Lrfn5 (leucine rich repeat and fibronectin type III domain containing 5) - Rat Genome Database

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Gene: Lrfn5 (leucine rich repeat and fibronectin type III domain containing 5) Rattus norvegicus
Analyze
Symbol: Lrfn5
Name: leucine rich repeat and fibronectin type III domain containing 5
RGD ID: 1309357
Description: Involved in synaptic membrane adhesion. Is integral component of postsynaptic density membrane. Orthologous to human LRFN5 (leucine rich repeat and fibronectin type III domain containing 5); 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: leucine-rich repeat and fibronectin type-III domain-containing protein 5; LOC314164
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2679,466,403 - 79,822,821 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl679,467,961 - 79,822,815 (+)Ensembl
Rnor_6.0683,082,593 - 83,438,601 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl683,083,740 - 83,438,601 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0692,601,831 - 92,958,936 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4682,482,116 - 82,656,279 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1682,889,667 - 82,906,372 (+)NCBI
Celera678,123,282 - 78,474,424 (+)NCBICelera
Cytogenetic Map6q23NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:16828986   PMID:27152329  


Genomics

Comparative Map Data
Lrfn5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2679,466,403 - 79,822,821 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl679,467,961 - 79,822,815 (+)Ensembl
Rnor_6.0683,082,593 - 83,438,601 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl683,083,740 - 83,438,601 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0692,601,831 - 92,958,936 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4682,482,116 - 82,656,279 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1682,889,667 - 82,906,372 (+)NCBI
Celera678,123,282 - 78,474,424 (+)NCBICelera
Cytogenetic Map6q23NCBI
LRFN5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381441,606,876 - 41,904,549 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1441,606,876 - 41,904,549 (+)EnsemblGRCh38hg38GRCh38
GRCh371442,076,079 - 42,373,752 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361441,147,090 - 41,443,499 (+)NCBINCBI36hg18NCBI36
Build 341441,147,093 - 41,443,498NCBI
Celera1421,937,439 - 22,234,297 (+)NCBI
Cytogenetic Map14q21.1NCBI
HuRef1422,187,067 - 22,483,854 (+)NCBIHuRef
CHM1_11442,014,900 - 42,311,898 (+)NCBICHM1_1
T2T-CHM13v2.01435,797,646 - 36,095,321 (+)NCBI
Lrfn5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391261,569,356 - 61,913,554 (+)NCBIGRCm39mm39
GRCm39 Ensembl1261,569,936 - 61,905,128 (+)Ensembl
GRCm381261,522,851 - 61,857,928 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1261,523,150 - 61,858,342 (+)EnsemblGRCm38mm10GRCm38
MGSCv371262,625,619 - 62,946,245 (+)NCBIGRCm37mm9NCBIm37
MGSCv361262,442,645 - 62,763,271 (+)NCBImm8
Celera1262,712,498 - 63,024,396 (+)NCBICelera
Cytogenetic Map12C1NCBI
Lrfn5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540919,710,305 - 19,856,123 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540919,710,527 - 19,969,984 (-)NCBIChiLan1.0ChiLan1.0
LRFN5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11440,519,143 - 40,814,212 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1440,676,278 - 40,814,212 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01422,185,289 - 22,480,641 (+)NCBIMhudiblu_PPA_v0panPan3
LRFN5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1819,365,786 - 19,602,551 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl819,367,570 - 19,602,185 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha819,177,231 - 19,413,096 (+)NCBI
ROS_Cfam_1.0819,508,003 - 19,744,373 (+)NCBI
ROS_Cfam_1.0 Ensembl819,509,804 - 19,745,878 (+)Ensembl
UMICH_Zoey_3.1819,183,646 - 19,420,029 (+)NCBI
UNSW_CanFamBas_1.0819,256,859 - 19,493,267 (+)NCBI
UU_Cfam_GSD_1.0819,517,360 - 19,753,738 (+)NCBI
Lrfn5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864051,402,747 - 51,649,903 (+)NCBI
SpeTri2.0NW_00493649414,908,783 - 15,155,797 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRFN5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1171,906,198 - 172,177,950 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11171,906,130 - 172,177,726 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21191,439,600 - 191,710,127 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRFN5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12418,421,057 - 18,712,096 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2418,568,568 - 18,712,609 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660537,563,895 - 7,851,872 (+)NCBIVero_WHO_p1.0
Lrfn5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462481311,049,888 - 11,196,095 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462481310,930,009 - 11,196,036 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D6Got310  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2679,516,001 - 79,516,176 (+)MAPPERmRatBN7.2
Rnor_6.0683,131,842 - 83,132,016NCBIRnor6.0
Rnor_5.0692,651,058 - 92,651,232UniSTSRnor5.0
RGSC_v3.4682,607,395 - 82,607,569UniSTSRGSC3.4
Celera678,171,147 - 78,171,321UniSTS
Cytogenetic Map6q23UniSTS
D6Got304  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0683,101,929 - 83,102,019NCBIRnor6.0
Rnor_5.0692,621,145 - 92,621,235UniSTSRnor5.0
RGSC_v3.4682,637,423 - 82,637,513UniSTSRGSC3.4
Celera678,141,342 - 78,141,436UniSTS
Cytogenetic Map6q23UniSTS
RH136499  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2679,637,593 - 79,637,802 (+)MAPPERmRatBN7.2
mRatBN7.21346,731,287 - 46,731,496 (+)MAPPERmRatBN7.2
Rnor_6.01352,124,812 - 52,125,020NCBIRnor6.0
Rnor_6.0683,252,719 - 83,252,927NCBIRnor6.0
Rnor_5.01357,174,343 - 57,174,551UniSTSRnor5.0
Rnor_5.0692,772,158 - 92,772,366UniSTSRnor5.0
RGSC_v3.4682,484,770 - 82,484,978UniSTSRGSC3.4
RGSC_v3.41348,297,687 - 48,297,895UniSTSRGSC3.4
Celera1347,051,865 - 47,052,073UniSTS
Celera678,292,310 - 78,292,518UniSTS
Cytogenetic Map13q13UniSTS
Cytogenetic Map6q23UniSTS
Lrfn5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2679,806,365 - 79,807,251 (+)MAPPERmRatBN7.2
Rnor_6.0683,422,152 - 83,423,037NCBIRnor6.0
Rnor_5.0692,942,487 - 92,943,372UniSTSRnor5.0
RGSC_v3.4682,886,504 - 82,887,389UniSTSRGSC3.4
Celera678,457,967 - 78,458,852UniSTS
Cytogenetic Map6q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65672856290198260Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)67222764181132889Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:25
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000007600
Prediction methods: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 60
Low 2 8 22 31
Below cutoff 2 28 12 7 2 7 1 1 4 1 9 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007600   ⟹   ENSRNOP00000007600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl679,467,961 - 79,822,815 (+)Ensembl
Rnor_6.0 Ensembl683,083,740 - 83,438,601 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084258   ⟹   ENSRNOP00000073272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl683,421,882 - 83,432,133 (+)Ensembl
RefSeq Acc Id: NM_001108024   ⟹   NP_001101494
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2679,467,961 - 79,822,815 (+)NCBI
Rnor_6.0683,083,740 - 83,438,601 (+)NCBI
Rnor_5.0692,601,831 - 92,958,936 (+)NCBI
RGSC_v3.4682,482,116 - 82,656,279 (-)RGD
Celera678,123,282 - 78,474,424 (+)RGD
Sequence:
RefSeq Acc Id: XM_039112240   ⟹   XP_038968168
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2679,466,412 - 79,822,821 (+)NCBI
RefSeq Acc Id: XM_039112241   ⟹   XP_038968169
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2679,466,412 - 79,822,821 (+)NCBI
RefSeq Acc Id: XR_001838166
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2679,466,403 - 79,810,106 (+)NCBI
Rnor_6.0683,082,593 - 83,425,845 (+)NCBI
Sequence:
RefSeq Acc Id: XR_593049
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2679,466,403 - 79,810,102 (+)NCBI
Rnor_6.0683,082,593 - 83,425,840 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101494 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968168 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968169 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4A1J9 (Get FASTA)   NCBI Sequence Viewer  
  EDM03478 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101494   ⟸   NM_001108024
- Peptide Label: precursor
- UniProtKB: D4A1J9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007600   ⟸   ENSRNOT00000007600
RefSeq Acc Id: ENSRNOP00000073272   ⟸   ENSRNOT00000084258
RefSeq Acc Id: XP_038968169   ⟸   XM_039112241
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968168   ⟸   XM_039112240
- Peptide Label: isoform X1
Protein Domains
Fibronectin type-III   Ig-like   LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A1J9-F1-model_v2 AlphaFold D4A1J9 1-719 view protein structure

Transcriptome

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

Promoters
RGD ID:13694620
Promoter ID:EPDNEW_R5144
Type:single initiation site
Name:Lrfn5_1
Description:leucine rich repeat and fibronectin type III domain containing5
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_6.0683,083,834 - 83,083,894EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 83252473 83252474 T C snv M520/N (MCW), F344/NRrrc (MCW), Buf/N (MCW), WN/N (MCW), WKY/N (MCW)
6 83252475 83252476 A G snv F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), WN/N (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LH/MavRrrcAek (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), WKY/NCrl (2019), WKY/N (2020), BUF/N (2020), WKY/NCrl (RGD), LEW/Crl (RGD), GK/Ox (RGD), F344/NCrl (RGD), GK/FarMcwi (2019)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 92771914 92771915 A G snv WN/N (KNAW), DOB/Oda (KyushuU), MHS/Gib (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), GK/Ox (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), F344/Jcl (KyushuU), LH/MavRrrc (KNAW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 82485222 82485223 T C snv BUF/N (KNAW), F344/NHsd (ICAHN), M520/N (KNAW), WKY/N (KNAW), WN/N (KNAW), F344/NCrl (ICL), GK/Ox (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), MHS/Gib (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), F344/NRrrc (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309357 AgrOrtholog
BioCyc Gene G2FUF-37355 BioCyc
Ensembl Genes ENSRNOG00000005550 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007600 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073272 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007600 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000084258 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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
  Lrfn5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:314164 UniProtKB/Swiss-Prot
NCBI Gene 314164 ENTREZGENE
PANTHER PTHR45842:SF10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lrfn5 PhenoGen
PROSITE 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
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K532_RAT UniProtKB/TrEMBL
  D4A1J9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Lrfn5  leucine rich repeat and fibronectin type III domain containing 5  LOC100360181  leucine rich repeat and fibronectin type III domain containing 5  Data Merged 1643240 APPROVED
2010-05-06 LOC100360181  leucine rich repeat and fibronectin type III domain containing 5      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Lrfn5  leucine rich repeat and fibronectin type III domain containing 5   Lrfn5_predicted  leucine rich repeat and fibronectin type III domain containing 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lrfn5_predicted  leucine rich repeat and fibronectin type III domain containing 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED