IBSP Gene (Protein Coding)

Integrin Binding Sialoprotein

GC04P087799
GIFtS:
38
The protein encoded by this gene is a major structural protein of the bone matrix. It constitutes approximately 12% of the noncollagenous proteins in human bone and is synthesized by skeletal-associated cell types, including hypertrophic chondrocytes, osteoblasts, osteocytes, and osteoclasts. The only extraskeletal site of its synthesis is the trophoblast. This protein binds to... See more...

Aliases for IBSP Gene

Aliases for IBSP Gene

  • Integrin Binding Sialoprotein 2 3 5
  • Bone Sialoprotein II 2 3 4
  • Cell-Binding Sialoprotein 3 4
  • Bone Sialoprotein 2 3 4
  • BSP-II 2 3
  • BSP II 3 4
  • SP-II 2 3
  • BNSP 3 4
  • BSP 2 3
  • Integrin-Binding Sialoprotein 4
  • Bone Sialoprotein 2
  • IBSP 5

External Ids for IBSP Gene

Previous GeneCards Identifiers for IBSP Gene

  • GC04P088878
  • GC04P089022
  • GC04P089179
  • GC04P089077
  • GC04P088939
  • GC04P088720
  • GC04P084466

Summaries for IBSP Gene

Entrez Gene Summary for IBSP Gene

  • The protein encoded by this gene is a major structural protein of the bone matrix. It constitutes approximately 12% of the noncollagenous proteins in human bone and is synthesized by skeletal-associated cell types, including hypertrophic chondrocytes, osteoblasts, osteocytes, and osteoclasts. The only extraskeletal site of its synthesis is the trophoblast. This protein binds to calcium and hydroxyapatite via its acidic amino acid clusters, and mediates cell attachment through an RGD sequence that recognizes the vitronectin receptor. [provided by RefSeq, Jul 2008]

GeneCards Summary for IBSP Gene

IBSP (Integrin Binding Sialoprotein) is a Protein Coding gene. Diseases associated with IBSP include Fibrous Dysplasia and Chondromalacia. Among its related pathways are Focal Adhesion and PI3K-Akt signaling pathway.

UniProtKB/Swiss-Prot Summary for IBSP Gene

  • Binds tightly to hydroxyapatite. Appears to form an integral part of the mineralized matrix. Probably important to cell-matrix interaction. Promotes Arg-Gly-Asp-dependent cell attachment.

Gene Wiki entry for IBSP Gene

Additional gene information for IBSP Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IBSP Gene

Genomics for IBSP Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for IBSP 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
GH04J087799 Promoter 0.3 EPDnew 250.7 0.0 -19 0.1 IBSP piR-61532-221 DMP1
GH04J087657 Enhancer 1 Ensembl ENCODE 15.3 -140.8 -140794 3.9 FEZF1 CEBPB CUX1 ZNF639 EP300 ZNF843 STAT3 JUND PRDM6 ZNF2 IBSP ENSG00000249001 ENSG00000200024 DSPP DMP1 piR-51137-086 LOC105377323
GH04J087679 Enhancer 0.8 Ensembl ENCODE 4.9 -119.6 -119569 1.8 CTCF ZIC2 REST TRIM22 SMC3 RAD21 JUND CHD1 ATF2 ZNF143 DMP1 DSPP SPARCL1 IBSP ENSG00000249001 LOC105377323 piR-32325-122
GH04J087806 Enhancer 0.7 Ensembl ENCODE 5.3 +7.3 7347 2.6 CEBPB GATA3 ZNF217 FOXA1 DPF2 FOSL2 HLF CREB1 FOS CEBPG IBSP PPM1K HSALNG0035720 MEPE
GH04J087698 Enhancer 0.3 Ensembl 10.7 -101.0 -100953 0.4 CEBPB CEBPG DMP1 IBSP DSPP piR-32325-122 piR-33432-390 ENSG00000249001
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IBSP on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IBSP

Top Transcription factor binding sites by QIAGEN in the IBSP gene promoter:
  • aMEF-2
  • AML1a
  • HOXA3
  • HSF1 (long)
  • HSF1short
  • MEF-2A
  • Nkx6-1
  • SRY
  • TBP

Genomic Locations for IBSP Gene

Latest Assembly
chr4:87,799,554-87,812,435
(GRCh38/hg38)
Size:
12,882 bases
Orientation:
Plus strand

Previous Assembly
chr4:88,720,706-88,733,587
(GRCh37/hg19 by Entrez Gene)
Size:
12,882 bases
Orientation:
Plus strand

chr4:88,720,733-88,733,074
(GRCh37/hg19 by Ensembl)
Size:
12,342 bases
Orientation:
Plus strand

Genomic View for IBSP Gene

Genes around IBSP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for IBSP Gene

Proteins for IBSP Gene

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  3. Assay products for research

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

    Protein Symbol:
    P21815-SIAL_HUMAN
    Recommended name:
    Bone sialoprotein 2
    Protein Accession:
    P21815

    Protein attributes for IBSP Gene

    Size:
    317 amino acids
    Molecular mass:
    35148 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • It is possible that the segments of clustered carboxyl groups mediate the strong binding to hydroxyapatite.

neXtProt entry for IBSP Gene

Post-translational modifications for IBSP Gene

  • N-glycosylated; glycans consist of sialylated and core-fucosylated bi-, tri- and tetraantennary chains.
  • O-glycosylated at eight sites; mucin-type glycans contain Gal, GlcNAc, GalNAc and terminal NeuAc.
  • Sulfated on either Tyr-313 or Tyr-314.
  • Glycosylation at Asn104, Thr119, Thr122, Asn177, Asn182, Asn190, Thr227, Thr228, Thr229, Thr238, and Thr239
  • Modification sites at PhosphoSitePlus

Other Protein References for IBSP Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for IBSP Gene

Domains & Families for IBSP Gene

Gene Families for IBSP Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted secreted proteins

Protein Domains for IBSP Gene

InterPro:
Blocks:
  • Bone sialoprotein II
ProtoNet:

Suggested Antigen Peptide Sequences for IBSP Gene

GenScript: Design optimal peptide antigens:
  • Integrin-binding sialoprotein (SIAL_HUMAN)
genes like me logo Genes that share domains with IBSP: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for IBSP Gene

Function for IBSP Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for IBSP Gene

UniProtKB/Swiss-Prot Function:
Binds tightly to hydroxyapatite. Appears to form an integral part of the mineralized matrix. Probably important to cell-matrix interaction. Promotes Arg-Gly-Asp-dependent cell attachment.
GENATLAS Biochemistry:
sialoprotein,bone (cell adhesion molecule,RGD containing)

Phenotypes From GWAS Catalog for IBSP Gene

Gene Ontology (GO) - Molecular Function for IBSP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005178 integrin binding IMP 24103036
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with IBSP: view
genes like me logo Genes that share phenotypes with IBSP: view

Animal Models for IBSP Gene

MGI Knock Outs for IBSP:
  • Ibsp Ibsp<tm1Jeau>

Animal Models for research

miRNA for IBSP Gene

miRTarBase miRNAs that target IBSP

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IBSP

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

Localization for IBSP Gene

Subcellular locations from UniProtKB/Swiss-Prot for IBSP Gene

Secreted.

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 IBSP gene
Compartment Confidence
extracellular 5
plasma membrane 2
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for IBSP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space ISS --
GO:0016020 membrane HDA 16210410
GO:0031982 vesicle ISS --
genes like me logo Genes that share ontologies with IBSP: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for IBSP Gene

Pathways & Interactions for IBSP Gene

genes like me logo Genes that share pathways with IBSP: view

Pathways by source for IBSP Gene

1 GeneGo (Thomson Reuters) pathway for IBSP Gene
  • Development_Hedgehog and PTH signaling pathways in bone and cartilage development
2 Cell Signaling Technology pathways for IBSP Gene

SIGNOR curated interactions for IBSP Gene

Is activated by:

Gene Ontology (GO) - Biological Process for IBSP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001503 ossification IEA --
GO:0001649 osteoblast differentiation HDA 16210410
GO:0007155 cell adhesion ISS --
GO:0030198 extracellular matrix organization IEA,TAS --
GO:0030282 bone mineralization IEA,IBA 21873635
genes like me logo Genes that share ontologies with IBSP: view

Drugs & Compounds for IBSP Gene

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  1. Drug products for research

(31) Drugs for IBSP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(36) Additional Compounds for IBSP Gene - From: Novoseek

