Human Gene SDC1 (ENST00000254351.9_7) from GENCODE V47lift37
  Description: syndecan 1, transcript variant 2 (from RefSeq NM_002997.5)
Gencode Transcript: ENST00000254351.9_7
Gencode Gene: ENSG00000115884.11_11
Transcript (Including UTRs)
   Position: hg19 chr2:20,400,558-20,424,891 Size: 24,334 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr2:20,402,527-20,424,628 Size: 22,102 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 (chr2:20,400,558-20,424,891)mRNA (may differ from genome)Protein (310 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDC1_HUMAN
DESCRIPTION: RecName: Full=Syndecan-1; Short=SYND1; AltName: CD_antigen=CD138; Flags: Precursor;
FUNCTION: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.
SUBUNIT: Interacts with CDCP1.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the ectodomain produces a soluble form.
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.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/SDC1ID42223ch2p24.html";

-  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: SDC1
Diseases sorted by gene-association score: granulomatous endometritis (4), diverticulitis (3), multiple myeloma (3), mucinous bronchioloalveolar adenocarcinoma (3), diffuse large b-cell lymphoma (3), intestinal disease (3), ameloblastic carcinoma (3), lymphoplasmacyte-rich meningioma (2), mature b-cell neoplasm (2), extrahepatic bile duct adenocarcinoma (2), anterior spinal artery syndrome (1), miliaria (1), chronic dacryocystitis (1), solitary osseous plasmacytoma (1), diffuse infiltrative lymphocytosis syndrome (1), chronic inflammation of lacrimal passage (1), nominal aphasia (1), sed congenita (1), juvenile glaucoma (1)

-  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: 284.61 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 1544.15 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 -114.30263-0.435 Picture PostScript Text
3' UTR -785.701969-0.399 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 P18827
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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0042802 identical protein binding

