OMD Gene

Aliases
for OMD gene

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Previous GC identifers: GC09M086003 GC09M086904 GC09M088475 GC09M090517 GC09M092256 GC09M094216 GC09M064853

Summaries
for OMD gene

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Genomic Views
for OMD gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:

NC_000009.11  NC_018920.2  NT_008470.20  

SwitchGear Promoter luciferase reporter plasmid: OMD promoter sequence

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat OMD

OMD Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)


GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M095176:  view genomic region     (about GC identifiers)

Proteins
for OMD gene

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, antibodies-online, and/or GeneTex,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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Explore the universe of human proteins at neXtProt for OMD: NX_Q99983

Explore proteomics data for OMD at MOPED

Post-translational modifications: 

OMD Human Recombinant Protein Products:

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	antibodies-online peptides for OMD

OMD Antibody Products:

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	antibodies-online kits for OMD (8 products)

Domains /
Families
for OMD gene

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GenesLikeMe)
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ProtoNet protein and cluster: Q99983

Find genes that share domains with OMD           About GenesLikeMe

Function
for OMD gene

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
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     Gene Ontology (GO): 1 molecular function term:    About this table

(inferred from 1 allele) (MGI details for Omd)

genOway: Develop your customized and physiologically relevant rodent model for OMD

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		hsa-miR-576-5p hsa-miR-875-5p hsa-miR-3662 hsa-miR-578 hsa-miR-551b* hsa-miR-3144-3p
		SwitchGear 3'UTR luciferase reporter plasmid: OMD 3' UTR sequence

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		Predesigned siRNA for gene silencing in human, mouse, rat OMD

Gene Editing Products:

DNA2.0 Custom Protein Engineering Service for OMD

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		GenScript: all cDNA clones in your preferred vector: OMD (NM_005014)
		Sino Biological Human cDNA Clone for OMD
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for OMD
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat OMD

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for OMD
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In Situ Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OMD

Localization
for OMD gene

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
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Subcellular locations from COMPARTMENTS: 

Compartment	Confidence
extracellular	4
golgi apparatus	4
lysosome	4
vacuole	4
plasma membrane	2
endoplasmic reticulum	1

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Gene Ontology (GO): 4 cellular component terms:    About this table

Pathways & Interactions
for OMD gene

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GenesLikeMe, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
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SuperPaths for OMD About     See pathways by source

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	SuperPath	Selected contained pathways About (see all per SuperPath)
1	MPS VI - Maroteaux-Lamy syndrome	MPS VI - Maroteaux-Lamy syndrome 0.45 MPS IV - Morquio syndrome B 0.45 MPS IIIC - Sanfilippo syndrome C 0.45 MPS IX - Natowicz syndrome 0.45 MPS IIID - Sanfilippo syndrome D 0.45 MPS IV - Morquio syndrome A 0.45 MPS IIIA - Sanfilippo syndrome A 0.45 Mucopolysaccharidoses 0.45
2	Keratan sulfate/keratin metabolism	Keratan sulfate/keratin metabolism 0.85 Keratan sulfate degradation 0.00 Keratan sulfate biosynthesis 0.85
3	Metabolism	Metabolism 0.38
4	Disease	Disease

2 Reactome Pathways for OMD

	Keratan sulfate biosynthesis
	Keratan sulfate degradation

Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

Drugs & Compounds
for OMD gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, Sets of similar genes according to GenesLikeMe)
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Transcripts
for OMD gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Expression
for OMD gene

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GenesLikeMe, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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OMD expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

Bone (Muscoskeletal System)    fully expand to see all 16 entries
Micromass-induced chondrocytes
Cartilage (Muscoskeletal System)    fully expand to see all 14 entries
Micromass-induced chondrocytes
Neural Crest (Gastrulation Derivatives)    fully expand to see all 3 entries
PureStem 4D20.8, NCr-fac Progenitor
Adipose (Muscoskeletal System)    fully expand to see all 3 entries
HyStem+BMP4-induced E15 cells
Ovary (Reproductive System)    fully expand to see all 2 entries
Pre-Granulosa Cells Primordial Follicle

