Human Gene SDC2 (ENST00000522911.5) Description and Page Index
  Description: Cell surface proteoglycan (By similarity). (from UniProt E9PBI9)
RefSeq Summary (NM_002998): The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-2 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-2 expression has been detected in several different tumor types. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803615.250362.1, SRR1660809.243341.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000302190.9/ ENSP00000307046.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000522911.5
Gencode Gene: ENSG00000169439.12
Transcript (Including UTRs)
   Position: hg38 chr8:96,494,008-96,609,643 Size: 115,636 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr8:96,593,507-96,609,548 Size: 16,042 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:96,494,008-96,609,643)mRNA (may differ from genome)Protein (172 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCLynx
MGIPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: E9PBI9_HUMAN
DESCRIPTION: RecName: Full=Syndecan;
FUNCTION: Cell surface proteoglycan (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (By similarity).
SIMILARITY: Belongs to the syndecan proteoglycan family.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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

-  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 -11.1063-0.176 Picture PostScript Text
3' UTR -18.2095-0.192 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 E9PBI9
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF210242 - JP 2014500723-A/17745: Polycomb-Associated Non-Coding RNAs.
MA445819 - JP 2018138019-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.
MA449598 - JP 2018138019-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.
AK298939 - Homo sapiens cDNA FLJ50836 complete cds, highly similar to Syndecan-2 precursor.
JD125174 - Sequence 106198 from Patent EP1572962.
LF336105 - JP 2014500723-A/143608: Polycomb-Associated Non-Coding RNAs.
MA571682 - JP 2018138019-A/143608: Polycomb-Associated Non-Coding RNAs.
LF336106 - JP 2014500723-A/143609: Polycomb-Associated Non-Coding RNAs.
MA571683 - JP 2018138019-A/143609: Polycomb-Associated Non-Coding RNAs.
LF336107 - JP 2014500723-A/143610: Polycomb-Associated Non-Coding RNAs.
MA571684 - JP 2018138019-A/143610: Polycomb-Associated Non-Coding RNAs.
LF336108 - JP 2014500723-A/143611: Polycomb-Associated Non-Coding RNAs.
MA571685 - JP 2018138019-A/143611: Polycomb-Associated Non-Coding RNAs.
LF336109 - JP 2014500723-A/143612: Polycomb-Associated Non-Coding RNAs.
MA571686 - JP 2018138019-A/143612: Polycomb-Associated Non-Coding RNAs.
LF336110 - JP 2014500723-A/143613: Polycomb-Associated Non-Coding RNAs.
MA571687 - JP 2018138019-A/143613: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04512 - ECM-receptor interaction
hsa04514 - Cell adhesion molecules (CAMs)

-  Other Names for This Gene
  Alternate Gene Symbols: AK298643, E9PBI9, E9PBI9_HUMAN, uc064oup.1
UCSC ID: uc064oup.1
RefSeq Accession: NM_002998
Protein: E9PBI9

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.