Omd (osteomodulin) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Omd (osteomodulin) Rattus norvegicus
Analyze
Symbol: Omd
Name: osteomodulin
RGD ID: 621818
Description: Predicted to be involved in cell adhesion and regulation of bone mineralization. Predicted to localize to extracellular matrix and extracellular space. Orthologous to human OMD (osteomodulin); INTERACTS WITH 1,2-dimethylhydrazine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: keratan sulfate proteoglycan osteomodulin; KSPG osteomodulin; LOC103690116; OSAD; osteoadherin; osteomodulin (osteoadherin)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Note: The locus_ids 83717 and 103690116 are annotated independently on Rnor_6.0 (AR 105) assembly. [29 May 2015]
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21715,060,217 - 15,068,441 (-)NCBI
Rnor_6.0 Ensembl1715,475,710 - 15,484,269 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1714,635,184 - 14,637,832 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01715,476,100 - 15,484,324 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01716,687,912 - 16,695,860 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41721,015,178 - 21,023,126 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11721,015,180 - 21,023,126 (-)NCBI
Celera1714,791,433 - 14,798,980 (-)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
berberine  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chloroprene  (ISO)
corticosterone  (EXP)
dexamethasone  (EXP,ISO)
dichloroacetic acid  (ISO)
Diisodecyl phthalate  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dopamine  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenoldopam  (EXP)
furan  (EXP)
indole-3-methanol  (EXP)
indometacin  (ISO)
isoprenaline  (ISO)
lead diacetate  (EXP)
levofloxacin  (EXP)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
orphenadrine  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (EXP,ISO)
rotenone  (EXP)
sevoflurane  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
Trapidil  (EXP)
triadimefon  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
valproic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:12648264   PMID:14673660   PMID:23533145  


