Olfm4 (olfactomedin 4) - Rat Genome Database

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Gene: Olfm4 (olfactomedin 4) Rattus norvegicus
Analyze
Symbol: Olfm4
Name: olfactomedin 4
RGD ID: 1311708
Description: Predicted to enable cadherin binding activity and structural molecule activity. Predicted to be involved in positive regulation of substrate adhesion-dependent cell spreading and signal transduction. Predicted to act upstream of or within negative regulation of canonical NF-kappaB signal transduction and negative regulation of immune response. Predicted to be located in several cellular components, including intercellular bridge; perinuclear region of cytoplasm; and specific granule. Predicted to be part of protein-containing complex. Predicted to be active in extracellular space. Orthologous to human OLFM4 (olfactomedin 4); INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC290409; olfactomedin-4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81561,790,889 - 61,838,773 (+)NCBIGRCr8
mRatBN7.21555,385,100 - 55,429,687 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1555,407,148 - 55,429,681 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1559,532,623 - 59,555,138 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01560,650,998 - 60,673,516 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01557,475,894 - 57,498,416 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01562,384,263 - 62,429,450 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1562,406,873 - 62,429,449 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01566,064,452 - 66,086,655 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41561,267,802 - 61,290,288 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11561,222,799 - 61,304,901 (+)NCBI
Celera1554,981,171 - 55,003,416 (+)NCBICelera
Cytogenetic Map15q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14962908   PMID:16502470   PMID:16566923   PMID:19056867   PMID:19199708   PMID:20534456   PMID:23376485   PMID:23533145   PMID:23922742  


Genomics

Comparative Map Data
Olfm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81561,790,889 - 61,838,773 (+)NCBIGRCr8
mRatBN7.21555,385,100 - 55,429,687 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1555,407,148 - 55,429,681 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1559,532,623 - 59,555,138 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01560,650,998 - 60,673,516 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01557,475,894 - 57,498,416 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01562,384,263 - 62,429,450 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1562,406,873 - 62,429,449 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01566,064,452 - 66,086,655 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41561,267,802 - 61,290,288 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11561,222,799 - 61,304,901 (+)NCBI
Celera1554,981,171 - 55,003,416 (+)NCBICelera
Cytogenetic Map15q12NCBI
OLFM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381353,028,813 - 53,052,057 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1353,028,813 - 53,052,057 (+)EnsemblGRCh38hg38GRCh38
GRCh371353,602,948 - 53,626,192 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361352,500,973 - 52,524,193 (+)NCBINCBI36Build 36hg18NCBI36
Build 341352,500,972 - 52,524,187NCBI
Celera1334,589,022 - 34,612,243 (+)NCBICelera
Cytogenetic Map13q14.3NCBI
HuRef1334,317,261 - 34,340,581 (+)NCBIHuRef
CHM1_11353,570,960 - 53,594,281 (+)NCBICHM1_1
T2T-CHM13v2.01352,244,407 - 52,267,681 (+)NCBIT2T-CHM13v2.0
Olfm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391480,237,742 - 80,260,581 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1480,221,521 - 80,260,579 (+)EnsemblGRCm39 Ensembl
GRCm381480,000,302 - 80,023,141 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1479,984,081 - 80,023,139 (+)EnsemblGRCm38mm10GRCm38
MGSCv371480,400,109 - 80,421,737 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361478,734,457 - 78,756,085 (+)NCBIMGSCv36mm8
Celera1477,496,092 - 77,517,728 (+)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1442.78NCBI
Olfm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540450,549,151 - 50,570,305 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540450,549,218 - 50,570,302 (-)NCBIChiLan1.0ChiLan1.0
OLFM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21454,369,604 - 54,393,154 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11353,017,773 - 53,041,321 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01334,066,155 - 34,089,468 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11352,873,289 - 52,896,616 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1352,873,289 - 52,896,827 (+)Ensemblpanpan1.1panPan2
OLFM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12210,053,494 - 10,075,759 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl229,944,025 - 10,074,722 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2210,049,679 - 10,071,946 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02210,278,301 - 10,300,554 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2210,278,100 - 10,299,477 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1229,975,280 - 9,997,549 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02210,025,509 - 10,047,757 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02210,039,441 - 10,061,690 (+)NCBIUU_Cfam_GSD_1.0
Olfm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945150,976,186 - 150,997,332 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936667907,473 - 922,291 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936667905,556 - 923,105 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OLFM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1126,350,203 - 26,375,716 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11126,252,948 - 26,375,531 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21127,026,373 - 27,051,872 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OLFM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,753,677 - 30,810,980 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl330,787,999 - 30,810,980 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605713,002,697 - 13,025,716 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Olfm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474814,494,619 - 14,516,015 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474814,394,961 - 14,515,850 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Olfm4
296 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:206
Count of miRNA genes:142
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000047572
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155079449473699215Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2317050Aia24Adjuvant induced arthritis QTL 242.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)155284790873690657Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat


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 2 16 16 2 16 2
Low 1 4 17 10 12 10 60 35 24 11
Below cutoff 27 16 8 5 8 2 2 14 15 2

Sequence


RefSeq Acc Id: ENSRNOT00000047572   ⟹   ENSRNOP00000039120
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1555,407,148 - 55,429,681 (+)Ensembl
Rnor_6.0 Ensembl1562,406,873 - 62,429,449 (+)Ensembl
RefSeq Acc Id: NM_001106052   ⟹   NP_001099522
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,816,231 - 61,838,764 (+)NCBI
mRatBN7.21555,407,148 - 55,429,681 (+)NCBI
Rnor_6.01562,406,873 - 62,429,449 (+)NCBI
Rnor_5.01566,064,452 - 66,086,655 (+)NCBI
RGSC_v3.41561,267,802 - 61,290,288 (+)RGD
Celera1554,981,171 - 55,003,416 (+)RGD
Sequence:
RefSeq Acc Id: XM_008770863   ⟹   XP_008769085
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,790,889 - 61,838,773 (+)NCBI
mRatBN7.21555,385,100 - 55,429,687 (+)NCBI
Rnor_6.01562,384,263 - 62,429,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093182   ⟹   XP_038949110
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,828,469 - 61,838,773 (+)NCBI
mRatBN7.21555,419,391 - 55,429,687 (+)NCBI
RefSeq Acc Id: XM_063274167   ⟹   XP_063130237
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,820,831 - 61,838,773 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001099522 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769085 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949110 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130237 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02377 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000039120.3
RefSeq Acc Id: NP_001099522   ⟸   NM_001106052
- Peptide Label: precursor
- UniProtKB: D3ZMI6 (UniProtKB/TrEMBL),   A6HU14 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769085   ⟸   XM_008770863
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000039120   ⟸   ENSRNOT00000047572
RefSeq Acc Id: XP_038949110   ⟸   XM_039093182
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063130237   ⟸   XM_063274167
- Peptide Label: isoform X2
Protein Domains
Olfactomedin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZMI6-F1-model_v2 AlphaFold D3ZMI6 1-511 view protein structure

Transcriptome

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

Promoters
RGD ID:13699851
Promoter ID:EPDNEW_R10375
Type:multiple initiation site
Name:Olfm4_1
Description:olfactomedin 4
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_6.01562,406,879 - 62,406,939EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311708 AgrOrtholog
BioCyc Gene G2FUF-12972 BioCyc
Ensembl Genes ENSRNOG00000013280 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047572.4 UniProtKB/TrEMBL
InterPro Olfac-like UniProtKB/TrEMBL
KEGG Report rno:290409 UniProtKB/TrEMBL
NCBI Gene 290409 ENTREZGENE
PANTHER OLFACTOMEDIN-RELATED UniProtKB/TrEMBL
  PTHR23192:SF7 UniProtKB/TrEMBL
Pfam OLF UniProtKB/TrEMBL
PhenoGen Olfm4 PhenoGen
PROSITE OLF UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013280 RatGTEx
SMART OLF UniProtKB/TrEMBL
UniProt A6HU14 ENTREZGENE, UniProtKB/TrEMBL
  D3ZMI6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Olfm4  olfactomedin 4   Olfm4_predicted  olfactomedin 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Olfm4_predicted  olfactomedin 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED