Lrfn1 (leucine rich repeat and fibronectin type III domain containing 1) - Rat Genome Database

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Gene: Lrfn1 (leucine rich repeat and fibronectin type III domain containing 1) Rattus norvegicus
Analyze
Symbol: Lrfn1
Name: leucine rich repeat and fibronectin type III domain containing 1
RGD ID: 1304707
Description: Involved in regulation of postsynaptic density assembly. Localizes to integral component of postsynaptic density membrane. Orthologous to human LRFN1 (leucine rich repeat and fibronectin type III domain containing 1); INTERACTS WITH acrylamide; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 60S ribosomal protein L38-like; leucine-rich repeat and fibronectin type III domain-containing protein 1; LOC100911296; LOC365222; synaptic adhesion-like molecule 2
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
mRatBN7.2183,742,442 - 83,761,450 (+)NCBI
Rnor_6.0 Ensembl185,291,462 - 85,300,825 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0185,290,887 - 85,308,498 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0186,506,887 - 86,524,071 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,567,056 - 83,580,643 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,645,167 - 83,653,000 (+)NCBI
Celera178,143,426 - 78,157,015 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References

Additional References at PubMed
PMID:16828986  


Genomics

Comparative Map Data
Lrfn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2183,742,442 - 83,761,450 (+)NCBI
Rnor_6.0 Ensembl185,291,462 - 85,300,825 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0185,290,887 - 85,308,498 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0186,506,887 - 86,524,071 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,567,056 - 83,580,643 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,645,167 - 83,653,000 (+)NCBI
Celera178,143,426 - 78,157,015 (+)NCBICelera
Cytogenetic Map1q21NCBI
LRFN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1939,306,566 - 39,320,863 (-)EnsemblGRCh38hg38GRCh38
GRCh381939,306,566 - 39,320,863 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371939,797,206 - 39,811,503 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361944,489,297 - 44,497,816 (-)NCBINCBI36hg18NCBI36
Celera1936,599,137 - 36,607,655 (-)NCBI
Cytogenetic Map19q13.2NCBI
HuRef1936,243,970 - 36,252,487 (-)NCBIHuRef
CHM1_11939,798,264 - 39,806,781 (-)NCBICHM1_1
Lrfn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,151,227 - 28,167,667 (+)NCBIGRCm39mm39
GRCm39 Ensembl728,151,405 - 28,167,667 (+)Ensembl
GRCm38728,451,893 - 28,468,242 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,451,980 - 28,468,242 (+)EnsemblGRCm38mm10GRCm38
MGSCv37729,237,004 - 29,252,567 (+)NCBIGRCm37mm9NCBIm37
MGSCv36728,160,798 - 28,170,892 (+)NCBImm8
Celera723,010,018 - 23,029,505 (+)NCBICelera
Cytogenetic Map7A3NCBI
Lrfn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955468234,123 - 241,535 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955468231,164 - 240,924 (+)NCBIChiLan1.0ChiLan1.0
LRFN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11944,951,724 - 44,965,757 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1944,952,799 - 44,960,507 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01936,405,065 - 36,419,178 (-)NCBIMhudiblu_PPA_v0panPan3
LRFN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11113,888,736 - 113,898,240 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1113,891,484 - 113,898,140 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1113,287,918 - 113,299,713 (+)NCBI
ROS_Cfam_1.01114,485,184 - 114,496,978 (+)NCBI
UMICH_Zoey_3.11114,043,864 - 114,055,645 (+)NCBI
UNSW_CanFamBas_1.01113,676,649 - 113,688,444 (+)NCBI
UU_Cfam_GSD_1.01114,671,778 - 114,683,620 (+)NCBI
Lrfn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934913,739,195 - 13,751,202 (-)NCBI
SpeTri2.0NW_0049366612,167,264 - 2,179,193 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRFN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl647,971,275 - 47,978,430 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1647,971,270 - 47,981,532 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214143,764,593 - 143,776,877 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRFN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1633,913,147 - 33,927,320 (-)NCBI
ChlSab1.1 Ensembl633,912,176 - 33,922,162 (-)Ensembl
Vero_WHO_p1.0NW_02366607311,933,514 - 11,947,822 (-)NCBI
Lrfn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479412,651,391 - 12,663,781 (-)NCBI

Position Markers
D1Uwm1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2183,746,356 - 83,746,486 (-)MAPPER
Rnor_6.0185,305,849 - 85,305,978NCBIRnor6.0
Rnor_5.0186,520,928 - 86,521,057UniSTSRnor5.0
RGSC_v3.4183,566,126 - 83,566,256RGDRGSC3.4
RGSC_v3.4183,566,127 - 83,566,256UniSTSRGSC3.4
RGSC_v3.1183,644,237 - 83,644,367RGD
Celera178,142,497 - 78,142,626UniSTS
Cytogenetic Map1q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14190724986907249Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17968976594909507Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:218
Count of miRNA genes:159
Interacting mature miRNAs:171
Transcripts:ENSRNOT00000026900, ENSRNOT00000057073
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 66 5
Low 2 27 28 12 19 12 1 8 33 36 10
Below cutoff 1 16 29 29 29 8 10 2 1 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001127694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006228626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006228628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039084977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC110862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026900   ⟹   ENSRNOP00000026900
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl185,297,239 - 85,300,825 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000057073   ⟹   ENSRNOP00000053905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl185,291,462 - 85,300,825 (-)Ensembl
RefSeq Acc Id: NM_001108910   ⟹   NP_001102380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0185,297,226 - 85,305,049 (-)NCBI
Rnor_5.0186,506,887 - 86,524,071 (-)NCBI
RGSC_v3.4183,567,056 - 83,580,643 (+)RGD
Celera178,143,426 - 78,151,199 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001127694   ⟹   NP_001121166
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,747,292 - 83,761,449 (+)NCBI
Rnor_6.0185,291,462 - 85,300,825 (-)NCBI
Rnor_5.0186,506,887 - 86,524,071 (-)NCBI
RGSC_v3.4183,567,056 - 83,580,643 (+)RGD
Celera178,147,600 - 78,157,015 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228626   ⟹   XP_006228688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,746,313 - 83,761,450 (+)NCBI
Rnor_6.0185,290,887 - 85,306,746 (-)NCBI
Rnor_5.0186,506,887 - 86,524,071 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006228628   ⟹   XP_006228690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,745,594 - 83,761,450 (+)NCBI
Rnor_6.0185,290,887 - 85,306,746 (-)NCBI
Rnor_5.0186,506,887 - 86,524,071 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759174   ⟹   XP_008757396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,742,442 - 83,761,450 (+)NCBI
Rnor_6.0185,290,887 - 85,308,498 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759175   ⟹   XP_008757397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0185,290,887 - 85,308,498 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589471   ⟹   XP_017444960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,746,313 - 83,761,450 (+)NCBI
Rnor_6.0185,290,887 - 85,306,746 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589472   ⟹   XP_017444961
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,742,442 - 83,761,450 (+)NCBI
Rnor_6.0185,290,887 - 85,308,498 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589473   ⟹   XP_017444962
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,743,803 - 83,761,450 (+)NCBI
Rnor_6.0185,290,887 - 85,307,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039084965   ⟹   XP_038940893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,744,639 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084966   ⟹   XP_038940894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,744,869 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084968   ⟹   XP_038940896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,744,639 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084971   ⟹   XP_038940899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,743,803 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084973   ⟹   XP_038940901
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,745,594 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084975   ⟹   XP_038940903
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,746,313 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084976   ⟹   XP_038940904
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,744,868 - 83,761,450 (+)NCBI
RefSeq Acc Id: XM_039084977   ⟹   XP_038940905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,746,313 - 83,761,450 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102380   ⟸   NM_001108910
- Peptide Label: isoform 2 precursor
- Sequence:
RefSeq Acc Id: NP_001121166   ⟸   NM_001127694
- Peptide Label: precursor
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006228690   ⟸   XM_006228628
- Peptide Label: isoform X1
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006228688   ⟸   XM_006228626
- Peptide Label: isoform X1
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008757397   ⟸   XM_008759175
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008757396   ⟸   XM_008759174
- Peptide Label: isoform X1
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017444961   ⟸   XM_017589472
- Peptide Label: isoform X1
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017444962   ⟸   XM_017589473
- Peptide Label: isoform X1
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017444960   ⟸   XM_017589471
- Peptide Label: isoform X1
- UniProtKB: P0C7J6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000053905   ⟸   ENSRNOT00000057073
RefSeq Acc Id: ENSRNOP00000026900   ⟸   ENSRNOT00000026900
RefSeq Acc Id: XP_038940899   ⟸   XM_039084971
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940896   ⟸   XM_039084968
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940893   ⟸   XM_039084965
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940904   ⟸   XM_039084976
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940894   ⟸   XM_039084966
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940901   ⟸   XM_039084973
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940903   ⟸   XM_039084975
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940905   ⟸   XM_039084977
- Peptide Label: isoform X1
Protein Domains
Fibronectin type-III   Ig-like   LRRCT   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)
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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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304707 AgrOrtholog
Ensembl Genes ENSRNOG00000019869 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026900 UniProtKB/TrEMBL
  ENSRNOP00000053905 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026900 UniProtKB/TrEMBL
  ENSRNOT00000057073 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot
  FN3_sf UniProtKB/Swiss-Prot
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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
KEGG Report rno:365222 UniProtKB/Swiss-Prot
NCBI Gene 365222 ENTREZGENE
Pfam fn3 UniProtKB/Swiss-Prot
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lrfn1 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot
UniProt D4A5B8_RAT UniProtKB/TrEMBL
  LRFN1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Lrfn1  leucine rich repeat and fibronectin type III domain containing 1  LOC100911296  60S ribosomal protein L38-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100911296  60S ribosomal protein L38-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Lrfn1  leucine rich repeat and fibronectin type III domain containing 1   Lrfn1_predicted  leucine rich repeat and fibronectin type III domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lrfn1_predicted  leucine rich repeat and fibronectin type III domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED