Aliases for OMD Gene

Aliases for OMD Gene

  • Osteomodulin 2 3 4 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 Oromandibular Dystonia and Occult Macular Dystrophy. Among its related pathways are Defective ST3GAL3 causes MCT12 and EIEE15 and Keratan sulfate/keratin metabolism. An important paralog of this gene is KERA.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for OMD Gene

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

Genomics for OMD Gene

GeneHancer (GH) Regulatory Elements for OMD Gene

Promoters and enhancers for OMD 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
GH09J092423 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 -1.3 -1253 4.6 MXI1 YY1 POLR2A OMD CENPP NOL8 OGN ECM2 lnc-ECM2-2
GH09J092422 Enhancer 0.3 Ensembl dbSUPER 500.7 +1.7 1653 0.6 OMD CENPP OGN
GH09J092533 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.8 -111.4 -111408 4.3 FOXA2 MEF2B SPI1 JUND ASH2L GATA3 MAFK EBF1 SMARCA4 HNF4A ECM2 CENPP ASPN OMD OGN IPPK BICD2 piR-55705-056
GH09J092561 Enhancer 0.9 Ensembl ENCODE 10.8 -138.6 -138647 4 ZSCAN5C ZNF639 ZNF10 RFX1 OSR2 ZBTB17 KLF8 OVOL3 ZNF513 IKZF3 RF00017-7710 CENPP OMD NOL8 ASPN OGN IPPK BICD2 piR-33605-487
GH09J092359 Enhancer 0.7 Ensembl ENCODE 12 +64.7 64653 1.4 MXI1 GATA3 SPI1 RCOR1 CHD2 YY1 GATA2 MTA2 DPF2 RUNX3 CENPP NOL8 OMD OGN piR-46847-282 lnc-OMD-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around OMD on UCSC Golden Path with GeneCards custom track

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

Top Transcription factor binding sites by QIAGEN in the OMD gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • FOXO3
  • FOXO3a
  • FOXO3b
  • POU2F1
  • POU2F1a
  • SRY

Genomic Locations for OMD Gene

Genomic Locations for OMD Gene
chr9:92,414,245-92,424,554
(GRCh38/hg38)
Size:
10,310 bases
Orientation:
Minus strand
chr9:95,176,527-95,186,836
(GRCh37/hg19)
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 StructureGene Density

RefSeq DNA sequence for OMD Gene

Proteins for OMD Gene

  • 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.

    Three dimensional structures from OCA and Proteopedia for OMD Gene

neXtProt entry for OMD Gene

Post-translational modifications for OMD Gene

  • Binds keratan sulfate chains.
  • Glycosylation at Asn113, Asn121, Asn187, Asn242, and Asn316
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for OMD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for OMD Gene

Domains & Families for OMD Gene

Gene Families for OMD Gene

Protein Domains for OMD Gene

Blocks:
  • Cysteine-rich flanking region, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for OMD Gene

GenScript: Design optimal peptide antigens:
  • Osteoadherin (OMD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q99983

UniProtKB/Swiss-Prot:

OMD_HUMAN :
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
genes like me logo Genes that share domains with OMD: view

Function for OMD Gene

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 From GWAS Catalog for OMD Gene

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

Animal Models for OMD Gene

MGI Knock Outs for OMD:
  • Omd Omd<tm1Lex>

Animal Model Products

  • Taconic Biosciences Mouse Models for OMD

CRISPR Products

Inhibitory RNA Products

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

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
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 OMD gene
Compartment Confidence
extracellular 5
lysosome 4
golgi apparatus 4
plasma membrane 2
endoplasmic reticulum 2
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
  • Nucleoli fibrillar center (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for OMD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005796 Golgi lumen TAS --
GO:0031012 extracellular matrix IEA --
GO:0043202 lysosomal lumen TAS --
GO:0062023 collagen-containing extracellular matrix IEA --
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

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: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

(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

mRNA/cDNA for OMD Gene

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

CRISPR Products

Inhibitory RNA Products

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

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

No ASD Table

Relevant External Links for OMD Gene

GeneLoc Exon Structure for
OMD

Expression for OMD Gene

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



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

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.

Evidence on tissue expression from TISSUES for OMD Gene

  • Bone(4.4)
  • Nervous system(4.3)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with OMD: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia OMD 31 30
  • 99.45 (n)
OneToOne
cow
(Bos Taurus)
Mammalia OMD 31 30
  • 88.86 (n)
OneToOne
dog
(Canis familiaris)
Mammalia OMD 31 30
  • 87.45 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Omd 17 31 30
  • 85.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia OMD 31
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves OMD 31 30
  • 68.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia OMD 31
  • 56 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii omd 31 30
  • 57.82 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 25 (a)
OneToMany
Species where no ortholog for OMD 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)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for OMD: view image

Paralogs for OMD Gene

Paralogs for OMD Gene

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

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

Variants for OMD Gene

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

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs34059114 - p.Cys353Trp
rs34069871 - p.Asp200Gly
rs34413259 - p.Glu212Gly
rs34860658 - p.Ser221Asn
rs35779901 - p.Ile282Thr

Additional dbSNP identifiers (rs#s) for OMD Gene

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

Variant ID Type Subtype PubMed ID
esv3621079 CNV loss 21293372
esv3891693 CNV gain 25118596
nsv1047337 CNV loss 25217958
nsv1049599 CNV loss 25217958
nsv1053205 CNV loss 25217958

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)

Additional Variant Information for OMD Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for OMD Gene

MalaCards: The human disease database

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

- elite association - COSMIC cancer census association via MalaCards
Search OMD in MalaCards View complete list of genes associated with diseases
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 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 … Heinegård D (The Journal of biological chemistry 2009) 3 23 54
  2. 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 54
  3. Identification of tyrosine sulfation in extracellular leucine-rich repeat proteins using mass spectrometry. (PMID: 14551184) Onnerfjord P … Heinegård D (The Journal of biological chemistry 2004) 4 23 54
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 54
  5. TGF beta 1 signaling and stimulation of osteoadherin in human odontoblasts in vitro. (PMID: 12489179) Lucchini M … Farges JC (Connective tissue research 2002) 3 23 54

Products for OMD Gene

  • Signalway ELISA kits for OMD
  • Signalway Proteins for OMD

Sources for OMD Gene