Ltbp2 (latent transforming growth factor beta binding protein 2) - Rat Genome Database
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Gene: Ltbp2 (latent transforming growth factor beta binding protein 2) Rattus norvegicus
Analyze
Symbol: Ltbp2
Name: latent transforming growth factor beta binding protein 2
RGD ID: 68380
Description: Predicted to have microfibril binding activity. Predicted to be involved in supramolecular fiber organization. Predicted to localize to extracellular region. Human ortholog(s) of this gene implicated in Weill-Marchesani syndrome. Orthologous to human LTBP2 (latent transforming growth factor beta binding protein 2); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: latent-transforming growth factor beta-binding protein 2; LTBP-2 like protein
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
Rnor_6.06108,500,114 - 108,596,653 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,500,112 - 108,596,569 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06116,955,322 - 117,049,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46108,826,446 - 108,924,746 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16108,829,901 - 108,928,202 (-)NCBI
Celera6102,254,815 - 102,349,980 (-)NCBICelera
Cytogenetic Map6q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-butoxyethanol  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
chloropicrin  (ISO)
choline  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
glycidol  (EXP)
graphite  (EXP)
isoprenaline  (ISO)
L-methionine  (ISO)
methapyrilene  (ISO)
mitomycin C  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
paclitaxel  (ISO)
potassium chromate  (ISO)
pravastatin  (EXP,ISO)
rotenone  (EXP)
sodium arsenite  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
topotecan  (ISO)
trimellitic anhydride  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vincaleukoblastine  (ISO)
zaragozic acid A  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10743502   PMID:11104663   PMID:15326124   PMID:20551380   PMID:21362503   PMID:21700711   PMID:23376485   PMID:23533145   PMID:24006456   PMID:24908666   PMID:27068509   PMID:27559042  


Genomics

Comparative Map Data
Ltbp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.06108,500,114 - 108,596,653 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,500,112 - 108,596,569 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06116,955,322 - 117,049,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46108,826,446 - 108,924,746 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16108,829,901 - 108,928,202 (-)NCBI
Celera6102,254,815 - 102,349,980 (-)NCBICelera
Cytogenetic Map6q31NCBI
LTBP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1474,498,183 - 74,612,378 (-)EnsemblGRCh38hg38GRCh38
GRCh381474,498,183 - 74,612,593 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371474,964,886 - 75,079,034 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361474,034,639 - 74,148,787 (-)NCBINCBI36hg18NCBI36
Build 341474,034,639 - 74,148,787NCBI
Celera1455,003,271 - 55,117,403 (-)NCBI
Cytogenetic Map14q24.3NCBI
HuRef1455,133,330 - 55,247,309 (-)NCBIHuRef
CHM1_11474,904,422 - 75,018,171 (-)NCBICHM1_1
Ltbp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391284,829,986 - 84,923,581 (-)NCBIGRCm39mm39
GRCm381284,783,212 - 84,876,558 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1284,783,212 - 84,876,532 (-)EnsemblGRCm38mm10GRCm38
MGSCv371286,124,162 - 86,217,445 (-)NCBIGRCm37mm9NCBIm37
MGSCv361285,672,960 - 85,766,280 (-)NCBImm8
Celera1286,239,349 - 86,332,994 (-)NCBICelera
Cytogenetic Map12D1NCBI
Ltbp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955523932,347 - 1,003,256 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955523919,220 - 1,005,747 (+)NCBIChiLan1.0ChiLan1.0
LTBP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11473,899,154 - 74,012,203 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1473,901,851 - 74,011,914 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01455,051,325 - 55,164,613 (-)NCBIMhudiblu_PPA_v0panPan3
LTBP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl847,659,363 - 47,760,938 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1847,657,618 - 47,758,257 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ltbp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364883,682,044 - 3,790,988 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LTBP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl797,745,396 - 97,852,502 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1797,744,974 - 97,852,848 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27103,589,203 - 103,694,470 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LTBP2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12451,707,348 - 51,823,449 (-)NCBI
ChlSab1.1 Ensembl2451,708,479 - 51,823,347 (-)Ensembl
Ltbp2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473427,058,531 - 27,162,229 (+)NCBI

Position Markers
D6Got159  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06108,571,459 - 108,571,588NCBIRnor6.0
Rnor_5.06116,982,029 - 116,982,158UniSTSRnor5.0
RGSC_v3.46108,899,758 - 108,899,888RGDRGSC3.4
RGSC_v3.46108,899,759 - 108,899,888UniSTSRGSC3.4
RGSC_v3.16108,903,215 - 108,903,344RGD
Celera6102,325,132 - 102,325,261UniSTS
Cytogenetic Map6q31UniSTS
RH 3.4 Map6774.2RGD
RH 3.4 Map6774.2UniSTS
RH 2.0 Map6979.8RGD
D6Got324  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06108,547,383 - 108,547,472NCBIRnor6.0
Rnor_5.06117,005,741 - 117,005,830UniSTSRnor5.0
Celera6102,301,874 - 102,301,963UniSTS
Cytogenetic Map6q31UniSTS
RH134026  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06108,500,183 - 108,500,387NCBIRnor6.0
Rnor_5.06117,049,033 - 117,049,237UniSTSRnor5.0
RGSC_v3.46108,826,508 - 108,826,712UniSTSRGSC3.4
Celera6102,254,884 - 102,255,088UniSTS
Cytogenetic Map6q31UniSTS
RH 3.4 Map6781.0UniSTS
RH139165  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06108,529,381 - 108,529,510NCBIRnor6.0
Rnor_5.06117,023,190 - 117,023,319UniSTSRnor5.0
RGSC_v3.46108,856,295 - 108,856,424UniSTSRGSC3.4
Celera6102,283,983 - 102,284,112UniSTS
Cytogenetic Map6q31UniSTS
RH 3.4 Map6742.4UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
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)67009971115379601Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6108154445133849286Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:318
Count of miRNA genes:195
Interacting mature miRNAs:223
Transcripts:ENSRNOT00000031331
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 16 2 13 11
Low 2 27 33 17 17 17 7 7 23 35 22 7
Below cutoff 1 24 24 24 1 4 43 6 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_021586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAHX01045591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045596 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01045598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC113727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF016901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK358810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK479508 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV213994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y12760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000031331   ⟹   ENSRNOP00000038437
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6108,500,114 - 108,596,446 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077458   ⟹   ENSRNOP00000075533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6108,500,119 - 108,596,446 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082792   ⟹   ENSRNOP00000071831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6108,500,112 - 108,596,569 (-)Ensembl
RefSeq Acc Id: NM_021586   ⟹   NP_067597
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06108,500,114 - 108,596,446 (-)NCBI
Rnor_5.06116,955,322 - 117,049,306 (+)NCBI
RGSC_v3.46108,826,446 - 108,924,746 (-)RGD
Celera6102,254,815 - 102,349,980 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240350   ⟹   XP_006240412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06108,500,119 - 108,596,653 (-)NCBI
Rnor_5.06116,955,322 - 117,049,306 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_067597   ⟸   NM_021586
- UniProtKB: O35806 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240412   ⟸   XM_006240350
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K1G5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000038437   ⟸   ENSRNOT00000031331
RefSeq Acc Id: ENSRNOP00000071831   ⟸   ENSRNOT00000082792
RefSeq Acc Id: ENSRNOP00000075533   ⟸   ENSRNOT00000077458
Protein Domains
EGF-like   TB

Transcriptome

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

Promoters
RGD ID:13694744
Promoter ID:EPDNEW_R5256
Type:initiation region
Name:Ltbp2_1
Description:latent transforming growth factor beta binding protein 2
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_6.06108,596,555 - 108,596,615EPDNEW

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)
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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 116957015 116957016 C T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), ACI/N (KNAW), ZFDM (KyushuU), SBH/Ygl (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), Crl:SD (UDEL), LEC/Tj (KyushuU), ACI/EurMcwi (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 108596364 108596365 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), SBH/Ygl (RGD), ACI/N (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68380 AgrOrtholog
Ensembl Genes ENSRNOG00000012094 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000038437 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071831 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075533 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031331 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077458 UniProtKB/TrEMBL
  ENSRNOT00000082792 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.90.290.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TB_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TB_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:59106 UniProtKB/Swiss-Prot
NCBI Gene 59106 ENTREZGENE
Pfam EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hEGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00683 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ltbp2 PhenoGen
PROSITE ALDEHYDE_DEHYDR_CYS UniProtKB/Swiss-Prot
  ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS51364 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57184 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57581 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC206937
UniGene Rn.40921 ENTREZGENE
UniProt A0A0G2K1G5 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KAU7_RAT UniProtKB/TrEMBL
  F1M7L7_RAT UniProtKB/TrEMBL
  LTBP2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ltbp2  latent transforming growth factor beta binding protein 2       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference