Lhx5 (LIM homeobox protein 5) - Rat Genome Database

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Gene: Lhx5 (LIM homeobox protein 5) Mus musculus
Analyze
Symbol: Lhx5
Name: LIM homeobox protein 5
RGD ID: 732693
MGI Page MGI
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. Involved in positive regulation of transcription, DNA-templated and spinal cord association neuron differentiation. Acts upstream of or within brain development and cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation. Predicted to be active in nucleus. Is expressed in several structures, including future brain; limb; nervous system; sensory organ; and urinary system. Orthologous to human LHX5 (LIM homeobox 5); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; Benzo[ghi]perylene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Li; LIM homeo box protein 5; LIM/homeobox protein Lhx5; Lim2
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395120,569,951 - 120,579,522 (+)NCBIGRCm39mm39
GRCm39 Ensembl5120,569,764 - 120,579,288 (+)Ensembl
GRCm385120,431,886 - 120,441,457 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5120,431,699 - 120,441,223 (+)EnsemblGRCm38mm10GRCm38
MGSCv375120,881,895 - 120,891,466 (+)NCBIGRCm37mm9NCBIm37
MGSCv365120,692,518 - 120,702,074 (+)NCBImm8
Celera5117,516,048 - 117,525,759 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map560.62NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:8069910   PMID:8565076   PMID:8812449   PMID:8817562   PMID:9022063   PMID:9315901   PMID:10325223   PMID:10349636   PMID:10433919   PMID:10943837   PMID:11042159   PMID:11076861  
PMID:11161479   PMID:11217851   PMID:11239429   PMID:11306624   PMID:11502254   PMID:11566211   PMID:11567052   PMID:11567614   PMID:11877374   PMID:11944941   PMID:12062038   PMID:12062039  
PMID:12354394   PMID:12435629   PMID:12467588   PMID:12477932   PMID:12619132   PMID:12787506   PMID:12799141   PMID:14681479   PMID:14960494   PMID:15053981   PMID:15147765   PMID:15229603  
PMID:15240886   PMID:15469980   PMID:15489334   PMID:15528197   PMID:15607939   PMID:15618518   PMID:15691760   PMID:15733084   PMID:15769945   PMID:15901662   PMID:15917450   PMID:15922675  
PMID:15930101   PMID:16018995   PMID:16055717   PMID:16139370   PMID:16141072   PMID:16141073   PMID:16284245   PMID:16291784   PMID:16602821   PMID:16690754   PMID:16790481   PMID:16819978  
PMID:16855091   PMID:16957084   PMID:16971467   PMID:17122047   PMID:17123502   PMID:17150208   PMID:17166926   PMID:17219401   PMID:17468181   PMID:17475798   PMID:17611227   PMID:17664423  
PMID:17670789   PMID:17676639   PMID:17729296   PMID:17804629   PMID:17953485   PMID:18076286   PMID:18094027   PMID:18198335   PMID:18287559   PMID:18463247   PMID:18498101   PMID:18522874  
PMID:18547559   PMID:18579678   PMID:18694563   PMID:18700968   PMID:18721803   PMID:18942141   PMID:19029045   PMID:19048639   PMID:19088088   PMID:19135992   PMID:19141316   PMID:19304889  
PMID:19463901   PMID:19474326   PMID:19542358   PMID:19668217   PMID:19732765   PMID:19850875   PMID:19890917   PMID:19923199   PMID:19924827   PMID:20004188   PMID:20059953   PMID:20211142  
PMID:20400693   PMID:20436479   PMID:20495559   PMID:20503365   PMID:20562861   PMID:20589911   PMID:20685998   PMID:20711475   PMID:20809939   PMID:20932939   PMID:21215373   PMID:21246650  
PMID:21267068   PMID:21316586   PMID:21431469   PMID:21451052   PMID:21452208   PMID:21525287   PMID:21637844   PMID:21674568   PMID:21731673   PMID:21752929   PMID:21784065   PMID:21844226  
PMID:21873635   PMID:21880902   PMID:21925604   PMID:22090492   PMID:22102297   PMID:22159578   PMID:22291885   PMID:22307612   PMID:22326227   PMID:22419569   PMID:22485187   PMID:22492355  
PMID:22923088   PMID:22988430   PMID:23193182   PMID:23284619   PMID:23292680   PMID:23307637   PMID:23418536   PMID:23669529   PMID:24007338   PMID:24210661   PMID:24491816   PMID:24594479  
PMID:24715462   PMID:24803655   PMID:24924197   PMID:24952961   PMID:25113559   PMID:25176648   PMID:25179941   PMID:25369423   PMID:26444681   PMID:26520399   PMID:26527010   PMID:26911688  
PMID:26937009   PMID:27210758   PMID:27223328   PMID:27469598   PMID:27665712   PMID:27697904   PMID:27784329   PMID:28076782   PMID:28082864   PMID:28165338   PMID:28516904   PMID:28603487  
PMID:28850031   PMID:28893945   PMID:29679559   PMID:29795232   PMID:29874580   PMID:30063881   PMID:30121012   PMID:30456369   PMID:30635555   PMID:31152445   PMID:31869353   PMID:32325033  
PMID:32471461   PMID:33723434   PMID:33787491  


Genomics

Comparative Map Data
Lhx5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395120,569,951 - 120,579,522 (+)NCBIGRCm39mm39
GRCm39 Ensembl5120,569,764 - 120,579,288 (+)Ensembl
GRCm385120,431,886 - 120,441,457 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5120,431,699 - 120,441,223 (+)EnsemblGRCm38mm10GRCm38
MGSCv375120,881,895 - 120,891,466 (+)NCBIGRCm37mm9NCBIm37
MGSCv365120,692,518 - 120,702,074 (+)NCBImm8
Celera5117,516,048 - 117,525,759 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map560.62NCBI
LHX5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12113,462,033 - 113,472,280 (-)EnsemblGRCh38hg38GRCh38
GRCh3812113,462,033 - 113,471,871 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712113,899,838 - 113,909,676 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612112,385,077 - 112,394,260 (-)NCBINCBI36hg18NCBI36
Build 3412112,363,413 - 112,372,597NCBI
Celera12113,527,582 - 113,536,765 (-)NCBI
Cytogenetic Map12q24.13NCBI
HuRef12110,911,297 - 110,920,482 (-)NCBIHuRef
CHM1_112113,868,362 - 113,877,545 (-)NCBICHM1_1
Lhx5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21236,126,186 - 36,134,625 (-)NCBI
Rnor_6.0 Ensembl1241,663,000 - 41,671,437 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01241,663,000 - 41,671,437 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01243,513,076 - 43,521,513 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41237,323,820 - 37,332,257 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11237,187,214 - 37,195,645 (-)NCBI
Celera1237,784,186 - 37,792,623 (-)NCBICelera
Cytogenetic Map12q16NCBI
Lhx5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554829,682,526 - 9,691,530 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554829,682,671 - 9,691,155 (-)NCBIChiLan1.0ChiLan1.0
LHX5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112114,445,759 - 114,454,960 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12114,445,766 - 114,454,960 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012111,063,466 - 111,075,445 (-)NCBIMhudiblu_PPA_v0panPan3
LHX5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12610,776,991 - 10,785,820 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2610,777,242 - 10,785,815 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2610,901,082 - 10,909,374 (-)NCBI
ROS_Cfam_1.02611,027,504 - 11,035,796 (-)NCBI
UMICH_Zoey_3.12610,996,951 - 11,005,243 (-)NCBI
UNSW_CanFamBas_1.02611,059,577 - 11,067,865 (-)NCBI
UU_Cfam_GSD_1.02611,108,837 - 11,117,131 (-)NCBI
Lhx5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118148,746,922 - 148,756,459 (-)NCBI
SpeTri2.0NW_0049366683,246,456 - 3,255,353 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1438,446,730 - 38,457,177 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11438,446,781 - 38,456,460 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21440,911,815 - 40,920,132 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LHX5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111108,718,452 - 108,727,156 (-)NCBI
ChlSab1.1 Ensembl11108,718,925 - 108,727,139 (-)Ensembl
Vero_WHO_p1.0NW_023666037136,366,070 - 136,376,140 (+)NCBI
Lhx5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474719,088,372 - 19,097,406 (+)NCBI

