Human Gene SDCBP (ENST00000260130.9_7) from GENCODE V47lift37
  Description: syndecan binding protein, transcript variant 1 (from RefSeq NM_005625.4)
Gencode Transcript: ENST00000260130.9_7
Gencode Gene: ENSG00000137575.12_12
Transcript (Including UTRs)
   Position: hg19 chr8:59,465,820-59,495,417 Size: 29,598 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr8:59,477,593-59,494,299 Size: 16,707 Coding Exon Count: 8 

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 (chr8:59,465,820-59,495,417)mRNA (may differ from genome)Protein (298 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDCB1_HUMAN
DESCRIPTION: RecName: Full=Syntenin-1; AltName: Full=Melanoma differentiation-associated protein 9; Short=MDA-9; AltName: Full=Pro-TGF-alpha cytoplasmic domain-interacting protein 18; Short=TACIP18; AltName: Full=Scaffold protein Pbp1; AltName: Full=Syndecan-binding protein 1;
FUNCTION: Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.
SUBUNIT: Monomer and homodimer (By similarity). Interacts with SDC1, SDC2, SDC3, SDC4, NRXN2, EPHA7, EPHB1, NF2 isoform 1, TGFA and IL5RA. Interacts with neurofascin, SDCBP2 and PTPRJ (By similarity).
SUBCELLULAR LOCATION: Cell junction, focal adhesion. Cell junction, adherens junction. Cell membrane; Peripheral membrane protein. Endoplasmic reticulum membrane; Peripheral membrane protein. Nucleus. Melanosome. Cytoplasm, cytosol. Cytoplasm, cytoskeleton. Note=Mainly membrane-associated. Localized to adherens junctions, focal adhesions and endoplasmic reticulum. Colocalized with actin stress fibers. Also found in the nucleus. Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
TISSUE SPECIFICITY: Widely expressed. Expressed in fetal kidney, liver, lung and brain. In adult highest expression in heart and placenta.
INDUCTION: By IFNG/IFN-gamma in melanoma cells.
PTM: Phosphorylated on tyrosine residues.
SIMILARITY: Contains 2 PDZ (DHR) domains.

-  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: SDCBP
Diseases sorted by gene-association score: melanoma (5), pontiac fever (3), asthenopia (2), disuse amblyopia (1)

-  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: 169.86 RPKM in Whole Blood
Total median expression: 2303.48 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 -14.8058-0.255 Picture PostScript Text
3' UTR -235.501118-0.211 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
IPR001478 - PDZ

Pfam Domains:
PF00595 - PDZ domain
PF13180 - PDZ domain
PF17820 - PDZ domain

SCOP Domains:
50156 - PDZ domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1N99 - X-ray MuPIT 1NTE - X-ray MuPIT 1OBX - X-ray MuPIT 1OBY - X-ray MuPIT 1OBZ - X-ray MuPIT 1R6J - X-ray MuPIT 1V1T - X-ray MuPIT 1W9E - X-ray MuPIT 1W9O - X-ray MuPIT 1W9Q - X-ray MuPIT 1YBO - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00560
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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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005109 frizzled binding
GO:0005137 interleukin-5 receptor binding
GO:0005515 protein binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0008093 cytoskeletal adaptor activity
GO:0008289 lipid binding
GO:0042802 identical protein binding
GO:0045545 syndecan binding
GO:0046982 protein heterodimerization activity
GO:0047485 protein N-terminus binding

Biological Process:
GO:0002091 negative regulation of receptor internalization
GO:0006612 protein targeting to membrane
GO:0006930 substrate-dependent cell migration, cell extension
GO:0007268 chemical synaptic transmission
GO:0007346 regulation of mitotic cell cycle
GO:0008284 positive regulation of cell proliferation
GO:0010718 positive regulation of epithelial to mesenchymal transition
GO:0010862 positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0030036 actin cytoskeleton organization
GO:0030307 positive regulation of cell growth
GO:0030335 positive regulation of cell migration
GO:0030511 positive regulation of transforming growth factor beta receptor signaling pathway
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0035556 intracellular signal transduction
GO:0042327 positive regulation of phosphorylation
GO:0043312 neutrophil degranulation
GO:0046330 positive regulation of JNK cascade
GO:0048013 ephrin receptor signaling pathway
GO:1903543 positive regulation of exosomal secretion
GO:1903553 positive regulation of extracellular exosome assembly

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005895 interleukin-5 receptor complex
GO:0005912 adherens junction
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030054 cell junction
GO:0031965 nuclear membrane
GO:0035578 azurophil granule lumen
GO:0042470 melanosome
GO:0043231 intracellular membrane-bounded organelle
GO:0045121 membrane raft
GO:0070062 extracellular exosome
GO:0072562 blood microparticle
GO:1903561 extracellular vesicle


-  Descriptions from all associated GenBank mRNAs
  AF000652 - Homo sapiens syntenin (sycl) mRNA, complete cds.
BC143915 - Homo sapiens syndecan binding protein (syntenin), mRNA (cDNA clone MGC:177450 IMAGE:9052433), complete cds.
BC113674 - Homo sapiens syndecan binding protein (syntenin), mRNA (cDNA clone MGC:142234 IMAGE:8322726), complete cds.
BC113676 - Homo sapiens syndecan binding protein (syntenin), mRNA (cDNA clone MGC:142236 IMAGE:8322728), complete cds.
BC143916 - Homo sapiens syndecan binding protein (syntenin), mRNA (cDNA clone MGC:177451 IMAGE:9052434), complete cds.
AK300647 - Homo sapiens cDNA FLJ54164 complete cds, highly similar to Syntenin-1.
AF006636 - Homo sapiens melanoma differentiation associated protein-9 (mda-9) mRNA, complete cds.
AK295198 - Homo sapiens cDNA FLJ55055 complete cds, moderately similar to Syntenin-1.
AK128645 - Homo sapiens cDNA FLJ46804 fis, clone TRACH3032570, highly similar to Homo sapiens syndecan binding protein (syntenin) (SDCBP).
AK312274 - Homo sapiens cDNA, FLJ92571, highly similar to Homo sapiens syndecan binding protein (syntenin) (SDCBP), mRNA.
AK298697 - Homo sapiens cDNA FLJ52996 complete cds, highly similar to Syntenin-1.
BC013254 - Homo sapiens syndecan binding protein (syntenin), mRNA (cDNA clone IMAGE:3853334).
U83463 - Human scaffold protein Pbp1 mRNA, complete cds.
AB464262 - Synthetic construct DNA, clone: pF1KB5554, Homo sapiens SDCBP gene for syndecan binding protein, without stop codon, in Flexi system.
HQ258156 - Synthetic construct Homo sapiens clone IMAGE:100072465 syndecan binding protein (syntenin) (SDCBP), transcript variant 2 (SDCBP) gene, encodes complete protein.
KJ892118 - Synthetic construct Homo sapiens clone ccsbBroadEn_01512 SDCBP gene, encodes complete protein.
JD182126 - Sequence 163150 from Patent EP1572962.
JD205688 - Sequence 186712 from Patent EP1572962.
JD064979 - Sequence 46003 from Patent EP1572962.
JD482235 - Sequence 463259 from Patent EP1572962.
JD040999 - Sequence 22023 from Patent EP1572962.
JD503500 - Sequence 484524 from Patent EP1572962.
JD268377 - Sequence 249401 from Patent EP1572962.
JD092443 - Sequence 73467 from Patent EP1572962.
JD269998 - Sequence 251022 from Patent EP1572962.
JD046930 - Sequence 27954 from Patent EP1572962.

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

Protein O00560 (Reactome details) participates in the following event(s):

R-HSA-373738 Neurofascin interacts with syntenin-1
R-HSA-4093329 EFNBs bind SDCBP
R-HSA-6798751 Exocytosis of azurophil granule lumen proteins
R-HSA-447043 Neurofascin interactions
R-HSA-3928664 Ephrin signaling
R-HSA-373760 L1CAM interactions
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-6798695 Neutrophil degranulation
R-HSA-422475 Axon guidance
R-HSA-168249 Innate Immune System
R-HSA-1266738 Developmental Biology
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5Q7, B4DUH3, B7ZLN2, ENST00000260130.1, ENST00000260130.2, ENST00000260130.3, ENST00000260130.4, ENST00000260130.5, ENST00000260130.6, ENST00000260130.7, ENST00000260130.8, MDA9, NM_005625, O00173, O00560, O43391, Q14CP2, SDCB1_HUMAN, SYCL, uc317giz.1, uc317giz.2
UCSC ID: ENST00000260130.9_7
RefSeq Accession: NM_005625.4
Protein: O00560 (aka SDCB1_HUMAN or SDB1_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.