Lhx9 (LIM homeobox 9) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Lhx9 (LIM homeobox 9) Rattus norvegicus
Analyze
Symbol: Lhx9
Name: LIM homeobox 9
RGD ID: 727956
Description: Predicted to have 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 dorsal spinal cord interneuron anterior axon guidance; gonad development; and regulation of transcription, DNA-templated. Predicted to localize to nucleus. Orthologous to human LHX9 (LIM homeobox 9); INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LIM homeobox 9-like; LIM homeobox protein 9; LIM-homeodomain type transcription factor 9; LIM/homeobox protein Lhx9; MGC156570
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21350,389,052 - 50,409,947 (-)NCBI
Rnor_6.0 Ensembl1355,861,015 - 55,878,094 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01355,854,543 - 55,879,305 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01360,880,668 - 60,905,112 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,143,492 - 52,160,922 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11352,157,571 - 52,175,002 (-)NCBI
Celera1350,673,951 - 50,690,517 (-)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:10706291   PMID:12477932   PMID:12617828   PMID:15585134  


Genomics

Comparative Map Data
Lhx9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21350,389,052 - 50,409,947 (-)NCBI
Rnor_6.0 Ensembl1355,861,015 - 55,878,094 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01355,854,543 - 55,879,305 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01360,880,668 - 60,905,112 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,143,492 - 52,160,922 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11352,157,571 - 52,175,002 (-)NCBI
Celera1350,673,951 - 50,690,517 (-)NCBICelera
Cytogenetic Map13q13NCBI
LHX9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1197,911,902 - 197,935,478 (+)EnsemblGRCh38hg38GRCh38
GRCh381197,912,464 - 197,935,478 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371197,881,594 - 197,904,608 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361196,148,258 - 196,165,896 (+)NCBINCBI36hg18NCBI36
Build 341194,618,173 - 194,630,930NCBI
Celera1171,004,535 - 171,021,892 (+)NCBI
Cytogenetic Map1q31.3NCBI
HuRef1169,037,610 - 169,054,968 (+)NCBIHuRef
CHM1_11199,303,970 - 199,321,613 (+)NCBICHM1_1
Lhx9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391138,752,924 - 138,776,577 (-)NCBIGRCm39mm39
GRCm39 Ensembl1138,752,924 - 138,776,315 (-)Ensembl
GRCm381138,825,186 - 138,848,839 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1138,825,186 - 138,848,577 (-)EnsemblGRCm38mm10GRCm38
MGSCv371140,721,763 - 140,744,156 (-)NCBIGRCm37mm9NCBIm37
MGSCv361140,641,597 - 140,663,730 (-)NCBImm8
Celera1141,453,531 - 141,475,838 (-)NCBICelera
Cytogenetic Map1E4NCBI
Lhx9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540634,342,887 - 34,366,131 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540634,341,972 - 34,363,351 (+)NCBIChiLan1.0ChiLan1.0
LHX9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11177,817,265 - 177,834,968 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1177,817,265 - 177,836,800 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01173,504,443 - 173,528,955 (+)NCBIMhudiblu_PPA_v0panPan3
LHX9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.174,881,134 - 4,897,136 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl74,881,627 - 4,896,011 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha74,565,594 - 4,581,012 (-)NCBI
ROS_Cfam_1.074,568,411 - 4,583,880 (-)NCBI
UMICH_Zoey_3.174,513,941 - 4,529,370 (-)NCBI
UNSW_CanFamBas_1.074,614,595 - 4,629,997 (-)NCBI
UU_Cfam_GSD_1.074,646,577 - 4,662,020 (-)NCBI
Lhx9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934476,760,409 - 76,784,699 (-)NCBI
SpeTri2.0NW_0049365675,997,947 - 6,019,298 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1020,742,398 - 20,764,009 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11020,742,323 - 20,764,006 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21025,350,311 - 25,373,704 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LHX9
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12531,471,999 - 31,499,270 (-)NCBI
ChlSab1.1 Ensembl2531,474,303 - 31,487,521 (-)Ensembl
Lhx9
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247982,505,983 - 2,526,604 (-)NCBI

