LHX9_MOUSE
ID LHX9_MOUSE Reviewed; 397 AA.
AC Q9WUH2; Q6GQU4; Q9QYQ5; Q9QYQ6; Q9QZ00; Q9WU44;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 3.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=LIM/homeobox protein Lhx9;
DE Short=LIM homeobox protein 9;
GN Name=Lhx9;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [GENOMIC DNA]
RP OF 32-397 (ISOFORM 1/3), NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 32-397
RP (ISOFORM 1/2), AND ALTERNATIVE SPLICING.
RC STRAIN=C57BL/6J; TISSUE=Embryonic brain;
RX PubMed=10756098; DOI=10.1006/geno.2000.6123;
RA Failli V., Rogard M., Mattei M.-G., Vernier P., Retaux S.;
RT "Lhx9 and Lhx9alpha LIM-homeodomain factors: genomic structure, expression
RT patterns, chromosomal localization, and phylogenetic analysis.";
RL Genomics 64:307-317(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-309 (ISOFORM 1/2), INTERACTION WITH LDB1
RP AND LDB2, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=C57BL/6J; TISSUE=Embryonic head;
RX PubMed=9880598; DOI=10.1523/jneurosci.19-02-00783.1999;
RA Retaux S., Rogard M., Bach I., Failli V., Besson M.-J.;
RT "Lhx9: a novel LIM-homeodomain gene expressed in the developing
RT forebrain.";
RL J. Neurosci. 19:783-793(1999).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 20-397 (ISOFORM 1/3), INTERACTION WITH LDB1,
RP AND DEVELOPMENTAL STAGE.
RC STRAIN=NIH Swiss;
RX PubMed=10330499; DOI=10.1016/s0925-4773(98)00233-0;
RA Bertuzzi S., Porter F.D., Pitts A., Kumar M., Agulnick A., Wassif C.,
RA Westphal H.;
RT "Characterization of Lhx9, a novel LIM/homeobox gene expressed by the
RT pioneer neurons in the mouse cerebral cortex.";
RL Mech. Dev. 81:193-198(1999).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND DEVELOPMENTAL STAGE.
RX PubMed=10706291; DOI=10.1038/35002622;
RA Birk O.S., Casiano D.E., Wassif C.A., Cogliati T., Zhao L., Zhao Y.,
RA Grinberg A., Huang S., Kreidberg J.A., Parker K.L., Porter F.D.,
RA Westphal H.;
RT "The LIM homeobox gene Lhx9 is essential for mouse gonad formation.";
RL Nature 403:909-913(2000).
CC -!- FUNCTION: Involved in gonadal development.
CC {ECO:0000269|PubMed:10706291}.
CC -!- SUBUNIT: Interacts with LDB1 and LDB2. {ECO:0000269|PubMed:10330499,
CC ECO:0000269|PubMed:9880598}.
CC -!- INTERACTION:
CC Q9WUH2; Q9CYZ8: Ssbp2; NbExp=3; IntAct=EBI-309943, EBI-309962;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00108,
CC ECO:0000269|PubMed:10706291}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=3;
CC IsoId=Q9WUH2-3; Sequence=Displayed;
CC Name=1; Synonyms=Beta;
CC IsoId=Q9WUH2-1; Sequence=VSP_036430;
CC Name=2; Synonyms=Alpha;
CC IsoId=Q9WUH2-2; Sequence=VSP_036430, VSP_036431;
CC Name=4;
CC IsoId=Q9WUH2-4; Sequence=VSP_036431;
CC -!- TISSUE SPECIFICITY: Expressed in the dorsal thalamus and inner nuclei
CC of the cerebellum. {ECO:0000269|PubMed:9880598}.
CC -!- DEVELOPMENTAL STAGE: Expressed in urogenital ridges of mice at 9.5 dpc.
CC Expressed in the nervous system at 10.5 dpc. Expressed in the forelimb
CC and hindlimb buds, the caelomic cavity at the level of the urogenital
CC ridge, including the gonads, the pancreas and liver epithelium at 11.5
CC dpc. Expressed widespread throughout the CNS alar neuroepithelium from
CC 11.5 to 14.5 dpc. Expressed in pioneer neurons of the cerebral cortex.
