Loxl2 (lysyl oxidase-like 2) - Rat Genome Database
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Gene: Loxl2 (lysyl oxidase-like 2) Rattus norvegicus
Analyze
Symbol: Loxl2
Name: lysyl oxidase-like 2
RGD ID: 1308435
Description: Predicted to have metal ion binding activity; oligosaccharide binding activity; and protein-lysine 6-oxidase activity. Predicted to be involved in several processes, including collagen fibril organization; peptidyl-lysine oxidation; and positive regulation of cell differentiation. Localizes to basement membrane. Orthologous to human LOXL2 (lysyl oxidase like 2); INTERACTS WITH 4,4'-diaminodiphenylmethane; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC290350; lysyl oxidase homolog 2; lysyl oxidase-like protein 2; MGC189171
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
mRatBN7.21544,683,449 - 44,773,067 (+)NCBI
Rnor_6.0 Ensembl1551,303,909 - 51,365,234 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01551,276,022 - 51,365,238 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01555,005,461 - 55,092,980 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41549,982,103 - 50,068,902 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11550,024,097 - 50,084,571 (+)NCBI
Celera1544,366,507 - 44,453,187 (+)NCBICelera
Cytogenetic Map15p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bexarotene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
D-penicillamine  (ISO)
dexamethasone  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dopamine  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenoldopam  (EXP)
fenvalerate  (EXP)
folic acid  (ISO)
isotretinoin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodimethylamine  (EXP)
nickel dichloride  (EXP)
paracetamol  (ISO)
pentane-2,3-dione  (EXP)
phenobarbital  (ISO)
PhIP  (EXP)
progesterone  (ISO)
rotenone  (EXP)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (ISO)
tributylstannane  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
basement membrane  (IDA)
chromatin  (IEA,ISO,ISS)
endoplasmic reticulum  (IEA,ISO,ISS)
extracellular space  (IBA,IEA,ISO,ISS)
membrane  (IEA)
nucleoplasm  (IEA,ISO)
nucleus  (ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:16096638   PMID:21071451   PMID:22204712   PMID:23319596   PMID:23979707   PMID:24006456   PMID:24239292   PMID:24414204   PMID:25959397   PMID:27735137   PMID:28332555  
PMID:29581294   PMID:29966587  


Genomics

Comparative Map Data
Loxl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21544,683,449 - 44,773,067 (+)NCBI
Rnor_6.0 Ensembl1551,303,909 - 51,365,234 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01551,276,022 - 51,365,238 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01555,005,461 - 55,092,980 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41549,982,103 - 50,068,902 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11550,024,097 - 50,084,571 (+)NCBI
Celera1544,366,507 - 44,453,187 (+)NCBICelera
Cytogenetic Map15p11NCBI
LOXL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl823,296,897 - 23,425,328 (-)EnsemblGRCh38hg38GRCh38
GRCh38823,296,897 - 23,404,120 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37823,154,410 - 23,261,633 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37823,154,410 - 23,261,722 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36823,210,355 - 23,317,667 (-)NCBINCBI36hg18NCBI36
Build 34823,210,640 - 23,317,575NCBI
Celera822,116,981 - 22,224,289 (-)NCBI
Cytogenetic Map8p21.3NCBI
HuRef821,700,441 - 21,807,111 (-)NCBIHuRef
CHM1_1823,356,541 - 23,463,832 (-)NCBICHM1_1
Loxl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391469,846,085 - 69,933,283 (+)NCBIGRCm39mm39
GRCm381469,608,692 - 69,695,834 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1469,609,068 - 69,695,834 (+)EnsemblGRCm38mm10GRCm38
MGSCv371470,009,283 - 70,095,641 (+)NCBIGRCm37mm9NCBIm37
MGSCv361468,344,556 - 68,428,775 (+)NCBImm8
Celera1467,164,771 - 67,231,456 (+)NCBICelera
Cytogenetic Map14D2NCBI
Loxl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540346,504,440 - 46,584,016 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540346,503,226 - 46,583,807 (-)NCBIChiLan1.0ChiLan1.0
LOXL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1819,483,331 - 19,589,522 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl819,483,335 - 19,589,522 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0822,547,303 - 22,653,676 (-)NCBIMhudiblu_PPA_v0panPan3
LOXL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2534,126,335 - 34,185,969 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12534,095,858 - 34,186,775 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Loxl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365556,781,563 - 6,865,662 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOXL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl147,435,863 - 7,540,704 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1147,435,861 - 7,540,699 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOXL2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1821,416,821 - 21,516,923 (-)NCBI
ChlSab1.1 Ensembl821,416,787 - 21,516,854 (-)Ensembl
Loxl2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475818,567,367 - 18,644,528 (-)NCBI

