Lrfn2 (leucine rich repeat and fibronectin type III domain containing 2) - Rat Genome Database

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Gene: Lrfn2 (leucine rich repeat and fibronectin type III domain containing 2) Rattus norvegicus
Analyze
Symbol: Lrfn2
Name: leucine rich repeat and fibronectin type III domain containing 2
RGD ID: 1311831
Description: Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Is active in postsynaptic density membrane. Orthologous to human LRFN2 (leucine rich repeat and fibronectin type III domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine-rich repeat and fibronectin type-III domain-containing protein 2; LOC316205; Salm1; synaptic adhesion-like molecule 1
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
GRCr8919,395,099 - 19,563,849 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl919,395,145 - 19,561,163 (-)EnsemblGRCr8
mRatBN7.2911,897,425 - 12,066,177 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl911,897,468 - 11,939,931 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx920,403,200 - 20,434,776 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0925,469,396 - 25,500,976 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0923,856,849 - 23,888,562 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0913,845,756 - 14,015,360 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl913,845,757 - 13,877,130 (-)Ensemblrn6Rnor6.0
Rnor_5.0912,776,271 - 12,943,378 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.497,109,376 - 7,141,595 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera99,672,139 - 9,703,921 (-)NCBICelera
RGSC_v3.197,109,333 - 7,313,632 (-)NCBI
Cytogenetic Map9q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. A novel family of adhesion-like molecules that interacts with the NMDA receptor. Wang CY, etal., J Neurosci. 2006 Feb 22;26(8):2174-83.
Additional References at PubMed
PMID:8889548   PMID:16828986   PMID:18585462   PMID:28604739  


Genomics

Comparative Map Data
Lrfn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8919,395,099 - 19,563,849 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl919,395,145 - 19,561,163 (-)EnsemblGRCr8
mRatBN7.2911,897,425 - 12,066,177 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl911,897,468 - 11,939,931 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx920,403,200 - 20,434,776 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0925,469,396 - 25,500,976 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0923,856,849 - 23,888,562 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0913,845,756 - 14,015,360 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl913,845,757 - 13,877,130 (-)Ensemblrn6Rnor6.0
Rnor_5.0912,776,271 - 12,943,378 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.497,109,376 - 7,141,595 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera99,672,139 - 9,703,921 (-)NCBICelera
RGSC_v3.197,109,333 - 7,313,632 (-)NCBI
Cytogenetic Map9q12NCBI
LRFN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38640,391,591 - 40,587,364 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl640,391,591 - 40,587,364 (-)Ensemblhg38GRCh38
GRCh37640,359,330 - 40,555,103 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36640,467,351 - 40,663,104 (-)NCBIBuild 36Build 36hg18NCBI36
Celera641,912,256 - 42,107,705 (-)NCBICelera
Cytogenetic Map6p21.2-p21.1NCBI
HuRef640,076,973 - 40,272,680 (-)NCBIHuRef
CHM1_1640,361,750 - 40,557,459 (-)NCBICHM1_1
T2T-CHM13v2.0640,219,487 - 40,415,195 (-)NCBIT2T-CHM13v2.0
Lrfn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391749,238,630 - 49,404,619 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1749,239,407 - 49,404,616 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381748,931,590 - 49,097,591 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1748,932,379 - 49,097,588 (+)Ensemblmm10GRCm38
MGSCv371749,071,907 - 49,236,915 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361748,397,946 - 48,563,155 (+)NCBIMGSCv36mm8
Celera1752,367,169 - 52,531,112 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1724.66NCBI
Lrfn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554377,201,978 - 7,358,626 (-)Ensembl
ChiLan1.0NW_0049554377,202,466 - 7,358,616 (-)NCBIChiLan1.0ChiLan1.0
LRFN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2554,880,033 - 55,075,266 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1650,750,011 - 50,945,189 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0639,972,362 - 40,167,612 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1641,282,633 - 41,477,067 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl641,282,940 - 41,477,073 (-)EnsemblpanPan2panpan1.1
LRFN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1129,202,552 - 9,248,682 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl129,169,667 - 9,388,109 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha129,239,653 - 9,417,449 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0129,685,895 - 9,865,789 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl129,685,818 - 9,865,680 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1129,219,600 - 9,397,270 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0129,296,393 - 9,474,527 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0129,397,023 - 9,575,112 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lrfn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494644,591,901 - 44,752,579 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647619,330,102 - 19,366,081 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647619,207,623 - 19,368,301 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRFN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl735,723,797 - 35,914,467 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1735,720,969 - 35,914,392 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2740,906,665 - 40,952,914 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRFN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11731,569,027 - 31,760,252 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1731,680,934 - 31,763,037 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604440,394,513 - 40,587,572 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrfn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475418,169,513 - 18,201,639 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475418,054,520 - 18,201,529 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lrfn2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1480,831,606 - 80,997,634 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lrfn2
1294 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:220
Count of miRNA genes:150
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000015705
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
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9360535521031556Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9671488829567695Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat

Markers in Region
RH137795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,025,727 - 12,025,900 (+)MAPPERmRatBN7.2
Rnor_6.0913,975,483 - 13,975,657NCBIRnor6.0
Celera99,799,916 - 9,800,092UniSTS
RH 3.4 Map924.6UniSTS
Cytogenetic Map9q11-q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
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
8 7 123 32 27 16 59 16 2 134 73 3 115 37 69 11 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015705   ⟹   ENSRNOP00000015705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl919,395,145 - 19,464,165 (-)Ensembl
mRatBN7.2 Ensembl911,897,468 - 11,939,931 (-)Ensembl
Rnor_6.0 Ensembl913,845,757 - 13,877,130 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120679   ⟹   ENSRNOP00000098311
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl919,395,145 - 19,561,163 (-)Ensembl
RefSeq Acc Id: NM_001039699   ⟹   NP_001034788
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8919,395,144 - 19,426,859 (-)NCBI
mRatBN7.2911,897,467 - 11,929,185 (-)NCBI
Rnor_6.0913,845,756 - 13,877,130 (-)NCBI
Rnor_5.0912,776,271 - 12,943,378 (-)NCBI
RGSC_v3.497,109,376 - 7,141,595 (-)RGD
Celera99,672,139 - 9,703,921 (-)RGD
Sequence:
RefSeq Acc Id: XM_017596405   ⟹   XP_017451894
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8919,395,099 - 19,563,848 (-)NCBI
mRatBN7.2911,897,425 - 12,066,177 (-)NCBI
Rnor_6.0913,845,756 - 14,015,360 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596406   ⟹   XP_017451895
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8919,395,099 - 19,563,849 (-)NCBI
mRatBN7.2911,897,425 - 12,066,177 (-)NCBI
Rnor_6.0913,845,756 - 14,015,360 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001034788 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451894 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451895 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAZ20638 (Get FASTA)   NCBI Sequence Viewer  
  EDM18946 (Get FASTA)   NCBI Sequence Viewer  
  Q460M5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001034788   ⟸   NM_001039699
- Peptide Label: precursor
- UniProtKB: Q460M5 (UniProtKB/Swiss-Prot),   G3V7J3 (UniProtKB/TrEMBL),   A6JID6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451894   ⟸   XM_017596405
- Peptide Label: isoform X1
- UniProtKB: Q460M5 (UniProtKB/Swiss-Prot),   G3V7J3 (UniProtKB/TrEMBL),   A6JID6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451895   ⟸   XM_017596406
- Peptide Label: isoform X1
- UniProtKB: Q460M5 (UniProtKB/Swiss-Prot),   G3V7J3 (UniProtKB/TrEMBL),   A6JID6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015705   ⟸   ENSRNOT00000015705
Ensembl Acc Id: ENSRNOP00000098311   ⟸   ENSRNOT00000120679
Protein Domains
Fibronectin type-III   Ig-like   LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q460M5-F1-model_v2 AlphaFold Q460M5 1-788 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311831 AgrOrtholog
BioCyc Gene G2FUF-28328 BioCyc
Ensembl Genes ENSRNOG00000011803 Ensembl
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.80.10.10 UniProtKB/Swiss-Prot
InterPro Cys-rich_flank_reg_C UniProtKB/Swiss-Prot
  FN3_dom UniProtKB/Swiss-Prot
  FN3_sf UniProtKB/Swiss-Prot
  Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_I-set UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  Ig_sub2 UniProtKB/Swiss-Prot
  Leu-rich_rpt UniProtKB/Swiss-Prot
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot
  LRFN UniProtKB/Swiss-Prot
  LRR_dom_sf UniProtKB/Swiss-Prot
NCBI Gene 316205 ENTREZGENE
PANTHER LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE-III DOMAIN-CONTAINING PROTEIN 2 UniProtKB/Swiss-Prot
  SYNAPTIC ADHESION-LIKE MOLECULE SALM UniProtKB/Swiss-Prot
Pfam fn3 UniProtKB/Swiss-Prot
  I-set UniProtKB/Swiss-Prot
  LRR_8 UniProtKB/Swiss-Prot
PhenoGen Lrfn2 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot
  IG_LIKE UniProtKB/Swiss-Prot
  LRR UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000011803 RatGTEx
SMART IGc2 UniProtKB/Swiss-Prot
  LRR_TYP UniProtKB/Swiss-Prot
  LRRCT UniProtKB/Swiss-Prot
  SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP L domain-like UniProtKB/Swiss-Prot
  SSF48726 UniProtKB/Swiss-Prot
  SSF49265 UniProtKB/Swiss-Prot
UniProt A0ABK0L7V1_RAT UniProtKB/TrEMBL
  A6JID6 ENTREZGENE, UniProtKB/TrEMBL
  G3V7J3 ENTREZGENE, UniProtKB/TrEMBL
  LRFN2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Lrfn2  leucine rich repeat and fibronectin type III domain containing 2  Lrfn2_predicted  leucine rich repeat and fibronectin type III domain containing 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Lrfn2_predicted  leucine rich repeat and fibronectin type III domain containing 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED