LHX9 (LIM homeobox 9) - Rat Genome Database

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Gene: LHX9 (LIM homeobox 9) Homo sapiens
Analyze
Symbol: LHX9
Name: LIM homeobox 9
RGD ID: 1354474
HGNC Page HGNC:14222
Description: Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in dorsal spinal cord interneuron anterior axon guidance; negative regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within cell population proliferation and gonad development. Predicted to be located in chromatin. Predicted to be active in nucleus.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: LIM homeobox protein 9; LIM/homeobox protein Lhx9
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381197,912,464 - 197,935,478 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1197,911,902 - 197,935,478 (+)EnsemblGRCh38hg38GRCh38
GRCh371197,881,594 - 197,904,608 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361196,148,258 - 196,165,896 (+)NCBINCBI36Build 36hg18NCBI36
Build 341194,618,173 - 194,630,930NCBI
Celera1171,004,535 - 171,021,892 (+)NCBICelera
Cytogenetic Map1q31.3NCBI
HuRef1169,037,610 - 169,054,968 (+)NCBIHuRef
CHM1_11199,303,970 - 199,321,613 (+)NCBICHM1_1
T2T-CHM13v2.01197,171,857 - 197,194,877 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (ISA)
nucleus  (IBA,IEA)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7566098   PMID:9880598   PMID:11397841   PMID:12477932   PMID:14702039   PMID:15761153   PMID:16710414   PMID:19274049   PMID:19545367   PMID:19568415   PMID:21873635   PMID:25416956  
PMID:25910212   PMID:26186194   PMID:28473536   PMID:28514442   PMID:29565736   PMID:30419336   PMID:32296183   PMID:32513696   PMID:33961781   PMID:34536269   PMID:34548271   PMID:34732716  
PMID:37980488  


Genomics

Comparative Map Data
LHX9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381197,912,464 - 197,935,478 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1197,911,902 - 197,935,478 (+)EnsemblGRCh38hg38GRCh38
GRCh371197,881,594 - 197,904,608 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361196,148,258 - 196,165,896 (+)NCBINCBI36Build 36hg18NCBI36
Build 341194,618,173 - 194,630,930NCBI
Celera1171,004,535 - 171,021,892 (+)NCBICelera
Cytogenetic Map1q31.3NCBI
HuRef1169,037,610 - 169,054,968 (+)NCBIHuRef
CHM1_11199,303,970 - 199,321,613 (+)NCBICHM1_1
T2T-CHM13v2.01197,171,857 - 197,194,877 (+)NCBIT2T-CHM13v2.0
Lhx9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391138,752,924 - 138,776,577 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1138,752,924 - 138,776,315 (-)EnsemblGRCm39 Ensembl
GRCm381138,825,186 - 138,848,839 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1138,825,186 - 138,848,577 (-)EnsemblGRCm38mm10GRCm38
MGSCv371140,721,763 - 140,744,156 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361140,641,597 - 140,663,730 (-)NCBIMGSCv36mm8
Celera1141,453,531 - 141,475,838 (-)NCBICelera
Cytogenetic Map1E4NCBI
cM Map160.82NCBI
Lhx9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81352,941,207 - 52,961,436 (-)NCBIGRCr8
mRatBN7.21350,389,052 - 50,409,947 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1350,389,738 - 50,410,806 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1353,000,443 - 53,017,034 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01354,288,367 - 54,304,963 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01351,555,452 - 51,572,092 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01355,854,543 - 55,879,305 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1355,861,015 - 55,878,094 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01360,880,668 - 60,905,112 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,143,492 - 52,160,922 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11352,157,571 - 52,175,002 (-)NCBI
Celera1350,673,951 - 50,690,517 (-)NCBICelera
Cytogenetic Map13q13NCBI
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
NHGRI_mPanPan1-v2151,454,153 - 51,478,669 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1151,414,048 - 51,437,900 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01173,504,443 - 173,528,955 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11177,817,265 - 177,834,968 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1177,817,265 - 177,836,800 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.074,568,411 - 4,583,880 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl74,569,193 - 4,588,584 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.174,513,941 - 4,529,370 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.074,614,595 - 4,629,997 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.074,646,577 - 4,662,020 (-)NCBIUU_Cfam_GSD_1.0
Lhx9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934476,760,409 - 76,784,699 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365675,994,815 - 6,018,339 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 - 20,764,008 (+)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12531,471,999 - 31,499,270 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2531,474,303 - 31,487,521 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605532,370,969 - 32,391,119 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhx9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247982,502,407 - 2,526,130 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247982,505,983 - 2,526,604 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LHX9
18 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11		 pathogenic
GRCh38/hg38 1q25.2-32.1(chr1:179032905-199724897)x1 copy number loss See cases [RCV000053948] Chr1:179032905..199724897 [GRCh38]
Chr1:179002040..199694025 [GRCh37]
Chr1:177268663..197960648 [NCBI36]
Chr1:1q25.2-32.1		 pathogenic
GRCh38/hg38 1q31.1-32.1(chr1:189034483-199615866)x1 copy number loss See cases [RCV000135590] Chr1:189034483..199615866 [GRCh38]
Chr1:189003614..199584994 [GRCh37]
Chr1:187270237..197851617 [NCBI36]
Chr1:1q31.1-32.1		 pathogenic
GRCh37/hg19 1q31.3-42.13(chr1:197811907-228997888)x3 copy number gain See cases [RCV000240137] Chr1:197811907..228997888 [GRCh37]
Chr1:1q31.3-42.13		 pathogenic
GRCh37/hg19 1q31.3-44(chr1:195483439-249213000)x3 copy number gain See cases [RCV000449172] Chr1:195483439..249213000 [GRCh37]
Chr1:1q31.3-44		 pathogenic
GRCh37/hg19 1q25.2-32.1(chr1:179073386-200192265)x1 copy number loss See cases [RCV000448809] Chr1:179073386..200192265 [GRCh37]
Chr1:1q25.2-32.1		 pathogenic
GRCh37/hg19 1q25.2-32.1(chr1:179413479-201764737)x1 copy number loss See cases [RCV000445748] Chr1:179413479..201764737 [GRCh37]
Chr1:1q25.2-32.1		 pathogenic
GRCh37/hg19 1q25.2-32.1(chr1:179011314-199022759)x1 copy number loss See cases [RCV000512128] Chr1:179011314..199022759 [GRCh37]
Chr1:1q25.2-32.1		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q25.3-41(chr1:185644663-221698833)x3 copy number gain not provided [RCV000749265] Chr1:185644663..221698833 [GRCh37]
Chr1:1q25.3-41		 pathogenic
NM_020204.3(LHX9):c.1161C>T (p.Ser387=) single nucleotide variant not provided [RCV000957790] Chr1:197929226 [GRCh38]
Chr1:197898356 [GRCh37]
Chr1:1q31.3		 benign
GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1 copy number loss not provided [RCV001005157] Chr1:177551193..199599056 [GRCh37]
Chr1:1q25.2-32.1		 pathogenic
NM_020204.3(LHX9):c.791C>T (p.Ser264Leu) single nucleotide variant not specified [RCV004318468] Chr1:197927648 [GRCh38]
Chr1:197896778 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NM_020204.3(LHX9):c.1096A>T (p.Thr366Ser) single nucleotide variant not specified [RCV004288373] Chr1:197929161 [GRCh38]
Chr1:197898291 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1q25.3-44(chr1:182388773-249111240)x3 copy number gain not provided [RCV000845852] Chr1:182388773..249111240 [GRCh37]
Chr1:1q25.3-44		 pathogenic
GRCh37/hg19 1q31.3-32.1(chr1:196315481-200200856)x1 copy number loss not provided [RCV000847068] Chr1:196315481..200200856 [GRCh37]
Chr1:1q31.3-32.1		 uncertain significance
GRCh37/hg19 1q31.3-32.2(chr1:194356425-210988710)x3 copy number gain not provided [RCV001249273] Chr1:194356425..210988710 [GRCh37]
Chr1:1q31.3-32.2		 not provided
NM_020204.3(LHX9):c.947A>G (p.Gln316Arg) single nucleotide variant Inborn genetic diseases [RCV001266509] Chr1:197929012 [GRCh38]
Chr1:197898142 [GRCh37]
Chr1:1q31.3		 uncertain significance
