0419 (from clone DKFZp451A0419); complete cds.
AK123570 - Homo sapiens cDNA FLJ41576 fis, clone CTONG2019248.
DQ590336 - Homo sapiens piRNA piR-57448, complete sequence.
JD269058 - Sequence 250082 from Patent EP1572962.
JD066249 - Sequence 47273 from Patent EP1572962.
JD160171 - Sequence 141195 from Patent EP1572962.
JD524810 - Sequence 505834 from Patent EP1572962.
JD353885 - Sequence 334909 from Patent EP1572962.
JD268927 - Sequence 249951 from Patent EP1572962.
JD308625 - Sequence 289649 from Patent EP1572962.
JD538970 - Sequence 519994 from Patent EP1572962.
JD550893 - Sequence 531917 from Patent EP1572962.
JD233755 - Sequence 214779 from Patent EP1572962.
JD286395 - Sequence 267419 from Patent EP1572962.
JD306022 - Sequence 287046 from Patent EP1572962.
LF345922 - JP 2014500723-A/153425: Polycomb-Associated Non-Coding RNAs.
DQ596044 - Homo sapiens piRNA piR-34110, complete sequence.
JD086578 - Sequence 67602 from Patent EP1572962.
JD129370 - Sequence 110394 from Patent EP1572962.
JD172009 - Sequence 153033 from Patent EP1572962.
JD440912 - Sequence 421936 from Patent EP1572962.
JD330696 - Sequence 311720 from Patent EP1572962.
LF345923 - JP 2014500723-A/153426: Polycomb-Associated Non-Coding RNAs.
JD047799 - Sequence 28823 from Patent EP1572962.
JD070934 - Sequence 51958 from Patent EP1572962.
JD383890 - Sequence 364914 from Patent EP1572962.
JD536475 - Sequence 517499 from Patent EP1572962.
JD307222 - Sequence 288246 from Patent EP1572962.
JD438218 - Sequence 419242 from Patent EP1572962.
JD148464 - Sequence 129488 from Patent EP1572962.
JD228319 - Sequence 209343 from Patent EP1572962.
JD304832 - Sequence 285856 from Patent EP1572962.
JD503048 - Sequence 484072 from Patent EP1572962.
LF345924 - JP 2014500723-A/153427: Polycomb-Associated Non-Coding RNAs.
JD166992 - Sequence 148016 from Patent EP1572962.
DQ598621 - Homo sapiens piRNA piR-36687, complete sequence.
JD249122 - Sequence 230146 from Patent EP1572962.
JD237610 - Sequence 218634 from Patent EP1572962.
JD315520 - Sequence 296544 from Patent EP1572962.
JD085300 - Sequence 66324 from Patent EP1572962.
JD052319 - Sequence 33343 from Patent EP1572962.
JD363632 - Sequence 344656 from Patent EP1572962.
JD050635 - Sequence 31659 from Patent EP1572962.
JD097334 - Sequence 78358 from Patent EP1572962.
JD474560 - Sequence 455584 from Patent EP1572962.
JD275074 - Sequence 256098 from Patent EP1572962.
JD549134 - Sequence 530158 from Patent EP1572962.
JD526905 - Sequence 507929 from Patent EP1572962.
JD136771 - Sequence 117795 from Patent EP1572962.
JD358659 - Sequence 339683 from Patent EP1572962.
LF345925 - JP 2014500723-A/153428: Polycomb-Associated Non-Coding RNAs.
JD063351 - Sequence 44375 from Patent EP1572962.
JD387003 - Sequence 368027 from Patent EP1572962.
JD532375 - Sequence 513399 from Patent EP1572962.
JD080903 - Sequence 61927 from Patent EP1572962.
JD421176 - Sequence 402200 from Patent EP1572962.
JD535307 - Sequence 516331 from Patent EP1572962.
JD131936 - Sequence 112960 from Patent EP1572962.