Genomics

Comparative Map Data
Omd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21715,060,217 - 15,068,441 (-)NCBI
Rnor_6.0 Ensembl1715,475,710 - 15,484,269 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1714,635,184 - 14,637,832 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01715,476,100 - 15,484,324 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01716,687,912 - 16,695,860 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41721,015,178 - 21,023,126 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11721,015,180 - 21,023,126 (-)NCBI
Celera1714,791,433 - 14,798,980 (-)NCBICelera
Cytogenetic Map17p14NCBI
OMD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl992,412,380 - 92,424,471 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl992,414,245 - 92,424,461 (-)EnsemblGRCh38hg38GRCh38
GRCh38992,412,380 - 92,424,471 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37995,174,662 - 95,186,753 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36994,216,359 - 94,226,381 (-)NCBINCBI36hg18NCBI36
Build 34992,256,092 - 92,266,115NCBI
Celera965,618,561 - 65,628,868 (-)NCBI
Cytogenetic Map9q22.31NCBI
HuRef964,853,990 - 64,864,296 (-)NCBIHuRef
CHM1_1995,322,965 - 95,333,277 (-)NCBICHM1_1
Omd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391349,735,938 - 49,746,088 (+)NCBIGRCm39mm39
GRCm39 Ensembl1349,735,938 - 49,746,298 (+)Ensembl
GRCm381349,582,462 - 49,592,612 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1349,582,462 - 49,592,822 (+)EnsemblGRCm38mm10GRCm38
MGSCv371349,678,116 - 49,687,978 (+)NCBIGRCm37mm9NCBIm37
MGSCv361349,594,686 - 49,604,546 (+)NCBImm8
Celera1350,673,244 - 50,683,110 (+)NCBICelera
Cytogenetic Map13A5NCBI
Omd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555155,360,569 - 5,363,739 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555155,355,438 - 5,363,739 (+)NCBIChiLan1.0ChiLan1.0
OMD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1991,610,878 - 91,620,538 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl991,611,158 - 91,613,668 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0963,537,522 - 63,547,592 (-)NCBIMhudiblu_PPA_v0panPan3
OMD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1198,923,507 - 98,933,751 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl198,929,274 - 98,931,219 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha199,317,349 - 99,327,591 (+)NCBI
ROS_Cfam_1.0199,540,330 - 99,550,572 (+)NCBI
UMICH_Zoey_3.1199,153,410 - 99,163,649 (+)NCBI
UNSW_CanFamBas_1.0198,888,674 - 98,898,911 (+)NCBI
UU_Cfam_GSD_1.0199,645,439 - 99,655,679 (+)NCBI
Omd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049447,837,766 - 7,846,558 (-)NCBI
SpeTri2.0NW_0049364872,054,109 - 2,056,871 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OMD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl342,142,658 - 42,154,583 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1342,142,603 - 42,155,032 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2343,331,046 - 43,339,400 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OMD
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112102,938,402 - 102,948,626 (-)NCBI
ChlSab1.1 Ensembl12102,937,688 - 102,948,369 (-)Ensembl
Omd
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248683,930,861 - 3,939,380 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17124787908Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17132230361Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17133303755Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138243814Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)1751977023422380Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1751977036283402Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17333697224030841Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17333697224030841Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17333697237790462Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17341403928073589Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17471606727691136Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17471606727691136Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17842446716620067Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17973026321491085Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17973026321491085Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17973026321491085Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)171052970942542027Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)171400967923316697Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:40
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000020648, ENSRNOT00000074323
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 3 1 1 1 1 3 3 9 4
Below cutoff 1 14 21 7 12 7 7 8 34 26 21 10 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020648   ⟹   ENSRNOP00000020648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1715,476,100 - 15,484,269 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000074323   ⟹   ENSRNOP00000067041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1714,635,184 - 14,637,832 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078029   ⟹   ENSRNOP00000068868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1715,475,710 - 15,478,343 (-)Ensembl
RefSeq Acc Id: NM_031817   ⟹   NP_114005
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,060,217 - 15,068,441 (-)NCBI
Rnor_6.01715,476,100 - 15,484,324 (-)NCBI
Rnor_5.01716,687,912 - 16,695,860 (-)NCBI
RGSC_v3.41721,015,178 - 21,023,126 (-)RGD
Celera1714,791,433 - 14,798,980 (-)RGD
Sequence:
RefSeq Acc Id: XM_008771551   ⟹   XP_008769773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01715,476,100 - 15,479,265 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_114005 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD04570 (Get FASTA)   NCBI Sequence Viewer  
  EDL98111 (Get FASTA)   NCBI Sequence Viewer  
  Q9Z1S7 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_114005   ⟸   NM_031817
- Peptide Label: precursor
- UniProtKB: G3V7Y2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769773   ⟸   XM_008771551
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000068868   ⟸   ENSRNOT00000078029
RefSeq Acc Id: ENSRNOP00000067041   ⟸   ENSRNOT00000074323
RefSeq Acc Id: ENSRNOP00000020648   ⟸   ENSRNOT00000020648
Protein Domains
LRRNT

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 21016719 21016720 G A snv LE/Stm (ICL), LE/Stm (KNAW)
17 21016846 21016847 G A snv COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621818 AgrOrtholog
  RGD:9400356 AgrOrtholog
Ensembl Genes ENSRNOG00000039560 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000046658 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020648 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000067041 UniProtKB/TrEMBL
  ENSRNOP00000068868 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020648 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000074323 UniProtKB/TrEMBL
  ENSRNOT00000078029 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Osteomodulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:103690116 UniProtKB/TrEMBL
  rno:83717 UniProtKB/TrEMBL
NCBI Gene 83717 ENTREZGENE
PANTHER PTHR45712:SF3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Omd PhenoGen
PROSITE LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V7Y2 ENTREZGENE, UniProtKB/TrEMBL
  OMD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Omd  osteomodulin  LOC103690116  osteomodulin  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103690116  osteomodulin      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Omd  osteomodulin    osteomodulin (osteoadherin)  Name updated 1299863 APPROVED
2002-08-07 Omd  osteomodulin (osteoadherin)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in bone trabeculae 633418
gene_protein 423 amino acids 633418