Olfm2 (olfactomedin 2) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Olfm2 (olfactomedin 2) Rattus norvegicus
Analyze
Symbol: Olfm2
Name: olfactomedin 2
RGD ID: 1309741
Description: Involved in regulation of vascular associated smooth muscle cell dedifferentiation. Predicted to be located in several cellular components, including extracellular region; nucleus; and synaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in extracellular space and glutamatergic synapse. Predicted to be extrinsic component of postsynaptic density membrane. Orthologous to human OLFM2 (olfactomedin 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC313783; MGC109424; noelin-2; olfactomedin-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,480,703 - 27,558,416 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl827,480,711 - 27,558,460 (-)EnsemblGRCr8
mRatBN7.2819,204,472 - 19,282,154 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,204,475 - 19,282,117 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx823,224,798 - 23,283,196 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,522,638 - 21,581,036 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,434,221 - 19,493,166 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0821,684,307 - 21,762,000 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,681,266 - 21,743,338 (-)Ensemblrn6Rnor6.0
Rnor_5.0821,740,363 - 21,818,045 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4819,685,433 - 19,746,974 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera820,599,780 - 20,658,825 (-)NCBICelera
RGSC_v3.1819,685,433 - 19,746,974 (-)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
protein binding  (IPI,ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Olfactomedin 2 Regulates Smooth Muscle Phenotypic Modulation and Vascular Remodeling Through Mediating Runt-Related Transcription Factor 2 Binding to Serum Response Factor. Shi N, etal., Arterioscler Thromb Vasc Biol. 2017 Mar;37(3):446-454. doi: 10.1161/ATVBAHA.116.308606. Epub 2017 Jan 5.
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:21228389   PMID:22632720   PMID:25218043   PMID:25298399  


Genomics

Comparative Map Data
Olfm2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,480,703 - 27,558,416 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl827,480,711 - 27,558,460 (-)EnsemblGRCr8
mRatBN7.2819,204,472 - 19,282,154 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,204,475 - 19,282,117 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx823,224,798 - 23,283,196 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,522,638 - 21,581,036 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,434,221 - 19,493,166 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0821,684,307 - 21,762,000 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,681,266 - 21,743,338 (-)Ensemblrn6Rnor6.0
Rnor_5.0821,740,363 - 21,818,045 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4819,685,433 - 19,746,974 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera820,599,780 - 20,658,825 (-)NCBICelera
RGSC_v3.1819,685,433 - 19,746,974 (-)NCBI
Cytogenetic Map8q13NCBI
OLFM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38199,853,718 - 9,936,515 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl199,853,718 - 9,936,558 (-)Ensemblhg38GRCh38
GRCh37199,964,394 - 10,047,191 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36199,825,394 - 9,908,070 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34199,825,394 - 9,908,070NCBI
Celera199,859,823 - 9,942,535 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef199,545,037 - 9,627,331 (-)NCBIHuRef
CHM1_1199,964,109 - 10,046,786 (-)NCBICHM1_1
T2T-CHM13v2.0199,979,884 - 10,062,687 (-)NCBIT2T-CHM13v2.0
Olfm2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,578,986 - 20,657,660 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl920,578,986 - 20,657,645 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38920,667,690 - 20,746,333 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl920,667,690 - 20,746,349 (-)Ensemblmm10GRCm38
MGSCv37920,472,430 - 20,532,658 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36920,418,102 - 20,478,631 (-)NCBIMGSCv36mm8
Celera917,938,428 - 17,996,310 (-)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.6NCBI
Olfm2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,264,831 - 1,328,877 (-)Ensembl
ChiLan1.0NW_0049554951,264,831 - 1,328,877 (-)NCBIChiLan1.0ChiLan1.0
OLFM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22014,772,348 - 14,855,375 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11913,774,905 - 13,855,608 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0199,408,161 - 9,488,855 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11910,071,375 - 10,151,178 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1910,071,375 - 10,151,183 (-)EnsemblpanPan2panpan1.1
OLFM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12051,148,013 - 51,153,303 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2051,148,157 - 51,153,314 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2050,955,590 - 51,016,889 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02051,613,108 - 51,674,476 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2051,612,962 - 51,674,473 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12050,820,875 - 50,882,225 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02051,245,805 - 51,307,078 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02051,486,759 - 51,548,349 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Olfm2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,969,055 - 210,029,710 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936659325,436 - 372,225 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936659324,996 - 385,646 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OLFM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl268,734,081 - 68,807,191 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1268,734,078 - 68,807,207 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2269,063,856 - 69,135,514 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OLFM2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.168,939,966 - 8,947,913 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl68,939,603 - 8,947,678 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607411,068,366 - 11,161,713 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Olfm2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,135,245 - 2,200,332 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248282,134,728 - 2,200,354 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Olfm2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1816,934,731 - 17,010,976 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Olfm2
1050 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:320
Count of miRNA genes:162
Interacting mature miRNAs:179
Transcripts:ENSRNOT00000027829
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
D8Got19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,257,769 - 19,257,905 (+)MAPPERmRatBN7.2
Rnor_6.0821,737,631 - 21,737,766NCBIRnor6.0
Rnor_5.0821,793,692 - 21,793,827UniSTSRnor5.0
RGSC_v3.4819,741,292 - 19,741,428RGDRGSC3.4
RGSC_v3.4819,741,293 - 19,741,428UniSTSRGSC3.4
Celera820,653,144 - 20,653,279UniSTS
RGSC_v3.1819,741,293 - 19,741,428RGD
RH 3.4 Map8180.5UniSTS
RH 3.4 Map8180.5RGD
Cytogenetic Map8q13UniSTS
Olfm2  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8827,485,381 - 27,485,816 (+)Marker Load Pipeline
mRatBN7.2819,209,150 - 19,209,585 (+)MAPPERmRatBN7.2
Rnor_6.0821,688,981 - 21,689,415NCBIRnor6.0
Rnor_5.0821,745,042 - 21,745,476UniSTSRnor5.0
Celera820,604,454 - 20,604,888UniSTS
Cytogenetic Map8q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 157 79 78 47 71 47 6 308 171 11 136 66 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000027829   ⟹   ENSRNOP00000027829
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl827,480,711 - 27,540,382 (-)Ensembl
mRatBN7.2 Ensembl819,204,475 - 19,263,482 (-)Ensembl
Rnor_6.0 Ensembl821,681,266 - 21,743,338 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108558   ⟹   ENSRNOP00000097675
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl827,480,711 - 27,558,460 (-)Ensembl
mRatBN7.2 Ensembl819,204,695 - 19,282,117 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117797   ⟹   ENSRNOP00000083962
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl827,480,711 - 27,540,867 (-)Ensembl
mRatBN7.2 Ensembl819,204,478 - 19,282,096 (-)Ensembl
RefSeq Acc Id: NM_001015017   ⟹   NP_001015017
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,480,708 - 27,539,661 (-)NCBI
mRatBN7.2819,204,477 - 19,263,451 (-)NCBI
Rnor_6.0821,684,307 - 21,743,312 (-)NCBI
Rnor_5.0821,740,363 - 21,818,045 (-)NCBI
RGSC_v3.4819,685,433 - 19,746,974 (-)RGD
Celera820,599,780 - 20,658,825 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242643   ⟹   XP_006242705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,480,703 - 27,558,416 (-)NCBI
mRatBN7.2819,204,472 - 19,282,154 (-)NCBI
Rnor_6.0821,684,713 - 21,762,000 (-)NCBI
Rnor_5.0821,740,363 - 21,818,045 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001015017   ⟸   NM_001015017
- Peptide Label: precursor
- UniProtKB: A6JNL2 (UniProtKB/Swiss-Prot),   Q568Y7 (UniProtKB/Swiss-Prot),   A0A8I6A0A4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242705   ⟸   XM_006242643
- Peptide Label: isoform X1
- UniProtKB: A6JNL1 (UniProtKB/TrEMBL),   A0A8I6A0A4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027829   ⟸   ENSRNOT00000027829
Ensembl Acc Id: ENSRNOP00000083962   ⟸   ENSRNOT00000117797
Ensembl Acc Id: ENSRNOP00000097675   ⟸   ENSRNOT00000108558
Protein Domains
Olfactomedin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q568Y7-F1-model_v2 AlphaFold Q568Y7 1-478 view protein structure

Transcriptome

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

Promoters
RGD ID:13695762
Promoter ID:EPDNEW_R6287
Type:single initiation site
Name:Olfm2_1
Description:olfactomedin 2
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_6.0821,743,353 - 21,743,413EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309741 AgrOrtholog
BioCyc Gene G2FUF-31460 BioCyc
Ensembl Genes ENSRNOG00000020519 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027829 ENTREZGENE
  ENSRNOT00000027829.8 UniProtKB/Swiss-Prot
  ENSRNOT00000108558 ENTREZGENE
IMAGE_CLONE IMAGE:7319232 IMAGE-MGC_LOAD
InterPro Noelin_dom UniProtKB/Swiss-Prot
  Olfac-like_dom UniProtKB/Swiss-Prot
  Olfactomedin-like_domain UniProtKB/Swiss-Prot
KEGG Report rno:313783 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109424 IMAGE-MGC_LOAD
NCBI Gene 313783 ENTREZGENE
PANTHER OLFACTOMEDIN-RELATED UniProtKB/Swiss-Prot
  PTHR23192:SF27 UniProtKB/Swiss-Prot
Pfam Noelin-1 UniProtKB/Swiss-Prot
  OLF UniProtKB/Swiss-Prot
PhenoGen Olfm2 PhenoGen
PROSITE OLF UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000020519 RatGTEx
SMART OLF UniProtKB/Swiss-Prot
UniProt A0A8I6A0A4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GMM3_RAT UniProtKB/TrEMBL
  A6JNL1 ENTREZGENE, UniProtKB/TrEMBL
  A6JNL2 ENTREZGENE
  NOE2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A6JNL2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Olfm2  olfactomedin 2  Olfm2_predicted  olfactomedin 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Olfm2_predicted  olfactomedin 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED