Mouse Gene Sdc4 (ENSMUST00000017153.3) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus syndecan 4 (Sdc4), mRNA. (from RefSeq NM_011521)
Gencode Transcript: ENSMUST00000017153.3
Gencode Gene: ENSMUSG00000017009.3
Transcript (Including UTRs)
   Position: mm10 chr2:164,424,247-164,443,186 Size: 18,940 Total Exon Count: 5 Strand: -
Coding Region
   Position: mm10 chr2:164,426,086-164,443,164 Size: 17,079 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:164,424,247-164,443,186)mRNA (may differ from genome)Protein (198 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: Q3U5S6_MOUSE
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.

-  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           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.4022-0.109 Picture PostScript Text
3' UTR -625.001839-0.340 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 Q3U5S6
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

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

Biological Process:
GO:0001657 ureteric bud development
GO:0001843 neural tube closure
GO:0007165 signal transduction
GO:0010762 regulation of fibroblast migration
GO:0042060 wound healing
GO:0042130 negative regulation of T cell proliferation
GO:0045860 positive regulation of protein kinase activity
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:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043034 costamere
GO:0045121 membrane raft


-  Descriptions from all associated GenBank mRNAs
  D89571 - Mus musculus mRNA for ryudocan core protein, complete cds.
AK145805 - Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0047I02 product:syndecan 4, full insert sequence.
AK149784 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:G530016M04 product:syndecan 4, full insert sequence.
AK134326 - Mus musculus 13 days embryo male testis cDNA, RIKEN full-length enriched library, clone:6030423I07 product:syndecan 4, full insert sequence.
AK153445 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830162E12 product:syndecan 4, full insert sequence.
BC002312 - Mus musculus syndecan 4, mRNA (cDNA clone IMAGE:3592785), complete cds.
BC005679 - Mus musculus syndecan 4, mRNA (cDNA clone MGC:11456 IMAGE:3154160), complete cds.
AK164952 - Mus musculus 0 day neonate lung cDNA, RIKEN full-length enriched library, clone:E030048L13 product:syndecan 4, full insert sequence.
AK159215 - Mus musculus osteoclast-like cell cDNA, RIKEN full-length enriched library, clone:I420010F05 product:syndecan 4, full insert sequence.
AK158278 - Mus musculus adult inner ear cDNA, RIKEN full-length enriched library, clone:F930050A19 product:unclassifiable, full insert sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04512 - ECM-receptor interaction
mmu04514 - Cell adhesion molecules (CAMs)
mmu05144 - Malaria

-  Other Names for This Gene
  Alternate Gene Symbols: mCG_5428, NM_011521, Q3U5S6, Q3U5S6_MOUSE, uc008nuq.1, uc008nuq.2
UCSC ID: uc008nuq.2
RefSeq Accession: NM_011521
Protein: Q3U5S6 CCDS: CCDS17036.1

-  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.