Lhx8 (LIM homeobox 8) - Rat Genome Database

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Gene: Lhx8 (LIM homeobox 8) Rattus norvegicus
Analyze
Symbol: Lhx8
Name: LIM homeobox 8
RGD ID: 1308749
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 forebrain neuron development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including female gonad development; forebrain neuron differentiation; and odontogenesis of dentin-containing tooth. Predicted to be located in female germ cell nucleus. Predicted to be active in nucleus. Orthologous to human LHX8 (LIM homeobox 8); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Lhx7; LIM homeobox protein 8; LIM/homeobox protein Lhx8; LOC365963; MGC109530
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
mRatBN7.22243,244,958 - 243,269,631 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2243,244,961 - 243,269,416 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2251,069,403 - 251,090,965 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02248,963,243 - 248,984,805 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02243,862,639 - 243,884,232 (-)NCBIRnor_WKY
Rnor_6.02260,572,205 - 260,598,744 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,574,190 - 260,596,777 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02279,235,991 - 279,260,188 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42252,216,608 - 252,239,112 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12252,231,217 - 252,253,719 (-)NCBI
Celera2235,171,406 - 235,193,860 (-)NCBICelera
Cytogenetic Map2q45NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11801365   PMID:12477932   PMID:12703558   PMID:15217369   PMID:15978004   PMID:16690745   PMID:18753606   PMID:23150137   PMID:23385486   PMID:24265310   PMID:25475040  


Genomics

Comparative Map Data
Lhx8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22243,244,958 - 243,269,631 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2243,244,961 - 243,269,416 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2251,069,403 - 251,090,965 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02248,963,243 - 248,984,805 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02243,862,639 - 243,884,232 (-)NCBIRnor_WKY
Rnor_6.02260,572,205 - 260,598,744 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,574,190 - 260,596,777 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02279,235,991 - 279,260,188 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42252,216,608 - 252,239,112 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12252,231,217 - 252,253,719 (-)NCBI
Celera2235,171,406 - 235,193,860 (-)NCBICelera
Cytogenetic Map2q45NCBI
LHX8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38175,128,434 - 75,199,454 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl175,128,434 - 75,161,533 (+)EnsemblGRCh38hg38GRCh38
GRCh37175,594,119 - 75,627,218 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36175,366,707 - 75,399,806 (+)NCBINCBI36Build 36hg18NCBI36
Celera173,839,451 - 73,872,551 (+)NCBICelera
Cytogenetic Map1p31.1NCBI
HuRef173,728,993 - 73,762,092 (+)NCBIHuRef
CHM1_1175,709,516 - 75,742,604 (+)NCBICHM1_1
T2T-CHM13v2.0174,970,280 - 75,003,384 (+)NCBIT2T-CHM13v2.0
Lhx8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393154,011,925 - 154,036,197 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3154,011,931 - 154,036,296 (-)EnsemblGRCm39 Ensembl
GRCm383154,306,288 - 154,330,560 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3154,306,294 - 154,330,659 (-)EnsemblGRCm38mm10GRCm38
MGSCv373153,969,257 - 153,993,524 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363154,242,163 - 154,265,944 (-)NCBIMGSCv36mm8
Celera3160,766,458 - 160,790,689 (-)NCBICelera
Cytogenetic Map3H4NCBI
Lhx8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542317,644,871 - 17,668,781 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542317,644,691 - 17,668,969 (-)NCBIChiLan1.0ChiLan1.0
LHX8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1176,324,804 - 76,357,879 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl176,324,804 - 76,357,879 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0174,356,372 - 74,383,984 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LHX8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1671,329,711 - 71,355,851 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl671,329,820 - 71,352,945 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha673,992,529 - 74,018,201 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0671,921,509 - 71,947,201 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl671,920,999 - 71,947,701 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1671,416,782 - 71,442,453 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0671,362,129 - 71,387,952 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0671,856,878 - 71,882,562 (-)NCBIUU_Cfam_GSD_1.0
Lhx8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505886,811,952 - 86,842,076 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365712,326,920 - 2,351,779 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365712,326,851 - 2,352,428 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6138,074,855 - 138,099,810 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16138,074,673 - 138,102,025 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26128,034,492 - 128,061,739 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LHX8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12058,016,078 - 58,043,651 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2058,017,298 - 58,041,479 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603359,429,912 - 59,454,728 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhx8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474221,638,856 - 21,662,776 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474221,638,213 - 21,662,979 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lhx8
154 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:76
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000009370
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat


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 reproductive system respiratory system appendage
High
Medium 17 5
Low 17 12 5 12 30 14
Below cutoff 1 8 9 2 5 2 3 3 12 15 7 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009370   ⟹   ENSRNOP00000009370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2243,244,961 - 243,269,416 (-)Ensembl
Rnor_6.0 Ensembl2260,574,190 - 260,596,777 (-)Ensembl
RefSeq Acc Id: NM_001012219   ⟹   NP_001012219
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22243,244,958 - 243,267,578 (-)NCBI
Rnor_6.02260,574,187 - 260,596,777 (-)NCBI
Rnor_5.02279,235,991 - 279,260,188 (-)NCBI
RGSC_v3.42252,216,608 - 252,239,112 (-)RGD
Celera2235,171,406 - 235,193,860 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233528   ⟹   XP_006233590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22243,244,958 - 243,269,631 (-)NCBI
Rnor_6.02260,572,205 - 260,598,744 (-)NCBI
Rnor_5.02279,235,991 - 279,260,188 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001012219 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233590 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF29536 (Get FASTA)   NCBI Sequence Viewer  
  AAH90011 (Get FASTA)   NCBI Sequence Viewer  
  EDL82535 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001012219   ⟸   NM_001012219
- UniProtKB: G3V6V6 (UniProtKB/TrEMBL),   A0A8J8Y3T8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233590   ⟸   XM_006233528
- Peptide Label: isoform X1
- UniProtKB: Q5FVG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009370   ⟸   ENSRNOT00000009370
Protein Domains
Homeobox   LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6V6-F1-model_v2 AlphaFold G3V6V6 1-336 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:1308749 AgrOrtholog
BioCyc Gene G2FUF-50763 BioCyc
Ensembl Genes ENSRNOG00000028348 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009370 ENTREZGENE
  ENSRNOP00000009370.6 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009370 ENTREZGENE
  ENSRNOT00000009370.6 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7324565 IMAGE-MGC_LOAD
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:365963 UniProtKB/TrEMBL
MGC_CLONE MGC:109530 IMAGE-MGC_LOAD
NCBI Gene 365963 ENTREZGENE
Pfam Homeobox UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
PhenoGen Lhx8 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 A0A8J8Y3T8 ENTREZGENE, UniProtKB/TrEMBL
  G3V6V6 ENTREZGENE, UniProtKB/TrEMBL
  Q5FVG3 ENTREZGENE
UniProt Secondary Q5FVG3 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Lhx8  LIM homeobox 8  Lhx8  LIM homeobox protein 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-12 Lhx8  LIM homeobox protein 8  Lhx8  LIM homeobox protein 8  Data Merged 737654 APPROVED
2008-05-12 Lhx8  LIM homeobox protein 8  Lhx8_predicted  LIM homeobox protein 8 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 Lhx8  LIM homeobox protein 8      Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Lhx8_predicted  LIM homeobox protein 8 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Lhx8  LIM homeobox protein 8      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in cholinergic neurons of the basal forebrain 724413