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. 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
Previously 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
GRCr8169,862,161 - 9,926,338 (-)NCBIGRCr8
mRatBN7.2169,855,768 - 9,920,108 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx169,875,530 - 9,938,140 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01611,020,238 - 11,082,844 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0169,870,588 - 9,933,188 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera165,298,641 - 5,360,715 (+)NCBICelera
Cytogenetic Map16p15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Impaired binding of ZASP/Cypher with phosphoglucomutase 1 is associated with dilated cardiomyopathy. Arimura T, etal., Cardiovasc Res. 2009 Jul 1;83(1):80-8. doi: 10.1093/cvr/cvp119. Epub 2009 Apr 17.
2. A Cypher/ZASP mutation associated with dilated cardiomyopathy alters the binding affinity to protein kinase C. Arimura T, etal., J Biol Chem. 2004 Feb 20;279(8):6746-52. Epub 2003 Dec 3.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Zaspopathy in a large classic late-onset distal myopathy family. Griggs R, etal., Brain. 2007 Jun;130(Pt 6):1477-84. Epub 2007 Mar 2.
5. D117N in Cypher/ZASP may not be a causative mutation for dilated cardiomyopathy and ventricular arrhythmias. Levitas A, etal., Eur J Hum Genet. 2016 May;24(5):666-71. doi: 10.1038/ejhg.2015.195. Epub 2015 Sep 30.
6. A ZASP missense mutation, S196L, leads to cytoskeletal and electrical abnormalities in a mouse model of cardiomyopathy. Li Z, etal., Circ Arrhythm Electrophysiol. 2010 Dec;3(6):646-56. doi: 10.1161/CIRCEP.109.929240. Epub 2010 Sep 18.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. PKC-interacting proteins: from function to pharmacology. Poole AW, etal., Trends Pharmacol Sci. 2004 Oct;25(10):528-35.
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. Protein scaffolds, lipid domains and substrate recognition in protein kinase C function: implications for rational drug design. Walker JW Handb Exp Pharmacol. 2008;(186):185-203.
14. LDB3 splicing abnormalities are specific to skeletal muscles of patients with myotonic dystrophy type 1 and alter its PKC binding affinity. Yamashita Y, etal., Neurobiol Dis. 2014 Sep;69:200-5. doi: 10.1016/j.nbd.2014.05.026. Epub 2014 May 27.
15. Ablation of Cypher, a PDZ-LIM domain Z-line protein, causes a severe form of congenital myopathy. Zhou Q, etal., J Cell Biol. 2001 Nov 12;155(4):605-12. Epub 2001 Nov 5.
Additional References at PubMed
PMID:10391924   PMID:10427098   PMID:12477932   PMID:16481394   PMID:17987659   PMID:19047374   PMID:32922198   PMID:35352799  


Genomics

Comparative Map Data
Ldb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8169,862,161 - 9,926,338 (-)NCBIGRCr8
mRatBN7.2169,855,768 - 9,920,108 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,855,927 - 9,918,532 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx169,875,530 - 9,938,140 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01611,020,238 - 11,082,844 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0169,870,588 - 9,933,188 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera165,298,641 - 5,360,715 (+)NCBICelera
Cytogenetic Map16p15NCBI
LDB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381086,666,788 - 86,736,072 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1086,666,785 - 86,736,072 (+)EnsemblGRCh38hg38GRCh38
GRCh371088,426,545 - 88,495,829 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361088,418,301 - 88,485,805 (+)NCBINCBI36Build 36hg18NCBI36
Build 341088,418,407 - 88,484,731NCBI
Celera1082,430,979 - 82,498,948 (+)NCBICelera
Cytogenetic Map10q23.2NCBI
HuRef1082,282,449 - 82,350,075 (+)NCBIHuRef
CHM1_11088,709,859 - 88,777,554 (+)NCBICHM1_1
T2T-CHM13v2.01087,550,947 - 87,620,190 (+)NCBIT2T-CHM13v2.0
Ldb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391434,248,656 - 34,312,276 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1434,248,560 - 34,310,639 (-)EnsemblGRCm39 Ensembl
GRCm381434,526,699 - 34,590,314 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,526,603 - 34,588,682 (-)EnsemblGRCm38mm10GRCm38
MGSCv371435,339,885 - 35,401,867 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361433,355,797 - 33,417,766 (-)NCBIMGSCv36mm8
Celera1430,792,367 - 30,854,357 (-)NCBICelera
Cytogenetic Map14BNCBI
cM Map1420.83NCBI
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
NHGRI_mPanPan1-v2898,662,475 - 98,732,654 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11098,667,794 - 98,737,973 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01083,095,625 - 83,164,297 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0434,727,065 - 34,783,874 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl434,727,060 - 34,781,382 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1434,573,067 - 34,629,852 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0434,742,332 - 34,799,090 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0435,247,342 - 35,304,143 (+)NCBIUU_Cfam_GSD_1.0
Ldb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721344,085,476 - 44,150,650 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936804196,598 - 259,168 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl945,128,134 - 45,198,106 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660485,238,400 - 5,307,738 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ldb3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624841426,330 - 471,682 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624841426,300 - 471,855 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ldb3
312 total Variants

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 22.8liver 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

Markers in Region
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


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
  XM_063275630 (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
  JAXUCZ010000016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000081631   ⟹   ENSRNOP00000070370
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
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
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
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
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
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
GRCr8169,898,659 - 9,924,679 (-)NCBI
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
GRCr8169,898,659 - 9,924,679 (-)NCBI
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
GRCr8169,898,659 - 9,924,679 (-)NCBI
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
GRCr8169,862,161 - 9,924,679 (-)NCBI
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
GRCr8169,862,161 - 9,924,679 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,773 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,772 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,772 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,772 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,898,663 - 9,924,771 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,772 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,926,338 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,760 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,924,772 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,862,812 - 9,926,256 (-)NCBI
mRatBN7.2169,855,768 - 9,920,029 (-)NCBI
RefSeq Acc Id: XM_063275630   ⟹   XP_063131700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,898,663 - 9,924,755 (-)NCBI
RefSeq Acc Id: NP_001103960   ⟸   NM_001110490
- Peptide Label: isoform 4
- UniProtKB: Q5XIG1 (UniProtKB/TrEMBL),   D4A1A2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264094   ⟸   NM_001277165
- Peptide Label: isoform 1
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264095   ⟸   NM_001277166
- Peptide Label: isoform 2
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL),   A0A0G2K2C4 (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
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252702   ⟸   XM_006252640
- Peptide Label: isoform X4
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252703   ⟸   XM_006252641
- Peptide Label: isoform X5
- UniProtKB: A0A8I5Y5H4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252699   ⟸   XM_006252637
- Peptide Label: isoform X1
- UniProtKB: A0A096MJ01 (UniProtKB/TrEMBL),   A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252707   ⟸   XM_006252645
- Peptide Label: isoform X9
- UniProtKB: A0A0G2JXR0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455698   ⟸   XM_017600209
- Peptide Label: isoform X3
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455700   ⟸   XM_017600211
- Peptide Label: isoform X7
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455697   ⟸   XM_017600208
- Peptide Label: isoform X2
- UniProtKB: A0A0G2JYM0 (UniProtKB/TrEMBL),   A0A096MKD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455699   ⟸   XM_017600210
- Peptide Label: isoform X6
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
- 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
- UniProtKB: A0A096MKD4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000076700   ⟸   ENSRNOT00000104381
RefSeq Acc Id: XP_063131700   ⟸   XM_063275630
- Peptide Label: isoform X10
Protein Domains
LIM zinc-binding   PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JYM0-F1-model_v2 AlphaFold A0A0G2JYM0 1-729 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564875 AgrOrtholog
BioCyc Gene G2FUF-12056 BioCyc
Ensembl Genes ENSRNOG00000059166 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081631.2 UniProtKB/TrEMBL
  ENSRNOT00000083623.2 UniProtKB/TrEMBL
  ENSRNOT00000085414 ENTREZGENE
  ENSRNOT00000085414.2 UniProtKB/TrEMBL
  ENSRNOT00000086627.2 UniProtKB/TrEMBL
  ENSRNOT00000087521.2 UniProtKB/TrEMBL
  ENSRNOT00000104381.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
  Cysteine Rich Protein 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
PANTHER LIM DOMAIN-BINDING PROTEIN 3 UniProtKB/TrEMBL
  PDZ AND LIM DOMAIN PROTEIN ZASP UniProtKB/TrEMBL
Pfam DUF4749 UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
PhenoGen Ldb3 PhenoGen
PRINTS PRICHEXTENSN UniProtKB/TrEMBL
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000059166 RatGTEx
SMART LIM UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
  SM00735 UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
UniProt A0A096MJ01 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MKD4 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JXR0 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JYM0 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K2C4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5Y5H4 ENTREZGENE, UniProtKB/TrEMBL
  D4A1A2 ENTREZGENE
  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