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NM_020204.3(LHX9):c.1063C>A (p.Pro355Thr) single nucleotide variant Pituitary stalk interruption syndrome [RCV003214126] Chr1:197929128 [GRCh38]
Chr1:197898258 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1q31.3-44(chr1:197867914-249224684)x3 copy number gain See cases [RCV002287837] Chr1:197867914..249224684 [GRCh37]
Chr1:1q31.3-44		 pathogenic
GRCh37/hg19 1q31.1-32.1(chr1:189633885-199854163)x1 copy number loss not provided [RCV002472500] Chr1:189633885..199854163 [GRCh37]
Chr1:1q31.1-32.1		 likely pathogenic
GRCh37/hg19 1q31.2-32.1(chr1:193011753-199882947)x1 copy number loss not provided [RCV002474543] Chr1:193011753..199882947 [GRCh37]
Chr1:1q31.2-32.1		 pathogenic
NM_020204.3(LHX9):c.136C>A (p.Arg46Ser) single nucleotide variant not specified [RCV004205633] Chr1:197917959 [GRCh38]
Chr1:197887089 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1q25.2-32.1(chr1:179413479-201764737) copy number loss not specified [RCV002053780] Chr1:179413479..201764737 [GRCh37]
Chr1:1q25.2-32.1		 pathogenic
GRCh37/hg19 1q25.2-32.1(chr1:179073386-200192265) copy number loss not specified [RCV002053769] Chr1:179073386..200192265 [GRCh37]
Chr1:1q25.2-32.1		 pathogenic
NM_020204.3(LHX9):c.1090G>C (p.Asp364His) single nucleotide variant not specified [RCV004297298] Chr1:197929155 [GRCh38]
Chr1:197898285 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1q25.3-32.3(chr1:181453460-213107248)x3 copy number gain not provided [RCV002475637] Chr1:181453460..213107248 [GRCh37]
Chr1:1q25.3-32.3		 pathogenic
NM_020204.3(LHX9):c.1033C>T (p.Pro345Ser) single nucleotide variant not specified [RCV004137730] Chr1:197929098 [GRCh38]
Chr1:197898228 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.152C>T (p.Ala51Val) single nucleotide variant not specified [RCV004252578] Chr1:197917975 [GRCh38]
Chr1:197887105 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.1097C>A (p.Thr366Asn) single nucleotide variant not specified [RCV004284792] Chr1:197929162 [GRCh38]
Chr1:197898292 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.700G>T (p.Ala234Ser) single nucleotide variant not specified [RCV004415050] Chr1:197921626 [GRCh38]
Chr1:197890756 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.52C>T (p.Pro18Ser) single nucleotide variant not specified [RCV004415049] Chr1:197917875 [GRCh38]
Chr1:197887005 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1q31.3-32.1(chr1:197216705-203683110)x1 copy number loss not specified [RCV003986384] Chr1:197216705..203683110 [GRCh37]
Chr1:1q31.3-32.1		 likely pathogenic
NC_000001.10:g.(?_190829412)_(216061974_?)del deletion not provided [RCV004579260] Chr1:190829412..216061974 [GRCh37]
Chr1:1q31.2-41		 pathogenic
NM_020204.3(LHX9):c.227G>A (p.Gly76Asp) single nucleotide variant not specified [RCV004633975] Chr1:197920024 [GRCh38]
Chr1:197889154 [GRCh37]
Chr1:1q31.3		 uncertain significance
GRCh37/hg19 1q31.3(chr1:196670448-197898389)x1 copy number loss not provided [RCV002511626] Chr1:196670448..197898389 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.641C>T (p.Pro214Leu) single nucleotide variant not specified [RCV004161062] Chr1:197921567 [GRCh38]
Chr1:197890697 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.983G>A (p.Arg328Gln) single nucleotide variant not specified [RCV004200837] Chr1:197929048 [GRCh38]
Chr1:197898178 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.596T>C (p.Leu199Pro) single nucleotide variant not specified [RCV004283020] Chr1:197921522 [GRCh38]
Chr1:197890652 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.185C>G (p.Pro62Arg) single nucleotide variant not specified [RCV004340381] Chr1:197919982 [GRCh38]
Chr1:197889112 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.52C>G (p.Pro18Ala) single nucleotide variant not specified [RCV004343490] Chr1:197917875 [GRCh38]
Chr1:197887005 [GRCh37]
Chr1:1q31.3		 uncertain significance
NM_020204.3(LHX9):c.764A>G (p.Asp255Gly) single nucleotide variant not specified [RCV004415051] Chr1:197927621 [GRCh38]
Chr1:197896751 [GRCh37]
Chr1:1q31.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:4168
Count of miRNA genes:1203
Interacting mature miRNAs:1532
Transcripts:ENST00000337020, ENST00000367387, ENST00000367388, ENST00000367390, ENST00000367391, ENST00000475727, ENST00000561173, ENST00000606127
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 (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407341824GWAS990800_Heducational attainment QTL GWAS990800 (human)2e-12educational attainment1197921672197921673Human

Markers in Region
LHX9_2217  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371197,898,593 - 197,899,384UniSTSGRCh37
Build 361196,165,216 - 196,166,007RGDNCBI36
Celera1171,021,212 - 171,022,003RGD
HuRef1169,054,288 - 169,055,079UniSTS
Lhx9  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371197,896,759 - 197,898,201UniSTSGRCh37
Celera1171,019,377 - 171,020,820UniSTS
HuRef1169,052,455 - 169,053,896UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
877 980 2188 2060 2690 1044 1378 447 584 377 878 4596 4032 43 2634 347 1352 899 76 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001014434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001370213 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001410927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_020204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011509781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001849 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA316988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ296272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK097614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL590115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY273889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC131622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000367387   ⟹   ENSP00000356357
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,917,372 - 197,935,478 (+)Ensembl
Ensembl Acc Id: ENST00000367388   ⟹   ENSP00000356358
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,917,355 - 197,918,766 (+)Ensembl
Ensembl Acc Id: ENST00000367390   ⟹   ENSP00000356360
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,912,505 - 197,935,478 (+)Ensembl
Ensembl Acc Id: ENST00000367391   ⟹   ENSP00000356361
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,912,491 - 197,932,591 (+)Ensembl
Ensembl Acc Id: ENST00000475727   ⟹   ENSP00000482898
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,912,488 - 197,917,959 (+)Ensembl
Ensembl Acc Id: ENST00000561173   ⟹   ENSP00000453064
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,915,837 - 197,932,266 (+)Ensembl
Ensembl Acc Id: ENST00000606127   ⟹   ENSP00000483170
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,911,902 - 197,917,991 (+)Ensembl
Ensembl Acc Id: ENST00000615520
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1197,912,130 - 197,913,180 (+)Ensembl
RefSeq Acc Id: NM_001014434   ⟹   NP_001014434
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,912,464 - 197,935,478 (+)NCBI
GRCh371197,881,635 - 197,904,606 (+)NCBI
Build 361196,148,258 - 196,165,896 (+)NCBI Archive
Celera1171,004,535 - 171,021,892 (+)RGD
HuRef1169,037,610 - 169,054,968 (+)ENTREZGENE
CHM1_11199,303,970 - 199,321,613 (+)NCBI
T2T-CHM13v2.01197,171,857 - 197,194,877 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001370213   ⟹   NP_001357142
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,917,372 - 197,932,588 (+)NCBI
T2T-CHM13v2.01197,176,764 - 197,191,988 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001410927   ⟹   NP_001397856
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,916,074 - 197,932,588 (+)NCBI
T2T-CHM13v2.01197,175,466 - 197,191,988 (+)NCBI
RefSeq Acc Id: NM_020204   ⟹   NP_064589
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,917,372 - 197,935,478 (+)NCBI
GRCh371197,881,635 - 197,904,606 (+)NCBI
Build 361196,153,140 - 196,165,896 (+)NCBI Archive
Celera1171,004,535 - 171,021,892 (+)RGD
HuRef1169,037,610 - 169,054,968 (+)ENTREZGENE
CHM1_11199,308,851 - 199,321,613 (+)NCBI
T2T-CHM13v2.01197,176,764 - 197,194,877 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011509781   ⟹   XP_011508083
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,916,074 - 197,935,478 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054337758   ⟹   XP_054193733
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01197,175,346 - 197,194,877 (+)NCBI
RefSeq Acc Id: NP_001014434   ⟸   NM_001014434
- Peptide Label: isoform 2
- UniProtKB: Q9NQ69 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_064589   ⟸   NM_020204
- Peptide Label: isoform 1
- UniProtKB: Q9BYU6 (UniProtKB/Swiss-Prot),   Q86UH2 (UniProtKB/Swiss-Prot),   Q5VUE6 (UniProtKB/Swiss-Prot),   Q5VUE3 (UniProtKB/Swiss-Prot),   Q5VUE2 (UniProtKB/Swiss-Prot),   Q9NQ70 (UniProtKB/Swiss-Prot),   Q9NQ69 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011508083   ⟸   XM_011509781
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001357142   ⟸   NM_001370213
- Peptide Label: isoform 3
Ensembl Acc Id: ENSP00000453064   ⟸   ENST00000561173
Ensembl Acc Id: ENSP00000356361   ⟸   ENST00000367391
Ensembl Acc Id: ENSP00000356360   ⟸   ENST00000367390
Ensembl Acc Id: ENSP00000356358   ⟸   ENST00000367388
Ensembl Acc Id: ENSP00000356357   ⟸   ENST00000367387
Ensembl Acc Id: ENSP00000483170   ⟸   ENST00000606127
Ensembl Acc Id: ENSP00000482898   ⟸   ENST00000475727
RefSeq Acc Id: NP_001397856   ⟸   NM_001410927
- Peptide Label: isoform 4
- UniProtKB: H0YL54 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_054193733   ⟸   XM_054337758
- Peptide Label: isoform X1
Protein Domains
Homeobox   LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9NQ69-F1-model_v2 AlphaFold Q9NQ69 1-397 view protein structure

Promoters
RGD ID:6785931
Promoter ID:HG_KWN:6686
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   NB4
Transcripts:UC001GUJ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361196,151,551 - 196,152,051 (+)MPROMDB
RGD ID:6858490
Promoter ID:EPDNEW_H2410
Type:initiation region
Name:LHX9_3
Description:LIM homeobox 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2411  EPDNEW_H2412  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,912,480 - 197,912,540EPDNEW
RGD ID:6858492
Promoter ID:EPDNEW_H2411
Type:initiation region
Name:LHX9_2
Description:LIM homeobox 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2410  EPDNEW_H2412  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,916,074 - 197,916,134EPDNEW
RGD ID:6858494
Promoter ID:EPDNEW_H2412
Type:initiation region
Name:LHX9_1
Description:LIM homeobox 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2410  EPDNEW_H2411  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381197,917,372 - 197,917,432EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:14222 AgrOrtholog
COSMIC LHX9 COSMIC
Ensembl Genes ENSG00000143355 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000367387 ENTREZGENE
  ENST00000367387.6 UniProtKB/Swiss-Prot
  ENST00000367388.4 UniProtKB/TrEMBL
  ENST00000367390 ENTREZGENE
  ENST00000367390.7 UniProtKB/Swiss-Prot
  ENST00000367391 ENTREZGENE
  ENST00000367391.5 UniProtKB/Swiss-Prot
  ENST00000475727.1 UniProtKB/TrEMBL
  ENST00000561173 ENTREZGENE
  ENST00000561173.5 UniProtKB/TrEMBL
  ENST00000606127.2 UniProtKB/TrEMBL
Gene3D-CATH Cysteine Rich Protein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000143355 GTEx
HGNC ID HGNC:14222 ENTREZGENE
Human Proteome Map LHX9 Human Proteome Map
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_Homeobox_TF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:56956 UniProtKB/Swiss-Prot
NCBI Gene 56956 ENTREZGENE
OMIM 606066 OMIM
PANTHER LIM/HOMEOBOX PROTEIN LHX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM/HOMEOBOX PROTEIN LHX9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA30368 PharmGKB
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  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 Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087X083_HUMAN UniProtKB/TrEMBL
  A0A0C4DGY4_HUMAN UniProtKB/TrEMBL
  H0Y330_HUMAN UniProtKB/TrEMBL
  H0YL54 ENTREZGENE, UniProtKB/TrEMBL
  LHX9_HUMAN UniProtKB/Swiss-Prot
  Q5VUE2 ENTREZGENE
  Q5VUE3 ENTREZGENE
  Q5VUE6 ENTREZGENE
  Q86UH2 ENTREZGENE
  Q9BYU6 ENTREZGENE
  Q9NQ69 ENTREZGENE
  Q9NQ70 ENTREZGENE
UniProt Secondary Q5VUE2 UniProtKB/Swiss-Prot
  Q5VUE3 UniProtKB/Swiss-Prot
  Q5VUE6 UniProtKB/Swiss-Prot
  Q86UH2 UniProtKB/Swiss-Prot
  Q9BYU6 UniProtKB/Swiss-Prot
  Q9NQ70 UniProtKB/Swiss-Prot