Olfm1 (olfactomedin 1) - Rat Genome Database
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Gene: Olfm1 (olfactomedin 1) Rattus norvegicus
Analyze
Symbol: Olfm1
Name: olfactomedin 1
RGD ID: 620320
Description: Predicted to have amyloid-beta binding activity and identical protein binding activity. Predicted to be involved in several processes, including heart development; negative regulation of macromolecule metabolic process; and regulation of neurogenesis. Predicted to localize to several cellular components, including AMPA glutamate receptor complex; axonal growth cone; and glutamatergic synapse. Orthologous to human OLFM1 (olfactomedin 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 1B426B; D2Sut1e; neuronal olfactomedin-related ER localized protein; Noe1; noelin; olfactomedin related ER localized protein; olfactomedin-1; pancortin
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
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2311,520,522 - 11,558,240 (+)NCBI
Rnor_6.0 Ensembl36,773,813 - 6,798,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.036,761,031 - 6,798,739 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0312,114,825 - 12,152,487 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,170,421 - 7,195,345 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.137,170,720 - 7,195,645 (+)NCBI
Celera36,324,040 - 6,348,939 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-acetamidofluorene  (ISO)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
cisplatin  (ISO)
clomiphene  (ISO)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
coumestrol  (ISO)
dibutyl phthalate  (EXP,ISO)
diethyl phthalate  (EXP)
diethylstilbestrol  (ISO)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
estrone  (ISO)
ethanol  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
hexestrol  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mestranol  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
oxaliplatin  (EXP)
paracetamol  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
progesterone  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
topotecan  (EXP)
triclosan  (ISO)
undecane  (EXP)
valproic acid  (EXP,ISO)
vorinostat  (ISO)
zearalenone  (ISO)

References

Additional References at PubMed
PMID:15927402   PMID:16751333   PMID:22632720   PMID:22923615   PMID:22992957   PMID:25218043  


Genomics

Comparative Map Data
Olfm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2311,520,522 - 11,558,240 (+)NCBI
Rnor_6.0 Ensembl36,773,813 - 6,798,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.036,761,031 - 6,798,739 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0312,114,825 - 12,152,487 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,170,421 - 7,195,345 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.137,170,720 - 7,195,645 (+)NCBI
Celera36,324,040 - 6,348,939 (+)NCBICelera
Cytogenetic Map3p12NCBI
OLFM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9135,075,422 - 135,121,179 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl9135,075,422 - 135,121,180 (+)EnsemblGRCh38hg38GRCh38
GRCh389135,075,505 - 135,121,184 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379137,967,089 - 138,013,030 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh379137,967,351 - 138,013,030 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,106,910 - 137,152,851 (+)NCBINCBI36hg18NCBI36
Build 349135,193,115 - 135,195,180NCBI
Celera9108,481,187 - 108,526,613 (+)NCBI
Cytogenetic Map9q34.3NCBI
HuRef9107,430,180 - 107,476,065 (+)NCBIHuRef
CHM1_19138,116,020 - 138,161,923 (+)NCBICHM1_1
Olfm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,083,105 - 28,120,748 (+)NCBIGRCm39mm39
GRCm38228,193,093 - 28,230,736 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,192,992 - 28,230,736 (+)EnsemblGRCm38mm10GRCm38
MGSCv37228,048,613 - 28,086,256 (+)NCBIGRCm37mm9NCBIm37
MGSCv36228,015,102 - 28,052,745 (+)NCBImm8
Celera227,895,841 - 27,933,529 (+)NCBICelera
Cytogenetic Map2A3NCBI
Olfm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049557336,189 - 30,455 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049557336,189 - 30,455 (-)NCBIChiLan1.0ChiLan1.0
OLFM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19135,205,710 - 135,252,598 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9135,205,710 - 135,252,598 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09106,206,133 - 106,253,386 (+)NCBIMhudiblu_PPA_v0panPan3
OLFM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl950,979,146 - 50,996,602 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1950,972,035 - 50,996,770 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Olfm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366692,291,328 - 2,314,414 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OLFM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1274,224,454 - 274,261,328 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11274,236,241 - 274,261,322 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21308,316,240 - 308,353,274 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OLFM1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,028,681 - 3,063,754 (-)NCBI
Olfm1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247602,842,177 - 2,876,966 (+)NCBI

Position Markers
D78264  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.036,797,827 - 6,797,947NCBIRnor6.0
Rnor_5.0312,151,576 - 12,151,696UniSTSRnor5.0
RGSC_v3.437,194,435 - 7,194,555UniSTSRGSC3.4
Celera36,348,029 - 6,348,149UniSTS
Cytogenetic Map3p12UniSTS
AW742568  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.036,797,845 - 6,798,090NCBIRnor6.0
Rnor_5.0312,151,594 - 12,151,839UniSTSRnor5.0
RGSC_v3.437,194,453 - 7,194,698UniSTSRGSC3.4
Celera36,348,047 - 6,348,292UniSTS
Cytogenetic Map3p12UniSTS
Olfm1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05117,759,111 - 117,759,194NCBIRnor6.0
Rnor_6.036,780,879 - 6,780,962NCBIRnor6.0
Rnor_5.0312,134,628 - 12,134,711UniSTSRnor5.0
Rnor_5.05121,698,058 - 121,698,141UniSTSRnor5.0
Celera36,331,101 - 6,331,184UniSTS
Celera5112,322,358 - 112,322,441UniSTS
Cytogenetic Map3p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)3565463925105730Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)3600074851687917Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)3600074851687917Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)3600086634394121Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:749
Count of miRNA genes:289
Interacting mature miRNAs:353
Transcripts:ENSRNOT00000013443, ENSRNOT00000044951, ENSRNOT00000065953
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 74 19 15 8
Low 3 42 27 11 19 11 8 11 16 24 3 8
Below cutoff 1 30 30 30 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013443   ⟹   ENSRNOP00000013443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl36,773,813 - 6,798,737 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000065953   ⟹   ENSRNOP00000060981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl36,773,813 - 6,782,681 (+)Ensembl
RefSeq Acc Id: NM_053573   ⟹   NP_446025
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,533,308 - 11,558,239 (+)NCBI
Rnor_6.036,773,813 - 6,798,737 (+)NCBI
Rnor_5.0312,114,825 - 12,152,487 (+)NCBI
RGSC_v3.437,170,421 - 7,195,345 (+)RGD
Celera36,324,040 - 6,348,939 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233875   ⟹   XP_006233937
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,520,522 - 11,558,240 (+)NCBI
Rnor_6.036,761,031 - 6,798,739 (+)NCBI
Rnor_5.0312,114,825 - 12,152,487 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233876   ⟹   XP_006233938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,533,288 - 11,542,182 (+)NCBI
Rnor_6.036,773,777 - 6,782,686 (+)NCBI
Rnor_5.0312,114,825 - 12,152,487 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233877   ⟹   XP_006233939
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2311,520,528 - 11,542,182 (+)NCBI
Rnor_6.036,761,031 - 6,782,686 (+)NCBI
Rnor_5.0312,114,825 - 12,152,487 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592085   ⟹   XP_017447574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.036,780,534 - 6,798,739 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446025   ⟸   NM_053573
- Peptide Label: precursor
- UniProtKB: Q62609 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233937   ⟸   XM_006233875
- Peptide Label: isoform X1
- UniProtKB: Q62609 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233939   ⟸   XM_006233877
- Peptide Label: isoform X3
- UniProtKB: Q62609 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233938   ⟸   XM_006233876
- Peptide Label: isoform X2
- UniProtKB: Q62609 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447574   ⟸   XM_017592085
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000060981   ⟸   ENSRNOT00000065953
RefSeq Acc Id: ENSRNOP00000013443   ⟸   ENSRNOT00000013443
Protein Domains
Olfactomedin-like

Transcriptome

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

Promoters
RGD ID:13691931
Promoter ID:EPDNEW_R2455
Type:initiation region
Name:Olfm1_1
Description:olfactomedin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.036,773,812 - 6,773,872EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 6776271 6776272 G A snv ACI/N (MCW), MR/N (MCW)
3 6776291 6776292 G A snv ACI/N (MCW), MR/N (MCW)
3 6780931 6780932 G C snv Buf/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 7172879 7172880 G A snv ACI/N (KNAW), SS/JrHsdMcwi (MCW), MR/N (KNAW)
3 7172899 7172900 G A snv SS/JrHsdMcwi (MCW), MR/N (KNAW), ACI/N (KNAW)
3 7177474 7177475 A T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), LCR/1Mco (UMich), HCR/2Mco (UMich), GH/OmrMcwi (MCW), HCR/1Mco (UMich)
3 7193938 7193939 A T snv SS/JrHsdMcwi (MCW)
3 7193941 7193942 T C snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620320 AgrOrtholog
Ensembl Genes ENSRNOG00000009862 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000013443 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000060981 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013443 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000065953 UniProtKB/Swiss-Prot
InterPro Noelin UniProtKB/Swiss-Prot
  Noelin_dom UniProtKB/Swiss-Prot
  Olfac-like_dom UniProtKB/Swiss-Prot
  Quino_amine_DH_bsu UniProtKB/Swiss-Prot
KEGG Report rno:93667 UniProtKB/Swiss-Prot
NCBI Gene 93667 ENTREZGENE
PANTHER PTHR23192:SF34 UniProtKB/Swiss-Prot
Pfam Noelin-1 UniProtKB/Swiss-Prot
  OLF UniProtKB/Swiss-Prot
PhenoGen Olfm1 PhenoGen
PROSITE ER_TARGET UniProtKB/Swiss-Prot
  OLF UniProtKB/Swiss-Prot
SMART OLF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50969 UniProtKB/Swiss-Prot
UniProt NOE1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62606 UniProtKB/Swiss-Prot
  Q62607 UniProtKB/Swiss-Prot
  Q62608 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Olfm1  olfactomedin 1    olfactomedin related ER localized protein  Name updated 1299863 APPROVED
2002-08-07 Olfm1  olfactomedin related ER localized protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_transcript four different transcripts produced from differential promoter utilization and alternative splicing 729021