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		Pre-validated RT2 qPCR Primer Assay in human, mouse, rat OMD
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		QuantiFast Probe-based Assays in human, mouse, rat OMD

In Situ Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OMD

Orthologs
for OMD gene

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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Paralogs
for OMD gene

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68,Sets of similar genes according to GenesLikeMe)
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Paralogs for OMD gene

PODN²  FLRT1²  PODNL1²  FMOD²  KERA²  PRELP²  FLRT3²  ASPN²  

BGN²  DCN²  FLRT2²  ECM2²  LOC100509091²  LUM²  

4 SIMAP similar genes for OMD using alignment to 1 protein entry:     OMD_HUMAN:

KERA    LUM    PRELP    FMOD

Find genes that share paralogs with OMD           About GenesLikeMe

Genomic Variants
for OMD gene

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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5 SNPs for OMD    About this table

Genomic Data					Transcription Related Data				Allele Frequencies
SNP ID	Valid	Clinical significance	Chr 9 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
-1st2nd3rd	-1st2nd3rd	-1st2nd3rd	-1st2nd3rd	--	--	--	-1st2nd3rd	--	--	-1st2nd3rd	-1st2nd3rd	-1st2nd3rd
rs344132591,2,4		--	--	see VAR_052015	2		mis4		0	--	--	--	--
rs357799011,2,4		--	--	see VAR_052017	2		mis4		0	--	--	--	--
rs340698711,2,4		--	--	see VAR_052014	2		mis4		0	--	--	--	--
rs348606581,2,4		--	--	see VAR_052016	2		mis4		0	--	--	--	--
rs340591141,2,4		--	--	see VAR_052018	2		mis4		0	--	--	--	--

HapMap Linkage Disequilibrium report for OMD (95176527 - 95186836 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for OMD:    About this table    

Variant ID	Type	Subtype	PubMed ID
nsv893573	CNV	Gain	21882294

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing OMD

DNA2.0 Custom Variant and Variant Library Synthesis for OMD

Disorders / Diseases
for OMD gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB, Sets of similar genes according to GenesLikeMe)
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Publications
for OMD gene

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for OMD gene, integrated from 10 sources (see all 29): (articles sorted by number of sources associating them with OMD)

Utopia: connect your pdf to the dynamic world of online information

1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S.... Malek J. (Genome Res. 2004)
2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)^{1, 2} Clark H.F.... Gray A.M. (Genome Res. 2003)
3. Expression of the small leucine-rich proteoglycan osteoadherin/osteomodulin in human dental pulp and developing rat teeth. (PubMed id 10913920)^{1, 9} Buchaille R....Bleicher F. (Bone 2000)
4. TGF beta 1 signaling and stimulation of osteoadherin in human odontoblasts in vitro. (PubMed id 12489179)^{1, 9} Lucchini M....Farges J.C. (Connect. Tissue Res. 2002)
5. 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. (PubMed id 19700767)^{1, 9} Tillgren V....HeinegAYrd D. (J. Biol. Chem. 2009)
6. Identification of tyrosine sulfation in extracellular leucine-rich repeat proteins using mass spectrometry. (PubMed id 14551184)^{2, 9} Onnerfjord P.... Heinegaard D. (J. Biol. Chem. 2004)
7. Immunodetection of osteoadherin in murine tooth extracellular matrices. (PubMed id 14673660)¹ Couble M.L....Staquet M.J. (Histochem. Cell Biol. 2004)
8. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)² Humphray S.J.... Dunham I. (Nature 2004)
9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
10. Bone matrix proteins: isolation and characterization of a novel cell-binding keratan sulfate proteoglycan (osteoadherin) from bovine bone. (PubMed id 9566981)¹ Wendel M....HeinegAYrd D. (J. Cell Biol. 1998)

External Searches for OMD gene

Genome Databases showing OMD gene

Other Databases showing OMD gene

Specialized Databases showing OMD gene

Products
for OMD gene

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, GeneTex, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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