Position Markers
D15Mgh11  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01551,353,605 - 51,353,746NCBIRnor6.0
Rnor_5.01555,081,347 - 55,081,488UniSTSRnor5.0
RGSC_v3.41550,057,446 - 50,057,588RGDRGSC3.4
RGSC_v3.41550,057,447 - 50,057,588UniSTSRGSC3.4
RGSC_v3.11550,073,226 - 50,073,368RGD
Celera1544,441,732 - 44,441,873UniSTS
FHH x ACI Map1546.36UniSTS
FHH x ACI Map1546.36RGD
Cytogenetic Map15p11UniSTS
D15Arb7  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01551,353,526 - 51,353,744NCBIRnor6.0
Rnor_5.01555,081,268 - 55,081,486UniSTSRnor5.0
RGSC_v3.41550,057,367 - 50,057,586RGDRGSC3.4
RGSC_v3.41550,057,368 - 50,057,586UniSTSRGSC3.4
RGSC_v3.11550,073,147 - 50,073,366RGD
Celera1544,441,653 - 44,441,871UniSTS
Cytogenetic Map15p11UniSTS
D15Wox4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01551,353,543 - 51,353,744NCBIRnor6.0
Rnor_5.01555,081,285 - 55,081,486UniSTSRnor5.0
RGSC_v3.41550,057,385 - 50,057,586UniSTSRGSC3.4
Celera1544,441,670 - 44,441,871UniSTS
Cytogenetic Map15p11UniSTS
RH124140  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01551,361,065 - 51,362,317NCBIRnor6.0
Rnor_6.04113,882,579 - 113,882,809NCBIRnor6.0
Rnor_5.01555,088,807 - 55,090,059UniSTSRnor5.0
Rnor_5.04178,567,679 - 178,567,909UniSTSRnor5.0
RGSC_v3.41550,064,728 - 50,065,980UniSTSRGSC3.4
RGSC_v3.44117,261,114 - 117,261,344UniSTSRGSC3.4
Celera1544,449,013 - 44,450,265UniSTS
Celera4104,550,500 - 104,550,730UniSTS
Cytogenetic Map4q34UniSTS
Cytogenetic Map15p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154309747052831189Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:68
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000058663
Prediction methods:Microtar, Miranda, Rnahybrid
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 2 35 24 15 10 15 5 6 14 28 33 11 5
Low 1 8 33 26 9 26 3 5 60 7 8 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058663   ⟹   ENSRNOP00000055457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1551,304,059 - 51,365,124 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085237   ⟹   ENSRNOP00000073118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1551,303,909 - 51,365,234 (+)Ensembl
RefSeq Acc Id: NM_001106047   ⟹   NP_001099517
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,944 - 44,770,848 (+)NCBI
Rnor_6.01551,276,022 - 51,365,238 (+)NCBI
Rnor_5.01555,005,461 - 55,092,980 (+)NCBI
RGSC_v3.41549,982,103 - 50,068,902 (+)RGD
Celera1544,366,507 - 44,453,187 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093148   ⟹   XP_038949076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,475 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093149   ⟹   XP_038949077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,475 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093150   ⟹   XP_038949078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,477 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093151   ⟹   XP_038949079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,839 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093152   ⟹   XP_038949080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,838 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093153   ⟹   XP_038949081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,449 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093154   ⟹   XP_038949082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,479 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093155   ⟹   XP_038949083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,481 - 44,773,067 (+)NCBI
RefSeq Acc Id: XM_039093156   ⟹   XP_038949084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21544,683,843 - 44,773,067 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099517   ⟸   NM_001106047
- Peptide Label: precursor
- UniProtKB: B5DF27 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073118   ⟸   ENSRNOT00000085237
RefSeq Acc Id: ENSRNOP00000055457   ⟸   ENSRNOT00000058663
RefSeq Acc Id: XP_038949081   ⟸   XM_039093153
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038949076   ⟸   XM_039093148
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949077   ⟸   XM_039093149
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949078   ⟸   XM_039093150
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949082   ⟸   XM_039093154
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038949083   ⟸   XM_039093155
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038949080   ⟸   XM_039093152
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038949079   ⟸   XM_039093151
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038949084   ⟸   XM_039093156
- Peptide Label: isoform X7
Protein Domains
SRCR

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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:1308435 AgrOrtholog
Ensembl Genes ENSRNOG00000016758 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000055457 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073118 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058663 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085237 UniProtKB/TrEMBL
Gene3D-CATH 3.10.250.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Lysyl_oxidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lysyl_oxidase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRCR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRCR-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRCR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:290350 UniProtKB/Swiss-Prot
NCBI Gene 290350 ENTREZGENE
Pfam Lysyl_oxidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRCR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Loxl2 PhenoGen
PRINTS LYSYLOXIDASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPERACTRCPTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE LYSYL_OXIDASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRCR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRCR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00202 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56487 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K4P0_RAT UniProtKB/TrEMBL
  B5DF27 ENTREZGENE
  J3QTE1_RAT UniProtKB/TrEMBL
  LOXL2_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1LPM2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Loxl2  lysyl oxidase-like 2   Loxl2_predicted  lysyl oxidase-like 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Loxl2_predicted  lysyl oxidase-like 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED