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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
  • SITAC 3 4
  • Syndecan-Binding Protein 2 4
  • Similar To TACIP18 4
  • ST-2 3
  • ST2 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. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and protein C-terminus binding. An important paralog of this gene is SDCBP.

UniProtKB/Swiss-Prot for SDCBP2 Gene

  • Binds phosphatidylinositol 4,5-bisphosphate (PIP2). May play a role in the organization of nuclear PIP2, cell division and cell survival (PubMed:15961997).

Gene Wiki entry for SDCBP2 Gene

Additional gene information for SDCBP2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDCBP2 Gene

Genomics for SDCBP2 Gene

GeneHancer (GH) Regulatory Elements for SDCBP2 Gene

Promoters and enhancers for SDCBP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I001321 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 587 +2.1 2108 11.1 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 SDCBP2 SDCBP2-AS1 FKBP1A ENSG00000229728 SIRPB1 SIRPG ENSG00000280162 FKBP1A-SDCBP2 ENSG00000274322
GH20I001312 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 550.4 +15.6 15637 1.3 ELF3 RB1 ARID4B SIN3A ZNF2 THRB ZNF48 RAD21 ZNF335 ZNF207 SDCBP2 ENSG00000280162 PIR62557 FKBP1A-SDCBP2
GH20I001388 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 22.2 -62.2 -62190 6.7 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC30A9 MIR6869 FKBP1A-SDCBP2 FKBP1A ENSG00000274322 GC20M001394 GC20M001393 SDCBP2 ENSG00000229728 NSFL1C SIRPB2
GH20I001464 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 18 -138.8 -138753 6.7 MLX IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC SSRP1 NSFL1C SIRPB2 SDCBP2 SNPH FKBP1A GC20M001435
GH20I001815 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 17.3 -491.7 -491714 11.5 JUN MAX YBX1 PLRG1 ZNF48 ZFHX2 ZNF366 POLR2A PRDM10 FOSL2 SDCBP2 SIRPB2 SIRPB1 SIRPA ZNF343 LOC100533711 NSFL1C ENSG00000230839 PIR58932
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SDCBP2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SDCBP2 gene promoter:

Genomic Locations for SDCBP2 Gene

Genomic Locations for SDCBP2 Gene
chr20:1,309,909-1,329,239
(GRCh38/hg38)
Size:
19,331 bases
Orientation:
Minus strand
chr20:1,290,553-1,309,883
(GRCh37/hg19)

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:
    Q9H190-SDCB2_HUMAN
    Recommended name:
    Syntenin-2
    Protein Accession:
    Q9H190
    Secondary Accessions:
    • O95892
    • Q5W0X1
    • Q9BZ42
    • Q9H567
    • Q9NRY8

    Protein attributes for SDCBP2 Gene

    Size:
    292 amino acids
    Molecular mass:
    31594 Da
    Quaternary structure:
    • Monomer and homodimer (PubMed:11152476, PubMed:23300061). Interacts with SDCBP (PubMed:11152476). Interacts with TM4SF1 (PubMed:11102519).
    SequenceCaution:
    • Sequence=AAH02727.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SDCBP2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SDCBP2 Gene

Post-translational modifications for SDCBP2 Gene

No Post-translational modifications

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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SDCBP2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SDCBP2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H190

UniProtKB/Swiss-Prot:

SDCB2_HUMAN :
  • Binds phosphatidylinositol 4,5-bisphosphate (PIP2) via its two PDZ domains. These domains target SDCBP2 to the plasma membranes and nucleoli, two PIP2-rich regions.
Domain:
  • Binds phosphatidylinositol 4,5-bisphosphate (PIP2) via its two PDZ domains. These domains target SDCBP2 to the plasma membranes and nucleoli, two PIP2-rich regions.
genes like me logo Genes that share domains with SDCBP2: view

Function for SDCBP2 Gene

Molecular function for SDCBP2 Gene

UniProtKB/Swiss-Prot Function:
Binds phosphatidylinositol 4,5-bisphosphate (PIP2). May play a role in the organization of nuclear PIP2, cell division and cell survival (PubMed:15961997).
UniProtKB/Swiss-Prot Induction:
Down-regulated by HPV8 E6 papillomavirus (HPV) oncoprotein (at protein level).

