Lmx1b (LIM homeobox transcription factor 1 beta) - Rat Genome Database

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Gene: Lmx1b (LIM homeobox transcription factor 1 beta) Rattus norvegicus
Analyze
Symbol: Lmx1b
Name: LIM homeobox transcription factor 1 beta
RGD ID: 620843
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including memory; olfactory behavior; and regulation of autophagy. Predicted to act upstream of or within several processes, including collagen fibril organization; nervous system development; and trabecular meshwork development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in focal segmental glomerulosclerosis and nail-patella syndrome. Orthologous to human LMX1B (LIM homeobox transcription factor 1 beta); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LIM homeobox transcription factor 1-beta
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
mRatBN7.2316,862,195 - 16,940,899 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl316,862,195 - 16,940,899 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx319,930,667 - 20,009,835 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0328,515,689 - 28,594,855 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0326,766,677 - 26,845,838 (-)NCBIRnor_WKY
Rnor_6.0312,608,748 - 12,686,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl312,609,574 - 12,686,869 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0317,938,969 - 18,018,269 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4312,571,947 - 12,651,590 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1312,470,843 - 12,473,304 (-)NCBI
Celera311,596,841 - 11,674,265 (-)NCBICelera
Cytogenetic Map3p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
nucleus  (IBA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome. Dreyer SD, etal., Nat Genet. 1998 May;19(1):47-50.
2. The human LMX1B gene: transcription unit, promoter, and pathogenic mutations. Dunston JA, etal., Genomics. 2004 Sep;84(3):565-76.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. A second independent pathway for development of mesencephalic dopaminergic neurons requires Lmx1b. Smidt MP, etal., Nat Neurosci 2000 Apr;3(4):337-41.
Additional References at PubMed
PMID:10660670   PMID:10767331   PMID:12897786   PMID:15229182   PMID:17151281   PMID:17166916   PMID:18076286   PMID:19951692   PMID:20568247   PMID:20589901   PMID:21752929   PMID:24399192  
PMID:24785190   PMID:25915474  


Genomics

Comparative Map Data
Lmx1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2316,862,195 - 16,940,899 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl316,862,195 - 16,940,899 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx319,930,667 - 20,009,835 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0328,515,689 - 28,594,855 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0326,766,677 - 26,845,838 (-)NCBIRnor_WKY
Rnor_6.0312,608,748 - 12,686,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl312,609,574 - 12,686,869 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0317,938,969 - 18,018,269 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4312,571,947 - 12,651,590 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1312,470,843 - 12,473,304 (-)NCBI
Celera311,596,841 - 11,674,265 (-)NCBICelera
Cytogenetic Map3p11NCBI
LMX1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389126,613,928 - 126,701,032 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9126,613,928 - 126,701,032 (+)EnsemblGRCh38hg38GRCh38
GRCh379129,376,207 - 129,463,311 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369128,416,619 - 128,498,551 (+)NCBINCBI36Build 36hg18NCBI36
Build 349126,456,351 - 126,538,284NCBI
Celera9100,030,360 - 100,115,686 (+)NCBICelera
Cytogenetic Map9q33.3NCBI
HuRef998,989,870 - 99,079,726 (+)NCBIHuRef
CHM1_19129,527,362 - 129,614,009 (+)NCBICHM1_1
T2T-CHM13v2.09138,819,355 - 138,906,454 (+)NCBIT2T-CHM13v2.0
Lmx1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39233,450,977 - 33,531,219 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl233,450,977 - 33,530,620 (-)EnsemblGRCm39 Ensembl
GRCm38233,560,965 - 33,641,208 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl233,560,965 - 33,640,608 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl233,560,965 - 33,640,511 (-)EnsemblGRCm38mm10GRCm38
MGSCv37233,420,056 - 33,496,031 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36233,386,645 - 33,462,520 (-)NCBIMGSCv36mm8
Celera233,269,132 - 33,345,093 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.48NCBI
Lmx1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554191,782,566 - 1,857,375 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554191,782,566 - 1,857,375 (-)NCBIChiLan1.0ChiLan1.0
LMX1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19126,240,722 - 126,322,716 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9126,240,722 - 126,322,420 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0997,730,850 - 97,820,554 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LMX1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1956,542,844 - 56,625,609 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl956,542,826 - 56,625,530 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha955,744,662 - 55,827,799 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0957,463,555 - 57,546,781 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl957,467,707 - 57,547,344 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1956,222,283 - 56,305,769 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0956,538,211 - 56,621,349 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0956,629,212 - 56,712,418 (-)NCBIUU_Cfam_GSD_1.0
Lmx1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947194,744,769 - 194,819,262 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648714,513,290 - 14,587,902 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493648714,513,303 - 14,587,771 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LMX1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1267,207,419 - 267,287,729 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11267,207,273 - 267,290,862 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21301,155,404 - 301,230,939 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LMX1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11211,443,253 - 11,526,789 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1211,444,324 - 11,526,552 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660794,658,674 - 4,746,282 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lmx1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247608,698,139 - 8,772,147 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247608,701,204 - 8,772,147 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lmx1b
391 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:67
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000022953
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat

Markers in Region
D3Got11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,875,647 - 16,875,862 (+)MAPPERmRatBN7.2
Rnor_6.0312,622,203 - 12,622,417NCBIRnor6.0
Rnor_5.0317,953,540 - 17,953,754UniSTSRnor5.0
RGSC_v3.4312,584,673 - 12,584,888RGDRGSC3.4
RGSC_v3.4312,584,674 - 12,584,888UniSTSRGSC3.4
RGSC_v3.1312,481,046 - 12,481,260RGD
Celera311,610,296 - 11,610,510UniSTS
RH 3.4 Map3122.6UniSTS
RH 3.4 Map3122.6RGD
RH 2.0 Map30.0RGD
Cytogenetic Map3p11UniSTS
AU049321  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,877,744 - 16,877,891 (+)MAPPERmRatBN7.2
Rnor_6.0312,624,300 - 12,624,446NCBIRnor6.0
Rnor_5.0317,955,637 - 17,955,783UniSTSRnor5.0
RGSC_v3.4312,586,771 - 12,586,917UniSTSRGSC3.4
Celera311,612,393 - 11,612,539UniSTS
Cytogenetic Map3p11UniSTS


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 12 4 1
Low 4 4 4 27 31 13
Below cutoff 1 16 24 23 1 23 4 6 24 14 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022953   ⟹   ENSRNOP00000022953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl316,862,195 - 16,940,899 (-)Ensembl
Rnor_6.0 Ensembl312,609,574 - 12,686,869 (-)Ensembl
RefSeq Acc Id: NM_053709   ⟹   NP_446161
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2316,862,195 - 16,940,899 (-)NCBI
Rnor_6.0312,608,748 - 12,686,937 (-)NCBI
Celera311,596,841 - 11,674,265 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446161 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK70500 (Get FASTA)   NCBI Sequence Viewer  
  AAO17712 (Get FASTA)   NCBI Sequence Viewer  
  EDL93185 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446161   ⟸   NM_053709
- UniProtKB: G3V877 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022953   ⟸   ENSRNOT00000022953
Protein Domains
Homeobox   LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V877-F1-model_v2 AlphaFold G3V877 1-395 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620843 AgrOrtholog
BioCyc Gene G2FUF-50098 BioCyc
Ensembl Genes ENSRNOG00000017019 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022953 ENTREZGENE
  ENSRNOP00000022953.6 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022953 ENTREZGENE
  ENSRNOT00000022953.7 UniProtKB/TrEMBL
InterPro Homeobox_CS UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
NCBI Gene 114501 ENTREZGENE
Pfam Homeobox UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
PhenoGen Lmx1b PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt G3V877 ENTREZGENE, UniProtKB/TrEMBL
  Q91XM6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Lmx1b  LIM homeobox transcription factor 1 beta      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Lmx1b  LIM homeobox transcription factor 1 beta      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression enriched in mesencephalic dopamine (mesDA) systems in the substantia nigra pars compacta (SNc) and ventral tegmental area of embryos and adults 724433