Human Gene SDC4 (ENST00000372733.3_7) from GENCODE V47lift37
  Description: syndecan 4 (from RefSeq NM_002999.4)
Gencode Transcript: ENST00000372733.3_7
Gencode Gene: ENSG00000124145.6_9
Transcript (Including UTRs)
   Position: hg19 chr20:43,953,928-43,977,064 Size: 23,137 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr20:43,955,904-43,977,024 Size: 21,121 Coding Exon Count: 5 

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 (chr20:43,953,928-43,977,064)mRNA (may differ from genome)Protein (198 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDC4_HUMAN
DESCRIPTION: RecName: Full=Syndecan-4; Short=SYND4; AltName: Full=Amphiglycan; AltName: Full=Ryudocan core protein; Flags: Precursor;
FUNCTION: Cell surface proteoglycan that bears heparan sulfate.
SUBUNIT: Homodimer. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 (By similarity). Interacts with CDCP1 and SDCBP.
INTERACTION: P17252:PRKCA; NbExp=2; IntAct=EBI-3913237, EBI-1383528;
SUBCELLULAR LOCATION: Isoform 1: Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the ectodomain produces a soluble form (By similarity).
SUBCELLULAR LOCATION: Isoform 2: Secreted.
TISSUE SPECIFICITY: Expressed in epithelial and fibroblastic cells.
PTM: Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3.
SIMILARITY: Belongs to the syndecan proteoglycan family.

-  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

+  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: 136.36 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 2411.08 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 -11.2040-0.280 Picture PostScript Text
3' UTR -674.301976-0.341 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
IPR003585 - Neurexin-like
IPR001050 - Syndecan

Pfam Domains:
PF01034 - Syndecan domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1EJP - NMR 1EJQ - NMR 1OBY - X-ray MuPIT 1YBO - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P31431
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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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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001968 fibronectin binding
GO:0005080 protein kinase C binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0070053 thrombospondin receptor activity

Biological Process:
GO:0001523 retinoid metabolic process
GO:0001657 ureteric bud development
GO:0001843 neural tube closure
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006027 glycosaminoglycan catabolic process
GO:0007165 signal transduction
GO:0010762 regulation of fibroblast migration
GO:0016477 cell migration
GO:0042060 wound healing
GO:0042130 negative regulation of T cell proliferation
GO:0045860 positive regulation of protein kinase activity
GO:0050900 leukocyte migration
GO:0051496 positive regulation of stress fiber assembly
GO:0051894 positive regulation of focal adhesion assembly
GO:0060122 inner ear receptor stereocilium organization
GO:1903543 positive regulation of exosomal secretion
GO:1903553 positive regulation of extracellular exosome assembly

Cellular Component:
GO:0005576 extracellular region
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043034 costamere
GO:0043202 lysosomal lumen
GO:0045121 membrane raft
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  X67016 - H.sapiens mRNA for amphiglycan.
D13292 - Homo sapiens mRNA for ryudocan core protein, complete cds.
BC030805 - Homo sapiens syndecan 4, mRNA (cDNA clone MGC:22217 IMAGE:4690309), complete cds.
JD253759 - Sequence 234783 from Patent EP1572962.
JD124604 - Sequence 105628 from Patent EP1572962.
JD290746 - Sequence 271770 from Patent EP1572962.
JD426518 - Sequence 407542 from Patent EP1572962.
JD261556 - Sequence 242580 from Patent EP1572962.
JD493685 - Sequence 474709 from Patent EP1572962.
JD155473 - Sequence 136497 from Patent EP1572962.
JD122087 - Sequence 103111 from Patent EP1572962.
JD513294 - Sequence 494318 from Patent EP1572962.
JD491899 - Sequence 472923 from Patent EP1572962.
JD453572 - Sequence 434596 from Patent EP1572962.
JD487942 - Sequence 468966 from Patent EP1572962.
JD179884 - Sequence 160908 from Patent EP1572962.
JD234978 - Sequence 216002 from Patent EP1572962.
JD210201 - Sequence 191225 from Patent EP1572962.
JD503772 - Sequence 484796 from Patent EP1572962.
JD196259 - Sequence 177283 from Patent EP1572962.
JD146828 - Sequence 127852 from Patent EP1572962.
JD197435 - Sequence 178459 from Patent EP1572962.
JD556989 - Sequence 538013 from Patent EP1572962.
JD089665 - Sequence 70689 from Patent EP1572962.
JD182901 - Sequence 163925 from Patent EP1572962.
JD343913 - Sequence 324937 from Patent EP1572962.
JD266837 - Sequence 247861 from Patent EP1572962.
JD183212 - Sequence 164236 from Patent EP1572962.
JD360220 - Sequence 341244 from Patent EP1572962.
JD253614 - Sequence 234638 from Patent EP1572962.
JD476976 - Sequence 458000 from Patent EP1572962.
AK223243 - Homo sapiens mRNA for syndecan 4 precursor variant, clone: STM06491.
JD562425 - Sequence 543449 from Patent EP1572962.
AK303964 - Homo sapiens cDNA FLJ50358 complete cds, highly similar to Syndecan-4 precursor.
JD093808 - Sequence 74832 from Patent EP1572962.
JD232801 - Sequence 213825 from Patent EP1572962.
JD419508 - Sequence 400532 from Patent EP1572962.
JD296333 - Sequence 277357 from Patent EP1572962.
JD432868 - Sequence 413892 from Patent EP1572962.
JD296310 - Sequence 277334 from Patent EP1572962.
JD403708 - Sequence 384732 from Patent EP1572962.
JD287202 - Sequence 268226 from Patent EP1572962.
JD347017 - Sequence 328041 from Patent EP1572962.
JD375962 - Sequence 356986 from Patent EP1572962.
JD385269 - Sequence 366293 from Patent EP1572962.
JD307521 - Sequence 288545 from Patent EP1572962.
JD503788 - Sequence 484812 from Patent EP1572962.
JD291524 - Sequence 272548 from Patent EP1572962.
AK222695 - Homo sapiens mRNA for syndecan 4 precursor variant, clone: CBR08767.
JD551932 - Sequence 532956 from Patent EP1572962.
JD143832 - Sequence 124856 from Patent EP1572962.
JD363326 - Sequence 344350 from Patent EP1572962.
CR542074 - Homo sapiens full open reading frame cDNA clone RZPDo834F0836D for gene SDC4, syndecan 4 (amphiglycan, ryudocan); complete cds, incl. stopcodon.
AK312507 - Homo sapiens cDNA, FLJ92871, highly similar to Homo sapiens syndecan 4 (amphiglycan, ryudocan) (SDC4), mRNA.
KJ892117 - Synthetic construct Homo sapiens clone ccsbBroadEn_01511 SDC4 gene, encodes complete protein.
DQ890718 - Synthetic construct clone IMAGE:100003348; FLH165439.01X; RZPDo839C04160D syndecan 4 (amphiglycan, ryudocan) (SDC4) gene, encodes complete protein.
DQ893898 - Synthetic construct Homo sapiens clone IMAGE:100008358; FLH165435.01L; RZPDo839C04159D syndecan 4 (amphiglycan, ryudocan) (SDC4) gene, encodes complete protein.
CR542045 - Homo sapiens full open reading frame cDNA clone RZPDo834B0436D for gene SDC4, syndecan 4 (amphiglycan, ryudocan); complete cds, without stopcodon.
AB464261 - Synthetic construct DNA, clone: pF1KB6874, Homo sapiens SDC4 gene for syndecan 4, without stop codon, in Flexi system.

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

Protein P31431 (Reactome details) participates in the following event(s):

R-HSA-1878002 XYLTs transfer Xyl to core protein
R-HSA-1889955 B3GATs transfer GlcA to tetrasaccharide linker
R-HSA-2022919 EXT1:EXT2 transfers GlcNAc to the terminal GlcA residue
R-HSA-1889978 B3GALT6 transfers Gal to the tetrasaccharide linker
R-HSA-1889981 B4GALT7 transfers Gal group to xylosyl-unit of the tetrasaccharide linker
R-HSA-2076419 HS6STs sulfate GlcN at C6 in heparan sulfate/heparin
R-HSA-2022856 EXT1:EXT2 transfers GlcNAc to heparan
R-HSA-2022851 EXT1:EXT2 transfer GlcNAc to the heparan chain
R-HSA-2076371 GLCE epimerises more GlcA to IdoA as sulfate content rises
R-HSA-2076383 HS3ST1 sulfates GlcN at C3 in heparan sulfate
R-HSA-2076611 HS3STs sulfate GlcN at C3 in heparan sulfate
R-HSA-2076508 HS2ST1 sulfates IdoA at C2 in heparan sulfate
R-HSA-2024100 GLCE epimerises GlcA to IdoA
R-HSA-2022860 NDST1-4 can sulfate a glucosamine residue in heparan to form heparan sulfate (HS)
R-HSA-2076392 EXT1:EXT2 transfers GlcA to heparan
R-HSA-2022887 NDST1-4 N-deacetylates GlcNAc residues in heparan
R-HSA-1678694 Heparanase 2 (HPSE2) cleaves heparan sulfate from its proteoglycan (plasma membrane)
R-HSA-2731147 Syndecan-4 binds PI(4,5)P2
R-HSA-2731149 Syndecan-4 binds ACTN1
R-HSA-1667005 Heparanase (HPSE) cleaves heparan sulfate from its proteoglycan (lysosome)
R-HSA-2423785 CR:atREs binds apoE and HSPG
R-HSA-2429643 NREH hydrolyses atREs (HSPG:apoE) to atROL and FAs
R-HSA-2750187 Syndecan-4:PI(4,5)P2 binds PKC alpha:DAG
R-HSA-2684507 Syndecans 1, 2, 4, (3) bind FGF2
R-HSA-2731122 Syndecans 1, 2 & 4 bind VTN
R-HSA-2731078 Syndecans 2, (4) bind TGFB1
R-HSA-2404131 LRPs transport extracellular CR:atREs:HSPG:apoE to cytosol
R-HSA-8870732 PSGs bind proteoglycans and TGF-beta1
R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
R-HSA-2022928 HS-GAG biosynthesis
R-HSA-3656253 Defective EXT1 causes exostoses 1, TRPS2 and CHDS
R-HSA-3656237 Defective EXT2 causes exostoses 2
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
R-HSA-2024096 HS-GAG degradation
R-HSA-3000170 Syndecan interactions
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism
R-HSA-975634 Retinoid metabolism and transport
R-HSA-3000171 Non-integrin membrane-ECM interactions
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-3781865 Diseases of glycosylation
R-HSA-2187338 Visual phototransduction
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-1474244 Extracellular matrix organization
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1643685 Disease
R-HSA-418594 G alpha (i) signalling events
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-109582 Hemostasis
R-HSA-1430728 Metabolism
R-HSA-388396 GPCR downstream signalling
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000372733.1, ENST00000372733.2, NM_002999, O00773, P31431, Q16833, Q53FN9, Q6FGN3, SDC4 , SDC4_HUMAN, uc318ked.1, uc318ked.2
UCSC ID: ENST00000372733.3_7
RefSeq Accession: NM_002999.4
Protein: P31431 (aka SDC4_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.