Ldb3 (LIM domain binding 3) - Rat Genome Database

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Gene: Ldb3 (LIM domain binding 3) Rattus norvegicus
Analyze
Symbol: Ldb3
Name: LIM domain binding 3
RGD ID: 1564875
Description: Enables enzyme binding activity and protein C-terminus binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to act upstream of or within sarcomere organization. Located in Z disc. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1C; distal myopathy; and myofibrillar myopathy 4. Orthologous to human LDB3 (LIM domain binding 3); PARTICIPATES IN protein kinase C (PKC) signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Cypher; LIM domain-binding protein 3; LOC498587; RGD1564875; similar to mKIAA0613 protein; ZASP
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
mRatBN7.2169,855,768 - 9,920,108 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)Ensembl
Rnor_6.01610,878,348 - 10,943,016 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,878,334 - 10,941,501 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0169,203,392 - 9,267,999 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41610,221,362 - 10,247,798 (-)NCBIRGSC3.4rn4RGSC3.4
Celera165,298,641 - 5,360,715 (+)NCBICelera
Cytogenetic Map16p15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10391924   PMID:10427098   PMID:12477932   PMID:16481394   PMID:17987659   PMID:19047374   PMID:32922198  


Genomics

Comparative Map Data
Ldb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2169,855,768 - 9,920,108 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)Ensembl
Rnor_6.01610,878,348 - 10,943,016 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,878,334 - 10,941,501 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0169,203,392 - 9,267,999 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41610,221,362 - 10,247,798 (-)NCBIRGSC3.4rn4RGSC3.4
Celera165,298,641 - 5,360,715 (+)NCBICelera
Cytogenetic Map16p15NCBI
LDB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1086,668,507 - 86,736,072 (+)EnsemblGRCh38hg38GRCh38
GRCh381086,666,788 - 86,736,072 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371088,426,545 - 88,495,829 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361088,418,301 - 88,485,805 (+)NCBINCBI36hg18NCBI36
Build 341088,418,407 - 88,484,731NCBI
Celera1082,430,979 - 82,498,948 (+)NCBI
Cytogenetic Map10q23.2NCBI
HuRef1082,282,449 - 82,350,075 (+)NCBIHuRef
CHM1_11088,709,859 - 88,777,554 (+)NCBICHM1_1
Ldb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391434,248,656 - 34,312,276 (-)NCBIGRCm39mm39
GRCm39 Ensembl1434,248,560 - 34,310,639 (-)Ensembl
GRCm381434,526,699 - 34,590,314 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,526,603 - 34,588,682 (-)EnsemblGRCm38mm10GRCm38
MGSCv371435,339,885 - 35,401,867 (-)NCBIGRCm37mm9NCBIm37
MGSCv361433,355,797 - 33,417,766 (-)NCBImm8
Celera1430,792,367 - 30,854,357 (-)NCBICelera
Cytogenetic Map14BNCBI
Ldb3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555105,738,041 - 5,790,557 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555105,738,254 - 5,793,643 (+)NCBIChiLan1.0ChiLan1.0
LDB3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11086,641,517 - 86,722,159 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1086,654,737 - 86,722,148 (+)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl1086,641,746 - 86,653,143 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01083,095,625 - 83,164,297 (+)NCBIMhudiblu_PPA_v0panPan3
LDB3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1434,367,155 - 34,421,992 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl434,364,025 - 34,421,509 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha434,358,600 - 34,415,382 (+)NCBI
ROS_Cfam_1.0434,727,065 - 34,783,874 (+)NCBI
UMICH_Zoey_3.1434,573,067 - 34,629,852 (+)NCBI
UNSW_CanFamBas_1.0434,742,332 - 34,799,090 (+)NCBI
UU_Cfam_GSD_1.0435,247,342 - 35,304,143 (+)NCBI
Ldb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721344,085,476 - 44,150,650 (-)NCBI
SpeTri2.0NW_004936804196,592 - 259,168 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LDB3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1487,644,242 - 87,722,251 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11487,660,961 - 87,722,249 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21494,915,388 - 94,976,712 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LDB3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1945,130,015 - 45,199,585 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl945,128,134 - 45,198,106 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660485,238,400 - 5,307,738 (-)NCBIVero_WHO_p1.0
Ldb3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624841426,300 - 471,855 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH133236  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,892,613 - 9,892,810 (+)MAPPERmRatBN7.2
Rnor_6.01610,915,582 - 10,915,778NCBIRnor6.0
Rnor_5.0169,240,561 - 9,240,757UniSTSRnor5.0
RGSC_v3.41610,221,540 - 10,221,736UniSTSRGSC3.4
Celera165,324,319 - 5,324,515UniSTS
RH 3.4 Map1697.21UniSTS
Cytogenetic Map16p16-p15UniSTS
RH133871  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,856,808 - 9,857,026 (+)MAPPERmRatBN7.2
Rnor_6.01610,879,387 - 10,879,604NCBIRnor6.0
Rnor_5.0169,204,431 - 9,204,648UniSTSRnor5.0
RGSC_v3.41610,184,625 - 10,184,842UniSTSRGSC3.4
Celera165,359,616 - 5,359,833UniSTS
RH 3.4 Map1697.9UniSTS
Cytogenetic Map16p16-p15UniSTS
stSG622338  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0169,220,232 - 9,220,505NCBIRnor5.0
RGSC_v3.41610,201,457 - 10,201,729UniSTSRGSC3.4
Celera165,344,016 - 5,344,287UniSTS
Cytogenetic Map16p16-p15UniSTS
LDB3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,908,685 - 9,909,246 (+)MAPPERmRatBN7.2
Rnor_6.01610,931,655 - 10,932,215NCBIRnor6.0
Rnor_5.0169,256,634 - 9,257,194UniSTSRnor5.0
RGSC_v3.41610,237,613 - 10,238,173UniSTSRGSC3.4
Celera165,307,882 - 5,308,442UniSTS
Cytogenetic Map16p16-p15UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat


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 43 8 11 6 7 8
Low 3 32 16 19 16 58 35 33 4
Below cutoff 25 25 25 16 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001110490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001277158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001277159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001277165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001277166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC083721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM122871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FN804937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000081631   ⟹   ENSRNOP00000070370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,892,430 - 9,918,449 (-)Ensembl
Rnor_6.0 Ensembl1610,915,398 - 10,941,418 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083623   ⟹   ENSRNOP00000070707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)Ensembl
Rnor_6.0 Ensembl1610,878,334 - 10,941,501 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085414   ⟹   ENSRNOP00000072185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,855,927 - 9,918,449 (-)Ensembl
Rnor_6.0 Ensembl1610,878,505 - 10,941,418 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086627   ⟹   ENSRNOP00000075243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)Ensembl
Rnor_6.0 Ensembl1610,878,348 - 10,941,414 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087521   ⟹   ENSRNOP00000070984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)Ensembl
Rnor_6.0 Ensembl1610,878,348 - 10,941,428 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104381   ⟹   ENSRNOP00000076700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)Ensembl
RefSeq Acc Id: NM_001110490   ⟹   NP_001103960
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,892,430 - 9,918,449 (-)NCBI
Rnor_6.01610,915,398 - 10,941,418 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
RGSC_v3.41610,221,362 - 10,247,798 (-)RGD
Celera165,298,641 - 5,324,699 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001277158   ⟹   NP_001264087
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,892,430 - 9,918,449 (-)NCBI
Rnor_6.01610,915,398 - 10,941,418 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Celera165,298,641 - 5,324,699 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001277159   ⟹   NP_001264088
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,892,430 - 9,918,449 (-)NCBI
Rnor_6.01610,915,398 - 10,941,418 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Celera165,298,641 - 5,324,699 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001277165   ⟹   NP_001264094
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,927 - 9,918,449 (-)NCBI
Rnor_6.01610,878,505 - 10,941,418 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Celera165,298,641 - 5,360,715 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001277166   ⟹   NP_001264095
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,927 - 9,918,449 (-)NCBI
Rnor_6.01610,878,505 - 10,941,418 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Celera165,298,641 - 5,360,715 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252637   ⟹   XP_006252699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,543 (-)NCBI
Rnor_6.01610,878,348 - 10,941,456 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252640   ⟹   XP_006252702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,542 (-)NCBI
Rnor_6.01610,878,348 - 10,941,456 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252641   ⟹   XP_006252703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,542 (-)NCBI
Rnor_6.01610,878,348 - 10,941,456 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252644   ⟹   XP_006252706
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,542 (-)NCBI
Rnor_6.01610,878,348 - 10,941,456 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252645   ⟹   XP_006252707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,892,430 - 9,918,542 (-)NCBI
Rnor_6.01610,915,398 - 10,941,456 (-)NCBI
Rnor_5.0169,203,392 - 9,267,999 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600208   ⟹   XP_017455697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,542 (-)NCBI
Rnor_6.01610,878,348 - 10,941,456 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600209   ⟹   XP_017455698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,920,108 (-)NCBI
Rnor_6.01610,878,348 - 10,943,016 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600210   ⟹   XP_017455699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,533 (-)NCBI
Rnor_6.01610,878,348 - 10,941,443 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600211   ⟹   XP_017455700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,918,542 (-)NCBI
Rnor_6.01610,878,348 - 10,941,456 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039094753   ⟹   XP_038950681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,855,768 - 9,920,029 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001103960   ⟸   NM_001110490
- Peptide Label: isoform 4
- UniProtKB: Q5XIG1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264094   ⟸   NM_001277165
- Peptide Label: isoform 1
- UniProtKB: A0A096MJ01 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264095   ⟸   NM_001277166
- Peptide Label: isoform 2
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264087   ⟸   NM_001277158
- Peptide Label: isoform 3
- UniProtKB: A0A0G2JXR0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264088   ⟸   NM_001277159
- Peptide Label: isoform 3
- UniProtKB: A0A0G2JXR0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252706   ⟸   XM_006252644
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006252702   ⟸   XM_006252640
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006252703   ⟸   XM_006252641
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006252699   ⟸   XM_006252637
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252707   ⟸   XM_006252645
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017455698   ⟸   XM_017600209
- Peptide Label: isoform X3
- UniProtKB: A0A096MJ01 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455700   ⟸   XM_017600211
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017455697   ⟸   XM_017600208
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455699   ⟸   XM_017600210
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000070984   ⟸   ENSRNOT00000087521
RefSeq Acc Id: ENSRNOP00000072185   ⟸   ENSRNOT00000085414
RefSeq Acc Id: ENSRNOP00000070370   ⟸   ENSRNOT00000081631
RefSeq Acc Id: ENSRNOP00000070707   ⟸   ENSRNOT00000083623
RefSeq Acc Id: ENSRNOP00000075243   ⟸   ENSRNOT00000086627
RefSeq Acc Id: XP_038950681   ⟸   XM_039094753
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000076700   ⟸   ENSRNOT00000104381
Protein Domains
LIM zinc-binding   PDZ

Transcriptome

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

Promoters
RGD ID:13699961
Promoter ID:EPDNEW_R10484
Type:initiation region
Name:Ldb3_1
Description:LIM domain binding 3
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_6.01610,941,397 - 10,941,457EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
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/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/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
F344/Stm (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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
FXLE16/Stm (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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/FarMcwi (2019)
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Sequenced By: MCW
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
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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/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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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)
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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/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 (2019)
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Sequenced By: MCW
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/NCrl (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
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 (2020)
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Sequenced By: MCW
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
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:1564875 AgrOrtholog
Ensembl Genes ENSRNOG00000059166 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070370 UniProtKB/TrEMBL
  ENSRNOP00000070707 UniProtKB/TrEMBL
  ENSRNOP00000070984 UniProtKB/TrEMBL
  ENSRNOP00000072185 UniProtKB/TrEMBL
  ENSRNOP00000075243 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081631 UniProtKB/TrEMBL
  ENSRNOT00000083623 UniProtKB/TrEMBL
  ENSRNOT00000085414 UniProtKB/TrEMBL
  ENSRNOT00000086627 UniProtKB/TrEMBL
  ENSRNOT00000087521 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7190925 IMAGE-MGC_LOAD
InterPro DUF4749 UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  ZASP UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:498587 UniProtKB/TrEMBL
MGC_CLONE MGC:94616 IMAGE-MGC_LOAD
NCBI Gene 498587 ENTREZGENE
Pfam DUF4749 UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
PhenoGen Ldb3 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
SMART LIM UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
  SM00735 UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt A0A096MJ01 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MKD4 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JXR0 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JYM0_RAT UniProtKB/TrEMBL
  Q5XIG1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary D4A1A2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Ldb3  LIM domain binding 3  RGD1564875_predicted  similar to mKIAA0613 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564875_predicted  similar to mKIAA0613 protein (predicted)  LOC498587  similar to mKIAA0613 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498587  similar to mKIAA0613 protein      Symbol and Name status set to provisional 70820 PROVISIONAL