CC In the telencephalic vesicles, expressed in cerebral cortex, the
CC hippocampus, the claustrum primordium, olfactory bulb primordium and
CC the caudal ganglionic eminence (amygdaloid complex) at 13.5 dpc. In the
CC diencephalon, expressed in the pretectum (p1 prosomere), the dorsal
CC thalamus (except for a thin ventral band close to the alar-basal
CC boundary), the epithalamus, the epiphysis in prosomere p2, the
CC supraoptic-paraventricular area, the eminentia thalami (p4 prosomere),
CC the retrochiasmatic area and the tuberal hypothalamus at 13.5 dpc. In
CC the mesencephalon, expressed in the tectum, the walls of the hindbrain,
CC in nuclei of the ventral midbrain and hindbrain at 13.5 dpc. In the
CC spinal cord, expressed as a gradient in the dorsal part of the
CC neuroepithelium at 13.5 dpc. In the neocortical neuroepithelium,
CC expressed in the archicortex (in the dentate gyrus, CA3 and CA4), the
CC diencephalon, the midbrain and hindbrain at 14.5 and 16.5 dpc.
CC {ECO:0000269|PubMed:10330499, ECO:0000269|PubMed:10706291,
CC ECO:0000269|PubMed:9880598}.
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DR EMBL; AJ243851; CAB59907.1; -; mRNA.
DR EMBL; AJ243852; CAB59908.1; -; Genomic_DNA.
DR EMBL; AJ243853; CAB59908.1; JOINED; Genomic_DNA.
DR EMBL; AJ243854; CAB59908.1; JOINED; Genomic_DNA.
DR EMBL; AJ243855; CAB59908.1; JOINED; Genomic_DNA.
DR EMBL; AJ243856; CAB59908.1; JOINED; Genomic_DNA.
DR EMBL; AJ243852; CAB59909.1; -; Genomic_DNA.
DR EMBL; AJ243853; CAB59909.1; JOINED; Genomic_DNA.
DR EMBL; AJ243854; CAB59909.1; JOINED; Genomic_DNA.
DR EMBL; AJ243855; CAB59909.1; JOINED; Genomic_DNA.
DR EMBL; AJ243857; CAB59909.1; JOINED; Genomic_DNA.
DR EMBL; AC154398; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC072623; AAH72623.1; -; mRNA.
DR EMBL; AF134761; AAD30110.1; -; mRNA.
DR EMBL; AF113518; AAD22008.1; -; mRNA.
DR CCDS; CCDS15333.1; -. [Q9WUH2-2]
DR CCDS; CCDS15334.1; -. [Q9WUH2-4]
DR CCDS; CCDS35726.1; -. [Q9WUH2-3]
DR RefSeq; NP_001020736.1; NM_001025565.2. [Q9WUH2-4]
DR RefSeq; NP_001036042.1; NM_001042577.1. [Q9WUH2-3]
DR RefSeq; NP_034844.1; NM_010714.3. [Q9WUH2-2]
DR RefSeq; XP_006529234.1; XM_006529171.2. [Q9WUH2-1]
DR RefSeq; XP_006529235.1; XM_006529172.3. [Q9WUH2-1]
DR RefSeq; XP_006529236.1; XM_006529173.3. [Q9WUH2-1]
DR RefSeq; XP_017174117.1; XM_017318628.1.
DR RefSeq; XP_017174126.1; XM_017318637.1. [Q9WUH2-2]
DR AlphaFoldDB; Q9WUH2; -.
DR SMR; Q9WUH2; -.
DR BioGRID; 201161; 8.
DR IntAct; Q9WUH2; 7.
DR MINT; Q9WUH2; -.
DR STRING; 10090.ENSMUSP00000107657; -.
DR iPTMnet; Q9WUH2; -.
DR PhosphoSitePlus; Q9WUH2; -.
DR PaxDb; Q9WUH2; -.
DR PeptideAtlas; Q9WUH2; -.
DR PRIDE; Q9WUH2; -.
DR ProteomicsDB; 291948; -. [Q9WUH2-3]
DR ProteomicsDB; 291949; -. [Q9WUH2-1]
DR ProteomicsDB; 291950; -. [Q9WUH2-2]
DR ProteomicsDB; 291951; -. [Q9WUH2-4]
DR Antibodypedia; 1450; 94 antibodies from 18 providers.
DR DNASU; 16876; -.
DR Ensembl; ENSMUST00000019374; ENSMUSP00000019374; ENSMUSG00000019230. [Q9WUH2-4]
DR Ensembl; ENSMUST00000046870; ENSMUSP00000036480; ENSMUSG00000019230. [Q9WUH2-1]
DR Ensembl; ENSMUST00000093486; ENSMUSP00000091198; ENSMUSG00000019230. [Q9WUH2-2]
DR Ensembl; ENSMUST00000112026; ENSMUSP00000107657; ENSMUSG00000019230. [Q9WUH2-3]
DR Ensembl; ENSMUST00000112030; ENSMUSP00000107661; ENSMUSG00000019230. [Q9WUH2-2]
DR GeneID; 16876; -.
DR KEGG; mmu:16876; -.