Biological Process:
GO:0001523 retinoid metabolic process
GO:0001657 ureteric bud development
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006027 glycosaminoglycan catabolic process
GO:0006954 inflammatory response
GO:0009636 response to toxic substance
GO:0010033 response to organic substance
GO:0016477 cell migration
GO:0019221 cytokine-mediated signaling pathway
GO:0042060 wound healing
GO:0042476 odontogenesis
GO:0042542 response to hydrogen peroxide
GO:0048627 myoblast development
GO:0050900 leukocyte migration
GO:0051384 response to glucocorticoid
GO:0051591 response to cAMP
GO:0051592 response to calcium ion
GO:0055002 striated muscle cell development
GO:0060009 Sertoli cell development
GO:0060070 canonical Wnt signaling pathway
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:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032991 macromolecular complex
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF209473 - JP 2014500723-A/16976: Polycomb-Associated Non-Coding RNAs.
AJ551176 - Homo sapiens mRNA for Syndecan-1 (SDC-1 gene).
JD327577 - Sequence 308601 from Patent EP1572962.
JD439931 - Sequence 420955 from Patent EP1572962.
JD080508 - Sequence 61532 from Patent EP1572962.
JD223122 - Sequence 204146 from Patent EP1572962.
JD075688 - Sequence 56712 from Patent EP1572962.
JD111686 - Sequence 92710 from Patent EP1572962.
JD403210 - Sequence 384234 from Patent EP1572962.
JD100107 - Sequence 81131 from Patent EP1572962.
JD421738 - Sequence 402762 from Patent EP1572962.
JD264778 - Sequence 245802 from Patent EP1572962.
JD170729 - Sequence 151753 from Patent EP1572962.
JD305464 - Sequence 286488 from Patent EP1572962.
JD242450 - Sequence 223474 from Patent EP1572962.
JD141101 - Sequence 122125 from Patent EP1572962.
JD171884 - Sequence 152908 from Patent EP1572962.
AK222739 - Homo sapiens mRNA for syndecan 1 precursor variant, clone: DMC00339.
BC008765 - Homo sapiens syndecan 1, mRNA (cDNA clone MGC:1622 IMAGE:3347793), complete cds.
J05392 - Human syndecan mRNA, complete cds.
LF211508 - JP 2014500723-A/19011: Polycomb-Associated Non-Coding RNAs.
JD366078 - Sequence 347102 from Patent EP1572962.
JD551969 - Sequence 532993 from Patent EP1572962.
JD209606 - Sequence 190630 from Patent EP1572962.
JD071834 - Sequence 52858 from Patent EP1572962.
JD165459 - Sequence 146483 from Patent EP1572962.
JD232816 - Sequence 213840 from Patent EP1572962.
JD227202 - Sequence 208226 from Patent EP1572962.
JD134669 - Sequence 115693 from Patent EP1572962.
JD134668 - Sequence 115692 from Patent EP1572962.
JD204185 - Sequence 185209 from Patent EP1572962.
JD472904 - Sequence 453928 from Patent EP1572962.
LF380581 - JP 2014500723-A/188084: Polycomb-Associated Non-Coding RNAs.
LF328797 - JP 2014500723-A/136300: Polycomb-Associated Non-Coding RNAs.
AK299385 - Homo sapiens cDNA FLJ60837 complete cds, highly similar to Syndecan-1 precursor.
AK311409 - Homo sapiens cDNA, FLJ18451.
JD228877 - Sequence 209901 from Patent EP1572962.
JD562594 - Sequence 543618 from Patent EP1572962.
AK307313 - Homo sapiens cDNA, FLJ97261.
LF328796 - JP 2014500723-A/136299: Polycomb-Associated Non-Coding RNAs.
JD525050 - Sequence 506074 from Patent EP1572962.
JD325486 - Sequence 306510 from Patent EP1572962.
JD259456 - Sequence 240480 from Patent EP1572962.
JD516621 - Sequence 497645 from Patent EP1572962.
JD444222 - Sequence 425246 from Patent EP1572962.
JD419693 - Sequence 400717 from Patent EP1572962.
JD149019 - Sequence 130043 from Patent EP1572962.
JD104584 - Sequence 85608 from Patent EP1572962.
AK313974 - Homo sapiens cDNA, FLJ94623.
KJ897530 - Synthetic construct Homo sapiens clone ccsbBroadEn_06924 SDC1 gene, encodes complete protein.
DQ896595 - Synthetic construct Homo sapiens clone IMAGE:100011055; FLH195757.01L; RZPDo839F12151D syndecan 1 (SDC1) gene, encodes complete protein.
DQ893265 - Synthetic construct clone IMAGE:100005895; FLH195761.01X; RZPDo839F12152D syndecan 1 (SDC1) gene, encodes complete protein.
X60306 - H.sapiens RNA for syndecan.
AB464260 - Synthetic construct DNA, clone: pF1KB6425, Homo sapiens SDC1 gene for syndecan 1, without stop codon, in Flexi system.
CU679093 - Synthetic construct Homo sapiens gateway clone IMAGE:100018830 5' read SDC1 mRNA.
LF328795 - JP 2014500723-A/136298: Polycomb-Associated Non-Coding RNAs.
LF328794 - JP 2014500723-A/136297: Polycomb-Associated Non-Coding RNAs.
LF328793 - JP 2014500723-A/136296: Polycomb-Associated Non-Coding RNAs.
LF328792 - JP 2014500723-A/136295: Polycomb-Associated Non-Coding RNAs.
LF328791 - JP 2014500723-A/136294: Polycomb-Associated Non-Coding RNAs.
LF380580 - JP 2014500723-A/188083: Polycomb-Associated Non-Coding RNAs.
LF380579 - JP 2014500723-A/188082: Polycomb-Associated Non-Coding RNAs.
JD406472 - Sequence 387496 from Patent EP1572962.
JD141425 - Sequence 122449 from Patent EP1572962.
JD134719 - Sequence 115743 from Patent EP1572962.
JD283168 - Sequence 264192 from Patent EP1572962.
MA564374 - JP 2018138019-A/136300: Polycomb-Associated Non-Coding RNAs.
MA564373 - JP 2018138019-A/136299: Polycomb-Associated Non-Coding RNAs.
MA564372 - JP 2018138019-A/136298: Polycomb-Associated Non-Coding RNAs.
MA564371 - JP 2018138019-A/136297: Polycomb-Associated Non-Coding RNAs.
MA564370 - JP 2018138019-A/136296: Polycomb-Associated Non-Coding RNAs.
MA564369 - JP 2018138019-A/136295: Polycomb-Associated Non-Coding RNAs.
MA564368 - JP 2018138019-A/136294: Polycomb-Associated Non-Coding RNAs.
MA445050 - JP 2018138019-A/16976: Polycomb-Associated Non-Coding RNAs.
MA447085 - JP 2018138019-A/19011: Polycomb-Associated Non-Coding RNAs.
MA616158 - JP 2018138019-A/188084: Polycomb-Associated Non-Coding RNAs.
MA616157 - JP 2018138019-A/188083: Polycomb-Associated Non-Coding RNAs.
MA616156 - JP 2018138019-A/188082: Polycomb-Associated Non-Coding RNAs.

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

Protein P18827 (Reactome details) participates in the following event(s):

R-HSA-9009558 IL34 dimer binds SDC1
R-HSA-1678694 Heparanase 2 (HPSE2) cleaves heparan sulfate from its proteoglycan (plasma membrane)
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-1889981 B4GALT7 transfers Gal group to xylosyl-unit of the tetrasaccharide linker
R-HSA-1889978 B3GALT6 transfers Gal to 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-2076508 HS2ST1 sulfates IdoA at C2 in heparan sulfate
R-HSA-2024100 GLCE epimerises GlcA to IdoA
R-HSA-2022887 NDST1-4 N-deacetylates GlcNAc residues in heparan
R-HSA-2076392 EXT1:EXT2 transfers GlcA to heparan
R-HSA-2022860 NDST1-4 can sulfate a glucosamine residue in heparan to form heparan sulfate (HS)
R-HSA-2022851 EXT1:EXT2 transfer GlcNAc to the heparan chain
R-HSA-2022856 EXT1:EXT2 transfers GlcNAc to heparan
R-HSA-2076383 HS3ST1 sulfates GlcN at C3 in heparan sulfate
R-HSA-2076611 HS3STs sulfate GlcN at C3 in heparan sulfate
R-HSA-2681675 Syndecan-1 binds THBS1
R-HSA-2731074 Syndecan-1 binds Integrins alpha2beta1, (alpha6beta4)
R-HSA-2731075 Syndecan-1 binds collagen types I, III, V
R-HSA-2731081 Syndecan-1 binds Integrin alphaVBeta5
R-HSA-2731123 Syndecan-1 binds Integrin alphaVbeta3
R-NUL-2731130 Syndecan-1 binds integrin alphaVbeta5
R-HSA-2731141 Syndecan-1 binds fibronectin
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-2404131 LRPs transport extracellular CR:atREs:HSPG:apoE to cytosol
R-HSA-8870732 PSGs bind proteoglycans and TGF-beta1
R-HSA-449836 Other interleukin signaling
R-HSA-2024096 HS-GAG degradation
R-HSA-449147 Signaling by Interleukins
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-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
R-HSA-3000170 Syndecan interactions
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-1280215 Cytokine Signaling in Immune system
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-168256 Immune System
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: D6W523, ENST00000254351.1, ENST00000254351.2, ENST00000254351.3, ENST00000254351.4, ENST00000254351.5, ENST00000254351.6, ENST00000254351.7, ENST00000254351.8, NM_002997, P18827, Q53QV0, Q546D3, Q96HB7, SDC, SDC1 , SDC1_HUMAN, uc317fof.1, uc317fof.2
UCSC ID: ENST00000254351.9_7
RefSeq Accession: NM_002997.5
Protein: P18827 (aka SDC1_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.