JD221796 - Sequence 202820 from Patent EP1572962.
LF345926 - JP 2014500723-A/153429: Polycomb-Associated Non-Coding RNAs.
JD085468 - Sequence 66492 from Patent EP1572962.
JD487624 - Sequence 468648 from Patent EP1572962.
JD179169 - Sequence 160193 from Patent EP1572962.
JD538980 - Sequence 520004 from Patent EP1572962.
JD390294 - Sequence 371318 from Patent EP1572962.
LF345927 - JP 2014500723-A/153430: Polycomb-Associated Non-Coding RNAs.
DQ570869 - Homo sapiens piRNA piR-30981, complete sequence.
JD235717 - Sequence 216741 from Patent EP1572962.
JD401060 - Sequence 382084 from Patent EP1572962.
JD221180 - Sequence 202204 from Patent EP1572962.
JD485506 - Sequence 466530 from Patent EP1572962.
JD565749 - Sequence 546773 from Patent EP1572962.
JD191510 - Sequence 172534 from Patent EP1572962.
JD270815 - Sequence 251839 from Patent EP1572962.
JD352769 - Sequence 333793 from Patent EP1572962.
LF345928 - JP 2014500723-A/153431: Polycomb-Associated Non-Coding RNAs.
JD142038 - Sequence 123062 from Patent EP1572962.
JD060052 - Sequence 41076 from Patent EP1572962.
JD432863 - Sequence 413887 from Patent EP1572962.
JD444517 - Sequence 425541 from Patent EP1572962.
JD455556 - Sequence 436580 from Patent EP1572962.
JD036937 - Sequence 17961 from Patent EP1572962.
JD307887 - Sequence 288911 from Patent EP1572962.
JD482079 - Sequence 463103 from Patent EP1572962.
JD339339 - Sequence 320363 from Patent EP1572962.
LF345929 - JP 2014500723-A/153432: Polycomb-Associated Non-Coding RNAs.
JD332823 - Sequence 313847 from Patent EP1572962.
LF345930 - JP 2014500723-A/153433: Polycomb-Associated Non-Coding RNAs.
JD288567 - Sequence 269591 from Patent EP1572962.
JD464318 - Sequence 445342 from Patent EP1572962.
DQ583045 - Homo sapiens piRNA piR-50157, complete sequence.
JD289218 - Sequence 270242 from Patent EP1572962.
LF345931 - JP 2014500723-A/153434: Polycomb-Associated Non-Coding RNAs.
JD483827 - Sequence 464851 from Patent EP1572962.
JD287704 - Sequence 268728 from Patent EP1572962.
JD394301 - Sequence 375325 from Patent EP1572962.
JD123763 - Sequence 104787 from Patent EP1572962.
JD055529 - Sequence 36553 from Patent EP1572962.
JD291099 - Sequence 272123 from Patent EP1572962.
JD241737 - Sequence 222761 from Patent EP1572962.
JD542009 - Sequence 523033 from Patent EP1572962.
JD243655 - Sequence 224679 from Patent EP1572962.
JD486644 - Sequence 467668 from Patent EP1572962.
JD426655 - Sequence 407679 from Patent EP1572962.
JD109545 - Sequence 90569 from Patent EP1572962.
JD345239 - Sequence 326263 from Patent EP1572962.
JD465231 - Sequence 446255 from Patent EP1572962.
JD195477 - Sequence 176501 from Patent EP1572962.
JD546649 - Sequence 527673 from Patent EP1572962.
JD499388 - Sequence 480412 from Patent EP1572962.
JD118866 - Sequence 99890 from Patent EP1572962.
JD436795 - Sequence 417819 from Patent EP1572962.
JD062424 - Sequence 43448 from Patent EP1572962.
JD506971 - Sequence 487995 from Patent EP1572962.
JD286448 - Sequence 267472 from Patent EP1572962.
JD208459 - Sequence 189483 from Patent EP1572962.
