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Aliases & Descriptions for SDC1
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc
, and/or 7 Ensembl ,
8 miRBase )About This Section
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Aliases CD138 1 , 2 OTTHUMP00000115942 2 SDC 2 , 3 SYND1 1 , 2 , 3 syndecan 1 , 2
Descriptions CD138 antigen 2 , 3 heparan sulfate proteoglycan fibroblast growth factor receptor 2 syndecan 1 2 syndecan proteoglycan 1 2
Search outside databases for aliases for SDC1 genePrevious GC identifers: GC02M020292 GC02M020469 GC02M020368 GC02M020385 GC02M020322
Summaries for SDC1 (According to Entrez Gene ,
Wikipedia's
Gene Wiki ,
UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
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EntrezGene summary for SDC1 : The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is amember 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-1tat protein. The syndecan-1 protein functions as an integral membrane protein and participates incell proliferation, cell migration and cell-matrix interactions via its receptor for extracellularmatrix proteins. Altered syndecan-1 expression has been detected in several different tumor types.While several transcript variants may exist for this gene, the full-length natures of only twohave been described to date. These two represent the major variants of this gene and encode thesame protein. [provided by RefSeq] UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827 Function : Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate andthat links the cytoskeleton to the interstitial matrix
Gene Wiki entry for SDC1 (Syndecan_1)
Genomic Location for SDC1
(According to
GeneLoc and/or
HGNC , and/or
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and/or miRBase ,
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Transcription factor binding sites according to
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Genomic View : UCSC Golden Path with GeneCards custom track Transcription factor binding sites upstream to the SDC1 gene Entrez Gene cytogenetic band: 2p24.1 Ensembl cytogenetic band: 2p24.1 HGNC cytogenetic band: 2p24.1 SDC1 Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different) GeneLoc gene densities for chromosome 2 GeneLoc Exon Structure
GeneLoc location for GC02M020264:
(about GC identifiers )
Start:
20,264,039 bp from pter
End:
20,288,675 bp from pter
Size:
24,637 bases
Orientation:
minus strand
RefSeq DNA sequence: NC_000002.10 NT_015926.14 Proteins for SDC1
(According to
1 UniProtKB ,
and/or Ensembl ,
Phosphorylation sites according to 2 Phosphosite ,
RefSeq according to NCBI ,
PDB rendering according to OCA and/or Proteopedia ,
Recombinant Proteins
from Invitrogen ,
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Sigma-Aldrich ,
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Abnova ,
OriGene and/or,
Abcam ,
Biochemical Assays by
Invitrogen ,
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R&D Systems ,
Cell Signaling Technology , and/or
Enzo Life Sciences ,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene ,
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Millipore ,
Sigma-Aldrich ,
R&D Systems ,
Cell Signaling Technology ,
Abcam ,
Abnova , and/or
Novus Biologicals )
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UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827 (See
protein sequence )Recommended Name: Syndecan-1 precursor Size : 310 amino acids; 32462 Da
Subunit : Interacts with CDCP1
Subcellular location : Membrane; Single-pass type I membrane protein
Secondary accessions : Q53QV0 Q546D3 Q96HB7
Post-translational modifications:
View phosphorylation sites using PhosphoSite 2
REFSEQ proteins (2 alternative transcripts):
NP_001006947.1 NP_002988.3 ENSEMBL proteins: ENSP00000254351 ENSP00000370542 ENSP00000384613 Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 2 Gene Ontology (GO) cellular component terms (links to tree view) :
About this table Antibodies for SDC1: Assays for SDC1:
Protein
Domains/ Families for SDC1(According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
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Graphical View of Domain Structure for InterPro Entry P18827 ProtoNet protein and cluster: P18827
2 Blocks protein families : IPB001050 Syndecan IPB003585 Neurexin/syndecan/glycophorin C UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827 Similarity : Belongs to the syndecan proteoglycan family
Gene Function for SDC1
(According to MGI Jun 06 2009, UniProtKB ,
IUBMB ,and/or Genatlas ,
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Cell-based Assays from Millipore ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2 ): NM_002997 Applied Biosystems Silencer ® siRNAs for SDC1 Sigma-Aldrich siRNA and siRNA Panels for SDC1 Sigma-Aldrich shRNA for SDC1 Explore Sigma-Aldrich super-pooled esiRNAs                OriGene GFP tagged cDNA clones in CMV expression vector (see all 2 ): NM_001006946                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 2 ): NM_001006946                                  untagged cDNA clones in CMV expression vector (see all 2 ): NM_001006946  Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_002997 UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827 Function : Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate andthat links the cytoskeleton to the interstitial matrix
Genatlas biochemistry entry for SDC1 :syndecan,integral membrane heparan sulfate proteoglycan,matrix receptor,expressed in distinctstages of differentiation of normal lymphoid cells (pre-B) and in B chronic lymphoblastic leukemia(BCLL) in plamocytoid lymphomas and myelomas,underexpressed in squamous cell carcinoma of the headand neck
7 MGI mutant phenotypes (inferred from 2 alleles ) (MGI details for Sdc1) :2 Gene Ontology (GO) molecular function terms (links to tree view) :
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Pathways & Interactions for SDC1
(Pathways according to Invitrogen
(maps by GeneGo ),
Millipore ,
Cell Signaling Technology ,
Sigma-Aldrich ,
KEGG
and/or UniProtKB ,
Sets of similar genes according to GeneDecks ,
Proteins Network according to
SABiosciences ,
Interactions according to 1 UniProtKB ,
2 MINT , and/or
3 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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1 Sigma-Aldrich "Your Favorite Gene" Pathway for SDC1 (Your Favorite Gene powered by Ingenuity) Gene Network CentralTM Interacting Genes and Proteins Network for SDC1 5/122 Interacting proteins for SDC1 (ENSP00000370542 3 P18827 2 ) via UniProtKB, MINT, and/or STRING (see all 122
)About this table
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Novoseek and Drugs according to
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Browse Tocris compounds for SDC1
Transcripts for SDC1(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank , RefSeq according to Entrez Gene ,
DOTS (version 10), and/or
AceView ,
non coding RNAs according to
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ESTs according to GeneTide ,
exon structure from GeneLoc ,
alternative splicing isoforms according to ASD and/or
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2 ): NM_002997 Sigma-Aldrich siRNA and siRNA Panels for SDC1 Sigma-Aldrich shRNA for SDC1 Explore Sigma-Aldrich super-pooled esiRNAs
Applied Biosystems Silencer ® siRNAs: NM_001006946 NM_002997
REFSEQ mRNAs for SDC1 gene (2 alternative transcripts): NM_001006946.1 NM_002997.4
Applied Biosystems TaqMan ® Gene Expression Assays: NM_001006946 NM_002997
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2 ): NM_001006946                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 2 ): NM_001006946                                  untagged cDNA clones in CMV expression vector (see all 2 ): NM_001006946  
Additional cDNA sequence: AJ551176.1 AK222739.1 AK299385.1 AK307313.1 AK313974.1 BC008765.2 CR592915.1 CR600772.1 J05392.1 X60306.1
20 DOTS entries : DT.449752 DT.100727565 DT.100880464 DT.100880458 DT.100880469 DT.95269333 DT.100038526 DT.100880463 DT.91745597 DT.95269365 DT.120996810 DT.85105565 DT.100774836 DT.120996817 DT.120996820 DT.120996839 DT.92455346 DT.95269334 DT.100880451 DT.120996874
24/627 AceView cDNA sequences (see all 627
):BM750537 CB243800 BM758226 BM560731 BM772526 BM757645 BM758625 CB215596 BM756752 BI759105 BM772508 BU727183 BM791621 CB162558 BM755910 BM766329 BM756862 BU622242 CA426894 BQ896930 BE078507 BM998847 BM974052 CB306068
highest scoring ESTs for SDC1 :AA001108 AA001637 AA010621 AA010622 AA031960 AA032042 AA057472 AA074511 AA224261 AA299561
Unigene Cluster for SDC1: Syndecan 1 Hs.224607 [show with all ESTs ] Unigene Representative Sequence: NM_001006946 GeneLoc Exon Structure 5/7 Alternative Splicing Database (ASD) splice patterns (SP) for SDC1 (see all 7
) ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g ^ 7 ^ 8a · 8b SP1 :         -   -   -                         SP2 :   -   -     -   -   -                         SP3 :         -   -   -               -   -   -   -     SP4 :         -   -                           SP5 :         -   -   -     -                    
About this scheme ECgene alternative splicing isoforms for SDC1 3 Ensembl transcripts including schematic representations : ENST00000254351
ENST00000381150
ENST00000403076
Expression for SDC1
(Experimental results according to
1 GeneNote
and GNF BioGPS ,
probe sets-to-genes annotations according to
2 GeneAnnot ,
3 GeneTide ,
Sets of similar genes according to GeneDecks ,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP ,
plus additional links to
SOURCE , and/or
GNF
BioGPS , and/or
EXPOLDB , and/or
UniProtKB ,
Expression Assays from
Applied Biosystems
)
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SDC1 expression in normal and diseased human tissues Applied Biosystems TaqMan ® Gene Expression Assays for SDC1 1 / 2 / 3
5 probe-sets matching SDC1 gene Data from
(Publications) and GNF BioGPS About these images About these images CGAP SAGE TAG: AGCGACAAACSOURCE GeneReport for Unigene cluster: Hs.224607 Expression variation in blood from EXPOLDB for SDC1
Orthologs for SDC1
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
and/or
5 MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase ,
Gene Trees according to Ensembl )
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Orthologs for SDC1 gene from 5/7 species (see all 7
)
About this table Species with no ortholog for SDC1 ENSEMBL Gene Tree for SDC1 Paralogs for SDC1 (Paralogs according to 1 HomoloGene and 2 Ensembl , Pseudogenes according to 3 Pseudogene.org )About This Section
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Paralogs for SDC1 gene SDC4 2 SDC3 2 SDC2 2
SNPs/Variants for SDC1 (According to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE , and
UniProtKB ,
Linkage Disequilibrium by HapMap ,
Genotyping Reagents from
Applied Biosystems )
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HapMap Linkage Disequilibrium images for SDC1 (up to first 250kb)
Disorders & Mutations for SDC1
(in which this Gene is Involved, According to
OMIM, UniProtKB ,
Novoseek , PharmGKB ,
Genatlas , GeneTests ,
Blood group antigen gene mutations by BGMUT ,
HGMD, GAD ,
HuGE Navigator ,
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and/or TGDB .)
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OMIM: 186355 3 Novoseek disease relationships for SDC1 gene
About this table 1 PharmGKB disease relationship for SDC1 gene About this table Human Genome Epidemiology Navigator: SDC1 (1 document)
Medical News for SDC1 (Possibly Related Articles in
Doctor's Guide )
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--
Publications for SDC1 (in
PubMed .
Associations of this gene to articles via
1 Novoseek ,
2 HGNC ,
3 Entrez Gene ,
4 UniProtKB/Swiss-Prot ,
5 UniProtKB/TrEMBL ,
6 GAD , and/or
7 PharmGKB )
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10/130 PubMed articles for SDC1 gene (see all 130
): Adhesion signaling by a novel mitotic substrate of src kinases. (PubMed id 16007225) 3, 4 Bhatt A.S.... Moasser M.M. (2005) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334) 3, 4 Gerhard D.S....Malek J. (2004) The mapping and visual ordering of the human syndecan-1 and N-myc genes near the telomeric region of chromosome 2p. (PubMed id 9050911) 3, 4 Kaukonen J.... Palotie A. (1997) Differential expression of cell surface heparan sulfate proteoglycans in human mammary epithelial cells and lung fibroblasts. (PubMed id 1339431) 3, 4 Lories V.... David G. (1992) Sequence of human syndecan indicates a novel gene family of integral membrane proteoglycans. (PubMed id 2324102) 3, 4 Mali M.... Jalkanen M. (1990) Induction of syndecan-1 expression in stromal fibroblasts promotes proliferation of human breast cancer cells. (PubMed id 14744776) 1, 3 Maeda T....Friedl A. (2004) Syndecan-1 regulates alphavbeta3 and alphavbeta5 integrin activation during angiogenesis and is blocked by synstatin, a novel peptide inhibitor. (PubMed id 19255147) 1, 3 Beauvais D.M....Rapraeger A.C. (2009) Membrane type 1 matrix metalloproteinase-mediated stromal syndecan-1 shedding stimulates breast carcinoma cell proliferation. (PubMed id 19010933) 1, 3 Su G....Friedl A. (2008) Evaluation of the association with cervical cancer of polymorphisms in syndecan-1, a heparan sulfate proteoglycan involved with viral cell entry. (PubMed id 18006945) 1, 3 Yu K.J....Hildesheim A. (2007) Syndecan-1 expression is regulated in an isoform-specific manner by the farnesoid-X receptor. (PubMed id 12660231) 1, 3 Anisfeld A.M....Edwards P.A. (2003)
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Genome Databases showing SDC1
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
and/or
H-InvDB )
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Other Databases showing SDC1
(According to HUGE )
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Specialized Databases showing SDC1 (According to ATLAS , HORDE , IMGT , MTDB, LEIDEN , UniProtKB/Swiss-Prot , and/or UniProtKB/TrEMBL ,Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot )About This Section
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-- Services for SDC1 (Reagents available from Applied Biosystems , Antibodies and assays by Cell
Signaling Technology , Abcam , Novus Biologicals ,Sigma-Aldrich , R&D Systems , Millipore , Abnova , and/or Invitrogen , Clones available from OriGene ,and/or Invitrogen , Drugs and/or compounds by Sigma-Aldrich , Enzo Life Sciences , and/or Tocris Bioscience )About This Section
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