Position Markers
Lhx5  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5FUniSTS
cM Map564.0UniSTS
Lhx5  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5FUniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11341716Rvfs3_mRift Valley fever susceptibility 3 (mouse)526236236138457140Mouse
4142064Tmc1m4_mTmc1 modifier 4 (mouse)Not determined554342835126924008Mouse
26884395Humsd2_mhumerus midshaft diameter 2, 10 week (mouse)569900000132500000Mouse
27226719Tibw6_mtibia width 6, proximal, 16 week (mouse)572700000140000000Mouse
13506928Recrq8_mrecombination rate in male meiosis QTL 8 (mouse)574300000132500000Mouse
25314315Mlh1fc4_mMLH1 foci count 4 (mouse)574300000132500000Mouse
1300801Drb2_mdopamine receptor binding 2 (mouse)Not determined587239005121239199Mouse
1301399Cpfd3_mcerebellum pattern fissures (mouse)Not determined587239005121239199Mouse
1301126Bwem1_mbody weight day 30 males 1 (mouse)Not determined587239005121239199Mouse
10043958Chldq12_mcholesterol and HDL QTL 12 (mouse)Not determined587239005121239199Mouse
13464241Ahl18_mage related hearing loss, early onset 18 (mouse)587239005121239199Mouse
1300968Skts4_mskin tumor susceptibility 4 (mouse)Not determined589271017124100176Mouse
1301362Prnr1_mprion resistance 1 (mouse)Not determined589271017146851125Mouse
11049562Lmr24f_mleishmaniasis resistance 24f (mouse)590173096124173175Mouse
1301457Cfsw2_mcystic fibrosis survival to weaning 2 (mouse)Not determined590413140124413285Mouse
1300993Hycdc_mhypercapnic duty cycle (mouse)Not determined590413140124413285Mouse
9587780Afw16_mabdominal fat weight QTL 16 (mouse)Not determined592682300126682419Mouse
1301974Chab7_mcholesterol absorption 7 (mouse)Not determined595085348129085464Mouse
1357644Egrd1_mearly growth rate, direct effect 1 (mouse)Not determined595286714129286920Mouse
1558774Lith17_mlithogenic gene 17 (mouse)Not determined595317683129317856Mouse
10402486Dipa1_mdrug induced psychomotor activation 1 (mouse)Not determined595317683129317856Mouse
13464244Ahl19_mage related hearing loss, early onset 19 (mouse)595317683129317856Mouse
1300940Actd3_mactivity-distance traveled 3 (mouse)Not determined596172519130172667Mouse
1300659Pcd8ts1_mp-glycoprotein positive CD8 T cell subset 1 (mouse)Not determined596883692130883925Mouse
1301858Smdq1_msegregation of mitochondrial DNA QTL 1 (mouse)Not determined596883692130883925Mouse
4141519Hmtb5_mhemostasis and thrombosis bleeding time 5 (mouse)Not determined99801563126805880Mouse
12904945Tammq2_mtibialis anterior muscle mass QTL 2 (mouse)5100527900134527900Mouse
12904959Smmq1_msoleus muscle mass QTL 1 (mouse)5100527900134527900Mouse
12859290Criq2_mCitrobacter rodentium infection QTL 2 (mouse)5101194514135194514Mouse
1301624Aevm2_mautoimmune extremity vasculitis in MRL mice 2 (mouse)Not determined5101725767135725963Mouse
14746986Manh58_mmandible shape 58 (mouse)5102308218136308218Mouse
11532736Sluc33b_msusceptibility to lung cancer 33b (mouse)5102806972136807131Mouse
11528550Sluc33_msusceptibility to lung cancer 33 (mouse)5104239005120573921Mouse
10412202Bbaa26_mB.burgdorferi-associated arthritis 26 (mouse)Not determined5104435822138557193Mouse
10412239Alpq7_malcohol preference QTL 7 (mouse)Not determined5104567876138567876Mouse
4142473Chlq11_mcirculating hormone level QTL 11 (mouse)Not determined5107829235141829348Mouse
10043890Trigq4_mtriglyceride QTL 4 (mouse)Not determined5107829235141829348Mouse
13464243Ahl20_mage related hearing loss, early onset 20 (mouse)5107829235141829348Mouse
4141139Hmtb4_mhemostasis and thrombosis rebleeding time 4 (mouse)Not determined108614643126805880Mouse
10412197Bbaa25_mB.burgdorferi-associated arthritis 25 (mouse)Not determined5109090176143090317Mouse
13464251Ahl21_mage related hearing loss, early onset 21 (mouse)5109090176143090317Mouse
1301543Hypch_mhypercholesterolemia (mouse)Not determined5109090758139133150Mouse
1300913Bwefm_mbody weight females and males day 10 (mouse)Not determined5109362284143362395Mouse
1301102Cia14_mcollagen induced arthritis 14 (mouse)Not determined5113172519138557193Mouse
1357662Lprq4_mlipoprotein QTL 4 (mouse)Not determined5113883692129555542Mouse
1300827Cora1_mcorrelation in cytokine production 1 (mouse)Not determined5115128044149128176Mouse
1301226Bbaa2_mB.burgdorferi-associated arthritis 2 (mouse)Not determined5115128044149128176Mouse
1301857Bglq14_mbody growth late QTL 14 (mouse)Not determined5118920110151834684Mouse
10412191Bbaa24_mB.burgdorferi-associated arthritis 24 (mouse)Not determined5119806972141714711Mouse
4141081Nidd7k_mNidd7 on KK-A (mouse)Not determined119806972149423861Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:417
Count of miRNA genes:235
Interacting mature miRNAs:320
Transcripts:ENSMUST00000031591
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000031591   ⟹   ENSMUSP00000031591
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl5120,431,699 - 120,441,223 (+)Ensembl
RefSeq Acc Id: NM_008499   ⟹   NP_032525
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395120,569,951 - 120,579,522 (+)NCBI
GRCm385120,431,886 - 120,441,457 (+)ENTREZGENE
MGSCv375120,881,895 - 120,891,466 (+)RGD
Celera5117,516,048 - 117,525,759 (+)RGD
cM Map5 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_032525   ⟸   NM_008499
- UniProtKB: P61375 (UniProtKB/Swiss-Prot),   Q543P4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000031591   ⟸   ENSMUST00000031591
Protein Domains
Homeobox   LIM zinc-binding

Promoters
RGD ID:6887854
Promoter ID:EPDNEW_M7378
Type:multiple initiation site
Name:Lhx5_1
Description:Mus musculus LIM homeobox protein 5 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm385120,431,897 - 120,431,957EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:107792 AgrOrtholog
Ensembl Genes ENSMUSG00000029595 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000031591 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000031591 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:16873 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:107792 ENTREZGENE
NCBI Gene 16873 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lhx5 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt LHX5_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q543P4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary P50459 UniProtKB/Swiss-Prot