Human Gene SDC2 (ENST00000302190.9_4) from GENCODE V47lift37
  Description: syndecan 2 (from RefSeq NM_002998.4)
Gencode Transcript: ENST00000302190.9_4
Gencode Gene: ENSG00000169439.12_13
Transcript (Including UTRs)
   Position: hg19 chr8:97,506,041-97,624,018 Size: 117,978 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr8:97,506,500-97,621,776 Size: 115,277 Coding Exon Count: 5 

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 (chr8:97,506,041-97,624,018)mRNA (may differ from genome)Protein (201 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDC2_HUMAN
DESCRIPTION: RecName: Full=Syndecan-2; Short=SYND2; AltName: Full=Fibroglycan; AltName: Full=Heparan sulfate proteoglycan core protein; Short=HSPG; AltName: CD_antigen=CD362; Flags: Precursor;
FUNCTION: Cell surface proteoglycan that bears heparan sulfate.
INTERACTION: O14936:CASK; NbExp=2; IntAct=EBI-1172957, EBI-1215506; P21359:NF1; NbExp=4; IntAct=EBI-1172957, EBI-1172917;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
PTM: O-glycosylated with core 1 or possibly core 8 glycans. Contains heparan sulfate.
SIMILARITY: Belongs to the syndecan proteoglycan family.
SEQUENCE CAUTION: Sequence=AAA52701.1; 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: SDC2
Diseases sorted by gene-association score: chronic cholangitis (6), trichorhinophalangeal syndrome, type i (6)

-  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: 93.72 RPKM in Thyroid
Total median expression: 1209.94 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 -202.90459-0.442 Picture PostScript Text
3' UTR -544.802242-0.243 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

ModBase Predicted Comparative 3D Structure on P34741
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 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:0030165 PDZ domain binding
GO:0042802 identical protein binding

Biological Process:
GO:0001523 retinoid metabolic process
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006027 glycosaminoglycan catabolic process
GO:0007399 nervous system development
GO:0008150 biological_process
GO:0016477 cell migration
GO:0030154 cell differentiation
GO:0043687 post-translational protein modification
GO:0044267 cellular protein metabolic process
GO:0048013 ephrin receptor signaling pathway
GO:0048813 dendrite morphogenesis
GO:0048814 regulation of dendrite morphogenesis
GO:0050900 leukocyte migration

Cellular Component:
GO:0005788 endoplasmic reticulum lumen
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031012 extracellular matrix
GO:0043202 lysosomal lumen


-  Descriptions from all associated GenBank mRNAs
  LF210242 - JP 2014500723-A/17745: Polycomb-Associated Non-Coding RNAs.
BC030133 - Homo sapiens syndecan 2, mRNA (cDNA clone MGC:14928 IMAGE:4138627), complete cds.
FW340052 - Screening.
J04621 - Human heparan sulfate proteoglycan (HSPG) core protein, 3' end.
LF214021 - JP 2014500723-A/21524: Polycomb-Associated Non-Coding RNAs.
AK298643 - Homo sapiens cDNA FLJ55238 complete cds, highly similar to Syndecan-2 precursor.
AK300067 - Homo sapiens cDNA FLJ50203 complete cds, highly similar to Syndecan-2 precursor.
AK130131 - Homo sapiens cDNA FLJ26621 fis, clone MPC01076, highly similar to Syndecan-2 precursor.
AK097839 - Homo sapiens cDNA FLJ40520 fis, clone TESTI2046786, highly similar to SYNDECAN-2 PRECURSOR.
AK025488 - Homo sapiens cDNA: FLJ21835 fis, clone HEP01602.
AK074530 - Homo sapiens cDNA FLJ90049 fis, clone HEMBA1002421, highly similar to Syndecan-2 precursor.
BC049836 - Homo sapiens syndecan 2, mRNA (cDNA clone MGC:51965 IMAGE:4931549), complete cds.
HQ257944 - Synthetic construct Homo sapiens clone IMAGE:100072253 syndecan 2 (SDC2) gene, encodes complete protein.
KJ897531 - Synthetic construct Homo sapiens clone ccsbBroadEn_06925 SDC2 gene, encodes complete protein.
MA449598 - JP 2018138019-A/21524: Polycomb-Associated Non-Coding RNAs.
MA445819 - JP 2018138019-A/17745: Polycomb-Associated Non-Coding RNAs.
LF336096 - JP 2014500723-A/143599: Polycomb-Associated Non-Coding RNAs.
JD125174 - Sequence 106198 from Patent EP1572962.
JD127812 - Sequence 108836 from Patent EP1572962.
LF336097 - JP 2014500723-A/143600: Polycomb-Associated Non-Coding RNAs.
MA571673 - JP 2018138019-A/143599: Polycomb-Associated Non-Coding RNAs.
MA571674 - JP 2018138019-A/143600: Polycomb-Associated Non-Coding RNAs.
AK298939 - Homo sapiens cDNA FLJ50836 complete cds, highly similar to Syndecan-2 precursor.
LF336105 - JP 2014500723-A/143608: Polycomb-Associated Non-Coding RNAs.
LF336106 - JP 2014500723-A/143609: Polycomb-Associated Non-Coding RNAs.
LF336107 - JP 2014500723-A/143610: Polycomb-Associated Non-Coding RNAs.
LF336108 - JP 2014500723-A/143611: Polycomb-Associated Non-Coding RNAs.
LF336109 - JP 2014500723-A/143612: Polycomb-Associated Non-Coding RNAs.
LF336110 - JP 2014500723-A/143613: Polycomb-Associated Non-Coding RNAs.
JD284011 - Sequence 265035 from Patent EP1572962.
JD040476 - Sequence 21500 from Patent EP1572962.
JD550035 - Sequence 531059 from Patent EP1572962.
JD563868 - Sequence 544892 from Patent EP1572962.
JD547229 - Sequence 528253 from Patent EP1572962.
JD296734 - Sequence 277758 from Patent EP1572962.
JD288583 - Sequence 269607 from Patent EP1572962.
JD285953 - Sequence 266977 from Patent EP1572962.
JD026624 - Sequence 7648 from Patent EP1572962.
JD028799 - Sequence 9823 from Patent EP1572962.
LF336111 - JP 2014500723-A/143614: Polycomb-Associated Non-Coding RNAs.
JD047010 - Sequence 28034 from Patent EP1572962.
MA571682 - JP 2018138019-A/143608: Polycomb-Associated Non-Coding RNAs.
MA571683 - JP 2018138019-A/143609: Polycomb-Associated Non-Coding RNAs.
MA571684 - JP 2018138019-A/143610: Polycomb-Associated Non-Coding RNAs.
MA571685 - JP 2018138019-A/143611: Polycomb-Associated Non-Coding RNAs.
MA571686 - JP 2018138019-A/143612: Polycomb-Associated Non-Coding RNAs.
MA571687 - JP 2018138019-A/143613: Polycomb-Associated Non-Coding RNAs.
MA571688 - JP 2018138019-A/143614: Polycomb-Associated Non-Coding RNAs.

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

Protein P34741 (Reactome details) participates in the following event(s):

R-HSA-4093332 p-EPHB phosphorylates SDC2
R-HSA-1878002 XYLTs transfer Xyl to core protein
R-HSA-1889955 B3GATs transfer GlcA to tetrasaccharide linker
R-HSA-1889978 B3GALT6 transfers Gal to the tetrasaccharide linker
R-HSA-2022919 EXT1:EXT2 transfers GlcNAc to the terminal GlcA residue
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-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-2022887 NDST1-4 N-deacetylates GlcNAc residues in heparan
R-HSA-2076392 EXT1:EXT2 transfers GlcA to heparan
R-HSA-2022851 EXT1:EXT2 transfer GlcNAc to the heparan chain
R-HSA-2076508 HS2ST1 sulfates IdoA at C2 in heparan sulfate
R-HSA-2022856 EXT1:EXT2 transfers GlcNAc to heparan
R-HSA-2022860 NDST1-4 can sulfate a glucosamine residue in heparan to form heparan sulfate (HS)
R-HSA-2024100 GLCE epimerises GlcA to IdoA
R-HSA-2750177 Syndecan-2 binds TRAPPC4
R-HSA-2750181 Syndecan-2 binds CASK
R-HSA-1678694 Heparanase 2 (HPSE2) cleaves heparan sulfate from its proteoglycan (plasma membrane)
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-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-8952289 FAM20C phosphorylates FAM20C substrates
R-HSA-2404131 LRPs transport extracellular CR:atREs:HSPG:apoE to cytosol
R-HSA-8870732 PSGs bind proteoglycans and TGF-beta1
R-HSA-3928662 EPHB-mediated forward signaling
R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
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-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
R-HSA-3000170 Syndecan interactions
R-HSA-2024096 HS-GAG degradation
R-HSA-2682334 EPH-Ephrin signaling
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-422475 Axon guidance
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275 Post-translational protein phosphorylation
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-1266738 Developmental Biology
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification
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: B3KQA3, ENST00000302190.1, ENST00000302190.2, ENST00000302190.3, ENST00000302190.4, ENST00000302190.5, ENST00000302190.6, ENST00000302190.7, ENST00000302190.8, HSPG1, NM_002998, P34741, Q6PIS6, Q9H6V1, SDC2_HUMAN, uc317mzc.1, uc317mzc.2
UCSC ID: ENST00000302190.9_4
RefSeq Accession: NM_002998.4
Protein: P34741 (aka SDC2_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.