Position Markers
RH144410  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21350,389,889 - 50,390,114 (+)MAPPER
Rnor_6.01355,857,656 - 55,857,880NCBIRnor6.0
Rnor_5.01360,883,781 - 60,884,005UniSTSRnor5.0
RGSC_v3.41352,140,133 - 52,140,357UniSTSRGSC3.4
Celera1350,670,592 - 50,670,816UniSTS
Cytogenetic Map13q13UniSTS
BE117391  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21350,391,959 - 50,392,127 (+)MAPPER
Rnor_6.01355,859,726 - 55,859,893NCBIRnor6.0
Rnor_5.01360,885,851 - 60,886,018UniSTSRnor5.0
RGSC_v3.41352,142,203 - 52,142,370UniSTSRGSC3.4
Celera1350,672,662 - 50,672,829UniSTS
Cytogenetic Map13q13UniSTS
Lhx9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21350,393,443 - 50,394,752 (+)MAPPER
Rnor_6.01355,861,208 - 55,862,516NCBIRnor6.0
Rnor_5.01360,887,333 - 60,888,641UniSTSRnor5.0
RGSC_v3.41352,143,685 - 52,144,993UniSTSRGSC3.4
Celera1350,674,144 - 50,675,452UniSTS
Cytogenetic Map13q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:374
Count of miRNA genes:201
Interacting mature miRNAs:234
Transcripts:ENSRNOT00000013873, ENSRNOT00000014218
Prediction methods:Microtar, 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


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 47 24
Low 8 8 6 2 6 27 2 13 2
Below cutoff 2 24 31 17 17 17 8 10 28 4 9 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014218   ⟹   ENSRNOP00000014218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1355,861,015 - 55,878,094 (-)Ensembl
RefSeq Acc Id: NM_181367   ⟹   NP_852032
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21350,393,251 - 50,409,849 (-)NCBI
Rnor_6.01355,861,015 - 55,878,094 (-)NCBI
Rnor_5.01360,880,668 - 60,905,112 (-)NCBI
RGSC_v3.41352,143,492 - 52,160,922 (-)RGD
Celera1350,673,951 - 50,690,517 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249914   ⟹   XP_006249976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21350,390,906 - 50,404,854 (-)NCBI
Rnor_6.01355,860,955 - 55,873,122 (-)NCBI
Rnor_5.01360,880,668 - 60,905,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249915   ⟹   XP_006249977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21350,390,906 - 50,404,857 (-)NCBI
Rnor_6.01355,860,955 - 55,873,130 (-)NCBI
Rnor_5.01360,880,668 - 60,905,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249916   ⟹   XP_006249978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01355,858,672 - 55,879,305 (-)NCBI
Rnor_5.01360,880,668 - 60,905,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249918   ⟹   XP_006249980
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21350,389,052 - 50,404,848 (-)NCBI
Rnor_6.01355,854,543 - 55,873,105 (-)NCBI
Rnor_5.01360,880,668 - 60,905,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249919   ⟹   XP_006249981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21350,389,052 - 50,409,947 (-)NCBI
Rnor_6.01355,854,543 - 55,879,303 (-)NCBI
Rnor_5.01360,880,668 - 60,905,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598700   ⟹   XP_017454189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01355,860,955 - 55,873,583 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_852032   ⟸   NM_181367
- UniProtKB: Q80W90 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249981   ⟸   XM_006249919
- Peptide Label: isoform X4
- UniProtKB: Q80W90 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249980   ⟸   XM_006249918
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006249978   ⟸   XM_006249916
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006249977   ⟸   XM_006249915
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006249976   ⟸   XM_006249914
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454189   ⟸   XM_017598700
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000014218   ⟸   ENSRNOT00000014218
Protein Domains
LIM zinc-binding

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
F344/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
F344/NRrrc (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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
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/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
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
SBH/Ygl (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SHRSP/Gcrc (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
SR/JrHsd (MCW)
Visual CSV TAB Printer
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)
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
SS/Jr (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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
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)
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
WAG/Rij (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/Gcrc (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/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
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)
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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727956 AgrOrtholog
Ensembl Genes ENSRNOG00000010357 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014218 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014218 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:8362986 IMAGE-MGC_LOAD
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Znf_LIM UniProtKB/Swiss-Prot
KEGG Report rno:289048 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156570 IMAGE-MGC_LOAD
NCBI Gene 289048 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot
  LIM UniProtKB/Swiss-Prot
PhenoGen Lhx9 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
  LIM_DOMAIN_1 UniProtKB/Swiss-Prot
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot
SMART HOX UniProtKB/Swiss-Prot
  LIM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniProt LHX9_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A1A5M2 UniProtKB/Swiss-Prot
  Q811Z4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Lhx9  LIM homeobox 9  LOC100364075  LIM homeobox 9-like  Data Merged 1643240 APPROVED
2010-05-06 LOC100364075  LIM homeobox 9-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-08 Lhx9  LIM homeobox 9      Symbol and Name status set to approved 1299863 APPROVED