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

Transcripts for IBSP Gene

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  3. Inhibitory RNAs for research
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mRNA/cDNA for IBSP Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IBSP

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

No ASD Table

Relevant External Links for IBSP Gene

GeneLoc Exon Structure for
IBSP

Expression for IBSP Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for IBSP Gene
mRNA expression by GTEx for IBSP GenemRNA expression by BioGPS for IBSP Gene

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

This gene is overexpressed in Artery - Coronary (x10.7), Pituitary (x7.2), and Brain - Amygdala (x5.0).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IBSP

SOURCE GeneReport for Unigene cluster for IBSP Gene:

Hs.518726

Evidence on tissue expression from TISSUES for IBSP Gene

  • Bone(3.5)
  • Bone marrow(2.4)
  • Muscle(2.1)
  • Blood(2)
genes like me logo Genes that share expression patterns with IBSP: view

Primer products for research

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IBSP Gene

Orthologs for IBSP Gene

This gene was present in the common ancestor of chordates.

Orthologs for IBSP Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia IBSP 30 31
  • 98.53 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia IBSP 30 31
  • 81.73 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia IBSP 30 31
  • 80.68 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Ibsp 30 17 31
  • 71.96 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ibsp 30
  • 70.58 (n)
Oppossum
(Monodelphis domestica)
 Mammalia IBSP 31
  • 61 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia IBSP 31
  • 58 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves IBSP 31
  • 41 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia IBSP 31
  • 41 (a)
 OneToOne
Species where no ortholog for IBSP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Zebrafish (Danio rerio)

Evolution for IBSP Gene

ENSEMBL:
Gene Tree for IBSP (if available)
TreeFam:
Gene Tree for IBSP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for IBSP: view image

Paralogs for IBSP Gene

No data available for Paralogs for IBSP Gene

Variants for IBSP Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IBSP Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs114009564 Likely Benign: not provided 87,802,690(+) C/T
NM_004967.4(IBSP):c.142C>T (p.His48Tyr) 		MISSENSE
rs1054627 - p.Gly195Glu
rs1054628 - p.Ala268Val
rs1054629 - p.Glu270Asp
rs13144371 - p.Asp213Gly

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for IBSP Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv322n21 CNV loss 19592680
nsv515943 CNV gain+loss 19592680

Variation tolerance for IBSP Gene

Residual Variation Intolerance Score: 77.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.86; 97.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IBSP Gene

Human Gene Mutation Database (HGMD)
IBSP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
IBSP

SNP Genotyping and Copy Number Assays for research

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

Disorders for IBSP Gene

MalaCards: The human disease database

(43) MalaCards diseases for IBSP Gene - From: COP and GCD

Disorder Aliases PubMed IDs
fibrous dysplasia
  • fibrous dysplasia of bone
chondromalacia
autosomal recessive hypophosphatemic rickets
  • arhr
ankylosis
dentin dysplasia
  • dentinal dysplasia
- elite association - COSMIC cancer census association via MalaCards
Search IBSP in MalaCards View complete list of genes associated with diseases

Additional Disease Information for IBSP

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with IBSP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IBSP Gene

Publications for IBSP Gene

  1. Structural characterization of human recombinant and bone-derived bone sialoprotein. Functional implications for cell attachment and hydroxyapatite binding. (PMID: 11459848) Wuttke M … Maurer P (The Journal of biological chemistry 2001) 3 4 23
  2. Characterization of the human bone sialoprotein (BSP) gene and its promoter sequence. (PMID: 8061918) Kim RH … Sodek J (Matrix biology : journal of the International Society for Matrix Biology 1994) 3 4 23
  3. The human bone sialoprotein gene (IBSP): genomic localization and characterization. (PMID: 8406493) Kerr JM … Young MF (Genomics 1993) 2 3 4
  4. Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. (PMID: 21533022) Duncan EL … Brown MA (PLoS genetics 2011) 3 41
  5. Predictive significance of bone sialoprotein and osteopontin for bone metastases in resected Chinese non-small-cell lung cancer patients: a large cohort retrospective study. (PMID: 19376608) Zhang L … Wang X (Lung cancer (Amsterdam, Netherlands) 2010) 3 23

ExternalLinks

View latest publications for IBSP gene in Mastermind

Products for IBSP Gene

Sources for IBSP Gene