JD466992 - Sequence 448016 from Patent EP1572962.
JD261828 - Sequence 242852 from Patent EP1572962.
JD564834 - Sequence 545858 from Patent EP1572962.
JD385515 - Sequence 366539 from Patent EP1572962.
JD214940 - Sequence 195964 from Patent EP1572962.
JD378060 - Sequence 359084 from Patent EP1572962.
JD052684 - Sequence 33708 from Patent EP1572962.
JD364101 - Sequence 345125 from Patent EP1572962.
JD204228 - Sequence 185252 from Patent EP1572962.
DQ593885 - Homo sapiens piRNA piR-33997, complete sequence.
JD320818 - Sequence 301842 from Patent EP1572962.
JD276965 - Sequence 257989 from Patent EP1572962.
JD493711 - Sequence 474735 from Patent EP1572962.
JD107335 - Sequence 88359 from Patent EP1572962.
JD456573 - Sequence 437597 from Patent EP1572962.
JD220223 - Sequence 201247 from Patent EP1572962.
JD356191 - Sequence 337215 from Patent EP1572962.
JD170669 - Sequence 151693 from Patent EP1572962.
JD449404 - Sequence 430428 from Patent EP1572962.
JD286467 - Sequence 267491 from Patent EP1572962.
JD357449 - Sequence 338473 from Patent EP1572962.
JD218892 - Sequence 199916 from Patent EP1572962.
JD485843 - Sequence 466867 from Patent EP1572962.
JD088237 - Sequence 69261 from Patent EP1572962.
DQ580691 - Homo sapiens piRNA piR-48803, complete sequence.
JD476101 - Sequence 457125 from Patent EP1572962.
DQ586987 - Homo sapiens piRNA piR-54099, complete sequence.
DQ574090 - Homo sapiens piRNA piR-42202, complete sequence.
DQ584132 - Homo sapiens piRNA piR-51244, complete sequence.
MA581499 - JP 2018138019-A/153425: Polycomb-Associated Non-Coding RNAs.
MA581500 - JP 2018138019-A/153426: Polycomb-Associated Non-Coding RNAs.
MA581501 - JP 2018138019-A/153427: Polycomb-Associated Non-Coding RNAs.
MA581502 - JP 2018138019-A/153428: Polycomb-Associated Non-Coding RNAs.
MA581503 - JP 2018138019-A/153429: Polycomb-Associated Non-Coding RNAs.
MA581504 - JP 2018138019-A/153430: Polycomb-Associated Non-Coding RNAs.
MA581505 - JP 2018138019-A/153431: Polycomb-Associated Non-Coding RNAs.
MA581506 - JP 2018138019-A/153432: Polycomb-Associated Non-Coding RNAs.
MA581507 - JP 2018138019-A/153433: Polycomb-Associated Non-Coding RNAs.
MA581508 - JP 2018138019-A/153434: Polycomb-Associated Non-Coding RNAs.
MA446943 - JP 2018138019-A/18869: Polycomb-Associated Non-Coding RNAs.
JD437351 - Sequence 418375 from Patent EP1572962.

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

Protein Q5TCZ1 (Reactome details) participates in the following event(s):

R-HSA-8941234 SH3PXD2A binds ADAM12,ADAM15,ADAM19
R-HSA-8941237 Invadopodia formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: D3DR98, ENST00000369774.1, ENST00000369774.2, ENST00000369774.3, ENST00000369774.4, ENST00000369774.5, ENST00000369774.6, ENST00000369774.7, ENST00000369774.8, FISH, KIAA0418, NM_001394020, O43302, Q5TCZ1, Q5TCZ2, Q5TDQ8, SH3MD1, SPD2A_HUMAN, TKS5, uc318hvp.1, uc318hvp.2
UCSC ID: ENST00000369774.9_11
RefSeq Accession: NM_001394015.1
Protein: Q5TCZ1 (aka SPD2A_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.