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Aliases for SDCBP2 Gene

Aliases for SDCBP2 Gene

  • Syndecan Binding Protein 2 2 3 5
  • Syndecan Binding Protein (Syntenin) 2 2 3
  • Syntenin-2 2 3
  • SITAC18 3 4
  • Syndecan-Binding Protein 2 4
  • SITAC 3
  • ST-2 3

External Ids for SDCBP2 Gene

Previous GeneCards Identifiers for SDCBP2 Gene

  • GC20M001278
  • GC20M001285

Summaries for SDCBP2 Gene

Entrez Gene Summary for SDCBP2 Gene

  • The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2) and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. [provided by RefSeq, Sep 2011]

GeneCards Summary for SDCBP2 Gene

SDCBP2 (Syndecan Binding Protein 2) is a Protein Coding gene. GO annotations related to this gene include protein homodimerization activity and protein C-terminus binding. An important paralog of this gene is SDCBP.

Gene Wiki entry for SDCBP2 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDCBP2 Gene

Genomics for SDCBP2 Gene

Regulatory Elements for SDCBP2 Gene

Enhancers for SDCBP2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F001388 1.4 FANTOM5 ENCODE 22.1 -62.2 -62191 6.7 PKNOX1 MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC30A9 SDCBP2 ENSG00000229728 ACTG1P3 NSFL1C SIRPB2 SIRPB1 PSMF1 GC20M001393 GC20M001394
GH20F001815 1.6 FANTOM5 Ensembl ENCODE 17.3 -491.8 -491751 11.6 ELF3 YBX1 PLRG1 RAD21 ZNF48 ZNF335 ZNF366 CBX5 SCRT2 ZNF143 SDCBP2 SIRPB2 SIRPB1 SIRPA ZNF343 LOC100533711 NSFL1C ENSG00000230839 PIR58932
GH20F001415 1.7 FANTOM5 Ensembl ENCODE 14.2 -88.4 -88364 4.4 ARNT MLX ARID4B SIN3A DMAP1 ZNF143 FOS SP3 JUNB REST TBC1D20 ACTG1P3 SDCBP2 NSFL1C FKBP1A SIRPA LOC105372497 GC20M001435
GH20F001375 1.2 Ensembl ENCODE 19.6 -49.9 -49857 8.0 SIN3A ZNF121 ZNF366 SCRT2 FOS SMAD5 CEBPB JUNB SSRP1 KLF16 SDCBP2 SDCBP2-AS1 GC20M001393 GC20M001394 ENSG00000229728
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SDCBP2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SDCBP2 Gene

1,309,909 bp from pter
1,329,239 bp from pter
19,331 bases
Minus strand

Genomic View for SDCBP2 Gene

Genes around SDCBP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDCBP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDCBP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDCBP2 Gene

Proteins for SDCBP2 Gene

  • Protein details for SDCBP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • O95892
    • Q5W0X1
    • Q9BZ42
    • Q9H567
    • Q9NRY8

    Protein attributes for SDCBP2 Gene

    292 amino acids
    Molecular mass:
    31594 Da
    Quaternary structure:
    • Monomer and homodimer. Interacts with SDCBP (By similarity).
    • Sequence=AAH02727.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SDCBP2 Gene


neXtProt entry for SDCBP2 Gene

Post-translational modifications for SDCBP2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SDCBP2 Gene

No data available for DME Specific Peptides for SDCBP2 Gene

Domains & Families for SDCBP2 Gene

Gene Families for SDCBP2 Gene

Protein Domains for SDCBP2 Gene


Suggested Antigen Peptide Sequences for SDCBP2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 2 PDZ (DHR) domains.
  • Contains 2 PDZ (DHR) domains.
genes like me logo Genes that share domains with SDCBP2: view

Function for SDCBP2 Gene

Gene Ontology (GO) - Molecular Function for SDCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0008022 protein C-terminus binding IPI 11152476
GO:0042802 identical protein binding IPI 25416956
GO:0042803 protein homodimerization activity IDA 11152476
GO:0046982 protein heterodimerization activity IPI 11152476
genes like me logo Genes that share ontologies with SDCBP2: view
genes like me logo Genes that share phenotypes with SDCBP2: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SDCBP2 Gene

Localization for SDCBP2 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SDCBP2 gene
Compartment Confidence
extracellular 5
plasma membrane 4
nucleus 3
cytosol 3

Gene Ontology (GO) - Cellular Components for SDCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 11152476
GO:0005886 plasma membrane IC 11152476
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with SDCBP2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SDCBP2 Gene

Pathways & Interactions for SDCBP2 Gene

SuperPathways for SDCBP2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SDCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development NAS 11152476
GO:0035556 intracellular signal transduction NAS 11152476
GO:0046907 intracellular transport NAS 11152476
genes like me logo Genes that share ontologies with SDCBP2: view

No data available for Pathways by source and SIGNOR curated interactions for SDCBP2 Gene

Drugs & Compounds for SDCBP2 Gene

(1) Additional Compounds for SDCBP2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SDCBP2: view

Transcripts for SDCBP2 Gene

Unigene Clusters for SDCBP2 Gene

Syndecan binding protein (syntenin) 2:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDCBP2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b
SP1: - - - - - - -
SP2: - - - - - -
SP3: - -
SP4: - - - - -
SP5: - - -
SP6: - - - - - -
SP8: - -

Relevant External Links for SDCBP2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SDCBP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SDCBP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SDCBP2 Gene

This gene is overexpressed in Esophagus - Mucosa (x7.8) and Colon - Transverse (x6.2).

Protein differential expression in normal tissues from HIPED for SDCBP2 Gene

This gene is overexpressed in Cervix (50.7) and Skin (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SDCBP2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SDCBP2 Gene:


SOURCE GeneReport for Unigene cluster for SDCBP2 Gene:

genes like me logo Genes that share expression patterns with SDCBP2: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SDCBP2 Gene

Orthologs for SDCBP2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SDCBP2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SDCBP2 34 35
  • 98.63 (n)
(Bos Taurus)
Mammalia SDCBP2 34 35
  • 86.16 (n)
(Canis familiaris)
Mammalia SDCBP2 34 35
  • 84.03 (n)
(Rattus norvegicus)
Mammalia Sdcbp2 34
  • 81.28 (n)
(Mus musculus)
Mammalia Sdcbp2 34 16 35
  • 80.59 (n)
(Monodelphis domestica)
Mammalia SDCBP2 35
  • 76 (a)
(Gallus gallus)
Aves LOC100859439 34
  • 72.11 (n)
  • 65 (a)
(Anolis carolinensis)
Reptilia SDCBP2 35
  • 56 (a)
(Danio rerio)
Actinopterygii sdcbp2 35
  • 57 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6469 35
  • 47 (a)
Species where no ortholog for SDCBP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SDCBP2 Gene

Gene Tree for SDCBP2 (if available)
Gene Tree for SDCBP2 (if available)

Paralogs for SDCBP2 Gene

Paralogs for SDCBP2 Gene

(1) SIMAP similar genes for SDCBP2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SDCBP2: view

Variants for SDCBP2 Gene

Sequence variations from dbSNP and Humsavar for SDCBP2 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs35367003 A colorectal cancer sample 1,312,497(-) CCAGC(A/G)GACTG nc-transcript-variant, reference, missense
rs1018575 -- 1,317,753(-) AGCCG(A/G)TGAAA intron-variant
rs1018576 -- 1,317,613(-) ACAAG(C/G)ATGAG intron-variant
rs1018577 -- 1,317,583(-) AGAAC(G/T)GATGG intron-variant
rs1048621 -- 1,312,402(-) CGGCC(C/T)GCAAC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SDCBP2 Gene

Variant ID Type Subtype PubMed ID
esv2664030 CNV deletion 23128226
esv3644976 CNV loss 21293372
nsv1057097 CNV gain 25217958
nsv1071671 CNV deletion 25765185
nsv1138912 CNV deletion 24896259
nsv518295 CNV loss 19592680

Variation tolerance for SDCBP2 Gene

Residual Variation Intolerance Score: 95% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.87; 94.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SDCBP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDCBP2 Gene

Disorders for SDCBP2 Gene

Relevant External Links for SDCBP2

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SDCBP2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SDCBP2 Gene

Publications for SDCBP2 Gene

  1. The neural cell recognition molecule neurofascin interacts with syntenin-1 but not with syntenin-2, both of which reveal self- associating activity. (PMID: 11152476) Koroll M. … Volkmer H. (J. Biol. Chem. 2001) 2 3 4 22 64
  2. The prevalence and significance of PDZ domain-phosphoinositide interactions. (PMID: 16884951) Zimmermann P. (Biochim. Biophys. Acta 2006) 3 22 64
  3. Nuclear speckles and nucleoli targeting by PIP2-PDZ domain interactions. (PMID: 15961997) Mortier E. … Zimmermann P. (EMBO J. 2005) 3 22 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 3 4 64

Products for SDCBP2 Gene

Sources for SDCBP2 Gene

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