Phenotypes From GWAS Catalog for SDCBP2 Gene

Gene Ontology (GO) - Molecular Function for SDCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11102519
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding IDA 15961997
GO:0008022 protein C-terminus binding IPI 11152476
GO:0008289 lipid binding IEA --
GO:0042802 identical protein binding IPI 25416956
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

CRISPR Products

miRNA for SDCBP2 Gene

miRTarBase miRNAs that target SDCBP2

Inhibitory RNA Products

Clone Products

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

Localization for SDCBP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDCBP2 Gene

Cytoplasm. Nucleus, nucleolus. Nucleus, nucleoplasm. Cell membrane. Nucleus speckle. Note=Associates with intracellular membranes and enriched in the apical region of the cell and in intracellular compartments (PubMed:11102519). Colocalizes with TM4SF1 in the apical region of the cell (PubMed:11102519). Predominantly targeted to nuclear PIP2 pools. Shuttles between several subcellular compartments (PubMed:15961997). PIP2 plays an important role in the distribution of SDCBP2 (PubMed:23300061). {ECO:0000269 PubMed:11102519, ECO:0000269 PubMed:15961997, ECO:0000269 PubMed:23300061}.

Subcellular locations from

COMPARTMENTS
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
plasma membrane 5
extracellular 5
nucleus 5
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IEA,IDA 15961997
GO:0005737 cytoplasm IEA,IDA 11152476
GO:0005886 plasma membrane IEA,IDA 15961997
genes like me logo Genes that share ontologies with SDCBP2: view

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:0008283 cell proliferation IMP 15961997
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:

CRISPR Products

Inhibitory RNA Products

Clone 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: - - - - - -
SP7:
SP8: - -
SP9:

Relevant External Links for SDCBP2 Gene

GeneLoc Exon Structure for
SDCBP2
ECgene alternative splicing isoforms for
SDCBP2

Expression for SDCBP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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:

SDCBP2

SOURCE GeneReport for Unigene cluster for SDCBP2 Gene:

Hs.657015

mRNA Expression by UniProt/SwissProt for SDCBP2 Gene:

Q9H190-SDCB2_HUMAN
Tissue specificity: Preferentially expressed in cells of the digestive tract (PubMed:11102519). Low expression in skeletal muscle and kidney (PubMed:11102519). Detected in differentiated keratinocytes of normal and malignant epithelium (PubMed:22623796). In healthy skin, expression is localized in suprabasal epidermal layers (PubMed:22623796).

Evidence on tissue expression from TISSUES for SDCBP2 Gene

  • Nervous system(4.6)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with SDCBP2: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia SDCBP2 33 34
  • 98.63 (n)
cow
(Bos Taurus)
Mammalia SDCBP2 33 34
  • 86.16 (n)
dog
(Canis familiaris)
Mammalia SDCBP2 33 34
  • 84.03 (n)
rat
(Rattus norvegicus)
Mammalia Sdcbp2 33
  • 81.28 (n)
mouse
(Mus musculus)
Mammalia Sdcbp2 33 16 34
  • 80.59 (n)
oppossum
(Monodelphis domestica)
Mammalia SDCBP2 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100859439 33
  • 72.11 (n)
SDCBP2 34
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDCBP2 34
  • 56 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sdcbp2 34
  • 57 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6469 34
  • 47 (a)
OneToMany
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

ENSEMBL:
Gene Tree for SDCBP2 (if available)
TreeFam:
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 Variation AA Info Type
rs35367003 A colorectal cancer sample 1,312,497(-) C/G/T coding_sequence_variant, missense_variant
rs1000097636 -- 1,329,149(-) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1000138257 -- 1,321,607(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000186542 -- 1,322,007(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000322904 -- 1,322,321(-) G/C genic_upstream_transcript_variant, intron_variant

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)

Additional Variant Information for SDCBP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDCBP2

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

Disorders for SDCBP2 Gene

Additional Disease Information for SDCBP2

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 (The Journal of biological chemistry 2001) 2 3 4 22 58
  2. Nuclear speckles and nucleoli targeting by PIP2-PDZ domain interactions. (PMID: 15961997) Mortier E … Zimmermann P (The EMBO journal 2005) 3 4 22 58
  3. Human papillomavirus type 8 E6 oncoprotein inhibits transcription of the PDZ protein syntenin-2. (PMID: 22623796) Lazić D … Akgül B (Journal of virology 2012) 3 4 58
  4. The prevalence and significance of PDZ domain-phosphoinositide interactions. (PMID: 16884951) Zimmermann P (Biochimica et biophysica acta 2006) 3 22 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SDCBP2 Gene

Sources for SDCBP2 Gene

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