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OMD Gene(Protein Coding)

Osteomodulin

GCID:
GC09M092414
GIFtS:
55
Genes Participants
UDN Logo

Aliases for OMD Gene

Aliases for OMD Gene

  • Osteomodulin 2 3 5
  • Keratan Sulfate Proteoglycan Osteomodulin 3 4
  • Osteoadherin Proteoglycan 2 3
  • KSPG Osteomodulin 3 4
  • SLRR2C 3 4
  • OSAD 3 4
  • Osteoadherin 4

External Ids for OMD Gene

Previous GeneCards Identifiers for OMD Gene

  • GC09M086003
  • GC09M086904
  • GC09M088475
  • GC09M090517
  • GC09M092256
  • GC09M094216
  • GC09M095176
  • GC09M064853

Summaries for OMD Gene

GeneCards Summary for OMD Gene

OMD (Osteomodulin) is a Protein Coding gene. Diseases associated with OMD include Occult Macular Dystrophy and Hallermann-Streiff Syndrome. Among its related pathways are Glycosaminoglycan metabolism and Defective B3GAT3 causes JDSSDHD. An important paralog of this gene is ECM2.

UniProtKB/Swiss-Prot for OMD Gene

  • May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)-integrin (By similarity).

Gene Wiki entry for OMD Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for OMD Gene

Genomics for OMD Gene

Products:

  1. Regulatory Element

Regulatory Elements for OMD Gene

Enhancers for OMD Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around OMD on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the OMD gene promoter:

Genomic Location for OMD Gene

Chromosome:
9
Start:
92,414,245 bp from pter
End:
92,424,554 bp from pter
Size:
10,310 bases
Orientation:
Minus strand

Genomic View for OMD Gene

Genes around OMD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for OMD Gene

Proteins for OMD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    Q99983-OMD_HUMAN
    Recommended name:
    Osteomodulin
    Protein Accession:
    Q99983
    Secondary Accessions:
    • Q5TBF4

    Protein attributes for OMD Gene

    Size:
    421 amino acids
    Molecular mass:
    49492 Da
    Quaternary structure:
    • Binds the alpha(V)beta(3)-integrin.

neXtProt entry for OMD Gene

Proteomics data for OMD Gene at MOPED

Protein Expression for OMD Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for OMD Gene

Other Protein References for OMD Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for OMD (Osteoadherin/OSAD)
  • Abcam antibodies for OMD

No data available for DME Specific Peptides for OMD Gene

Domains & Families for OMD Gene

Gene Families for OMD Gene

HGNC:

Protein Domains for OMD Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for OMD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q99983

UniProtKB/Swiss-Prot:

OMD_HUMAN :
  • Contains 1 LRRNT domain.
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
  • Contains 11 LRR (leucine-rich) repeats.
Domain:
  • Contains 1 LRRNT domain.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
Similarity:
  • Contains 11 LRR (leucine-rich) repeats.
genes like me logo Genes that share domains with OMD: view

Function for OMD Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for OMD Gene

UniProtKB/Swiss-Prot Function:
May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)-integrin (By similarity).

Phenotypes for OMD Gene

MGI mutant phenotypes for OMD:
inferred from 1 alleles
GenomeRNAi human phenotypes for OMD:
genes like me logo Genes that share phenotypes with OMD: view

Animal Models for OMD Gene

MGI Knock Outs for OMD:

Animal Model Products

  • Taconic Biosciences Mouse Models for OMD

miRNA for OMD Gene

miRTarBase miRNAs that target OMD

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for OMD Gene

Localization for OMD Gene

Subcellular locations from UniProtKB/Swiss-Prot for OMD Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for OMD Gene COMPARTMENTS Subcellular localization image for OMD gene
Compartment Confidence
extracellular 5
golgi apparatus 4
lysosome 4
vacuole 4
plasma membrane 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for OMD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IBA --
genes like me logo Genes that share ontologies with OMD: view

Pathways & Interactions for OMD Gene

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

Interacting Proteins for OMD Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000364700%0d%0a9606.ENSP00000262551%0d%0a9606.ENSP00000345477%0d%0a9606.ENSP00000309096%0d%0a9606.ENSP00000387356%0d%0a9606.ENSP00000319636%0d%0a
Selected Interacting proteins: ENSP00000364700 for OMD Gene via STRING

SIGNOR curated interactions for OMD Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for OMD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process TAS --
GO:0007155 cell adhesion IEA --
GO:0018146 keratan sulfate biosynthetic process TAS --
GO:0030500 regulation of bone mineralization IEA --
GO:0042340 keratan sulfate catabolic process TAS --
genes like me logo Genes that share ontologies with OMD: view

Drugs & Compounds for OMD Gene

Products:

  1. Drug

(2) Drugs for OMD Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for OMD Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Keratan
  • Keratan 6'-sulfate
  • Keratan 6'-sulphate
  • Keratan sulfate
  • Keratan sulphate
  • Kerato 6'-sulfate
 69992-87-6
genes like me logo Genes that share compounds with OMD: view

Transcripts for OMD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for OMD Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(69) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for OMD Gene

Osteomodulin:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for OMD Gene

GeneLoc Exon Structure for
OMD
ECgene alternative splicing isoforms for
OMD

Expression for OMD Gene

Products:

  1. Primer

mRNA expression in normal human tissues for OMD Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Artery - Aorta (x9.7) and Artery - Coronary (x7.4).

Protein differential expression in normal tissues from HIPED for OMD Gene

This gene is overexpressed in Breast (40.3), Cerebrospinal fluid (10.0), and Urine (8.8).

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



SOURCE GeneReport for Unigene cluster for OMD Gene Hs.94070

mRNA Expression by UniProt/SwissProt for OMD Gene

Q99983-OMD_HUMAN
Tissue specificity: Bone specific.
genes like me logo Genes that share expression patterns with OMD: view

Primer Products

No data available for Protein tissue co-expression partners for OMD Gene

Orthologs for OMD Gene

This gene was present in the common ancestor of chordates.

Orthologs for OMD Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia OMD 35
  • 88.86 (n)
  • 84.6 (a)
OMD 36
  • 82 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia OMD 35
  • 87.45 (n)
  • 84.22 (a)
OMD 36
  • 81 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Omd 35
  • 85.39 (n)
  • 79.9 (a)
Omd 16
Omd 36
  • 79 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia OMD 35
  • 99.45 (n)
  • 99.05 (a)
OMD 36
  • 99 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia OMD 36
  • 66 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves OMD 35
  • 68.4 (n)
  • 61.54 (a)
OMD 36
  • 58 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia OMD 36
  • 56 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii omd 35
  • 57.82 (n)
  • 51.69 (a)
omd 36
  • 47 (a)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 36
  • 25 (a)
 OneToMany
Species with no ortholog for OMD:
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 OMD Gene

ENSEMBL:
Gene Tree for OMD (if available)
TreeFam:
Gene Tree for OMD (if available)

Paralogs for OMD Gene

Paralogs for OMD Gene

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

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

Variants for OMD Gene

Sequence variations from dbSNP and Humsavar for OMD Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
VAR_052014 -
VAR_052015 -
VAR_052016 -
VAR_052017 -
VAR_052018 -

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

Variant ID Type Subtype PubMed ID
nsv893573 CNV Gain 21882294

Variation tolerance for OMD Gene

Residual Variation Intolerance Score: 70.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.08; 60.90% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for OMD Gene

Disorders for OMD Gene

MalaCards: The human disease database

(2) MalaCards diseases for OMD Gene - From: DISEASES

Disorder Aliases PubMed IDs
occult macular dystrophy
  • ocmd
hallermann-streiff syndrome
  • francois dyscephalic syndrome
- elite association - COSMIC cancer census association via MalaCards
Search OMD in MalaCards View complete list of genes associated with diseases

Relevant External Links for OMD

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
OMD
genes like me logo Genes that share disorders with OMD: view

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

Publications for OMD Gene

  1. 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 67
  2. The tyrosine sulfate-rich domains of the LRR proteins fibromodulin and osteoadherin bind motifs of basic clusters in a variety of heparin-binding proteins, including bioactive factors. (PMID: 19700767) Tillgren V. … HeinegAYrd D. (J. Biol. Chem. 2009) 3 23
  3. TGF beta 1 signaling and stimulation of osteoadherin in human odontoblasts in vitro. (PMID: 12489179) Lucchini M. … Farges J.C. (Connect. Tissue Res. 2002) 3 23
  4. Expression of the small leucine-rich proteoglycan osteoadherin/osteomodulin in human dental pulp and developing rat teeth. (PMID: 10913920) Buchaille R. … Bleicher F. (Bone 2000) 3 23
  5. Distinct dysregulation of the small leucine-rich repeat protein family in osteoarthritic acetabular labrum compared to articular cartilage. (PMID: 25371314) Juchtmans N. … Elewaut D. ( 2015) 3

Products for OMD Gene

Sources for OMD Gene

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