DR UCSC; uc007cvr.1; mouse. [Q9WUH2-4]
DR UCSC; uc007cvs.1; mouse. [Q9WUH2-2]
DR UCSC; uc007cvu.2; mouse. [Q9WUH2-3]
DR CTD; 56956; -.
DR MGI; MGI:1316721; Lhx9.
DR VEuPathDB; HostDB:ENSMUSG00000019230; -.
DR eggNOG; KOG0490; Eukaryota.
DR GeneTree; ENSGT00940000158821; -.
DR HOGENOM; CLU_027802_4_1_1; -.
DR InParanoid; Q9WUH2; -.
DR OMA; MQINGRE; -.
DR OrthoDB; 1174930at2759; -.
DR PhylomeDB; Q9WUH2; -.
DR TreeFam; TF315442; -.
DR BioGRID-ORCS; 16876; 2 hits in 73 CRISPR screens.
DR ChiTaRS; Lhx9; mouse.
DR PRO; PR:Q9WUH2; -.
DR Proteomes; UP000000589; Chromosome 1.
DR RNAct; Q9WUH2; protein.
DR Bgee; ENSMUSG00000019230; Expressed in indifferent gonad and 116 other tissues.
DR ExpressionAtlas; Q9WUH2; baseline and differential.
DR Genevisible; Q9WUH2; MM.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:1990837; F:sequence-specific double-stranded DNA binding; ISO:MGI.
DR GO; GO:0008283; P:cell population proliferation; IMP:MGI.
DR GO; GO:0097380; P:dorsal spinal cord interneuron anterior axon guidance; ISS:UniProtKB.
DR GO; GO:0008585; P:female gonad development; IMP:MGI.
DR GO; GO:0035262; P:gonad morphogenesis; IMP:MGI.
DR GO; GO:0008584; P:male gonad development; IMP:MGI.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0030182; P:neuron differentiation; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd00086; homeodomain; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR001781; Znf_LIM.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF00412; LIM; 2.
DR SMART; SM00389; HOX; 1.
DR SMART; SM00132; LIM; 2.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
DR PROSITE; PS00478; LIM_DOMAIN_1; 2.
DR PROSITE; PS50023; LIM_DOMAIN_2; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; Homeobox; LIM domain; Metal-binding;
KW Nucleus; Reference proteome; Repeat; Zinc.
FT CHAIN 1..397
FT /note="LIM/homeobox protein Lhx9"
FT /id="PRO_0000075799"
FT DOMAIN 69..130
FT /note="LIM zinc-binding 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 131..193
FT /note="LIM zinc-binding 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DNA_BIND 267..326
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 248..272
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 330..365
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 378..397
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..18
FT /note="MEIVGCRAENNSCPFRPP -> MLNGTTLEA (in isoform 1 and
FT isoform 2)"
FT /evidence="ECO:0000303|PubMed:10756098"
FT /id="VSP_036430"
FT VAR_SEQ 313..397
FT /note="VWFQNARAKFRRNLLRQENGGVDKADGTSLPAPPSADSGALTPPGTATTLTD
FT LTNPTVTVVTTVTSNMDSHEPGSPSQTTLTNLF -> GEQILGHYSQTSRRLKIP (in
FT isoform 2 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:10756098,
FT ECO:0000303|PubMed:15489334"
FT /id="VSP_036431"
FT CONFLICT 58
FT /note="A -> T (in Ref. 5; AAD22008)"
FT /evidence="ECO:0000305"
FT CONFLICT 162
FT /note="S -> F (in Ref. 5; AAD22008)"
FT /evidence="ECO:0000305"
FT CONFLICT 377
FT /note="T -> I (in Ref. 1; CAB59908 and 5; AAD22008)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 397 AA; 44045 MW; 4E2DCF65B5EDFC54 CRC64;
MEIVGCRAEN NSCPFRPPAM LFHGISGGHI QGIMEEMERR SKTEARLTKG TQLNGRDAGM
PPLSPEKPAL CAGCGGKISD RYYLLAVDKQ WHLRCLKCCE CKLALESELT CFAKDGSIYC
KEDYYRRFSV QRCARCHLGI SASEMVMRAR DSVYHLSCFT CSTCNKTLTT GDHFGMKDSL
VYCRAHFETL LQGEYPPQLS YTELAAKSGG LALPYFNGTG TVQKGRPRKR KSPALGVDIV
NYNSGCNENE ADHLDRDQQP YPPSQKTKRM RTSFKHHQLR TMKSYFAINH NPDAKDLKQL
AQKTGLTKRV LQVWFQNARA KFRRNLLRQE NGGVDKADGT SLPAPPSADS GALTPPGTAT
TLTDLTNPTV TVVTTVTSNM DSHEPGSPSQ TTLTNLF
