LHX9_HUMAN
ID LHX9_HUMAN Reviewed; 397 AA.
AC Q9NQ69; Q5VUE2; Q5VUE3; Q5VUE6; Q86UH2; Q9BYU6; Q9NQ70;
DT 24-JAN-2001, 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 Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 2).
RC TISSUE=Testis;
RX PubMed=11397841; DOI=10.1210/jcem.86.6.7539;
RA Ottolenghi C., Moreira-Filho C., Mendonca B.B., Barbieri M., Fellous M.,
RA Berkovitz G.D., McElreavey K.;
RT "Absence of mutations involving the LIM homeobox domain gene LHX9 in 46,XY
RT gonadal agenesis and dysgenesis.";
RL J. Clin. Endocrinol. Metab. 86:2465-2469(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Shan Y.X., Pan J., Guo Z.K., Geng D.C., Huang C.Q., Yu L.;
RT "Cloning and characterization of human novel LIM-homeobox 9 gene.";
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [6]
RP STRUCTURE BY NMR OF 268-334.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of the homeobox domain of LIM/homeobox protein LHX9.";
RL Submitted (OCT-2006) to the PDB data bank.
CC -!- FUNCTION: Involved in gonadal development. {ECO:0000250}.
CC -!- SUBUNIT: Interacts with LDB1 and LDB2. {ECO:0000250}.
CC -!- INTERACTION:
CC Q9NQ69; P68400: CSNK2A1; NbExp=3; IntAct=EBI-10175218, EBI-347804;
CC Q9NQ69; Q2TBE0: CWF19L2; NbExp=3; IntAct=EBI-10175218, EBI-5453285;
CC Q9NQ69; Q86VF2-5: IGFN1; NbExp=3; IntAct=EBI-10175218, EBI-11955401;
CC Q9NQ69; P50053: KHK; NbExp=3; IntAct=EBI-10175218, EBI-1053974;
CC Q9NQ69; P50053-2: KHK; NbExp=3; IntAct=EBI-10175218, EBI-12204387;
CC Q9NQ69; Q86U70-2: LDB1; NbExp=3; IntAct=EBI-10175218, EBI-11979761;
CC Q9NQ69; P0CB47: UBTFL1; NbExp=3; IntAct=EBI-10175218, EBI-17208936;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00108}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1;
CC IsoId=Q9NQ69-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9NQ69-2; Sequence=VSP_036428;
CC Name=3;
CC IsoId=Q9NQ69-3; Sequence=VSP_036428, VSP_036429;
CC Name=4;
CC IsoId=Q9NQ69-4; Sequence=VSP_036429;
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DR EMBL; AJ277915; CAB97493.1; -; mRNA.
DR EMBL; AJ277916; CAB98128.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AJ277917; CAB98128.1; JOINED; Genomic_DNA.
DR EMBL; AJ277918; CAB98128.1; JOINED; Genomic_DNA.
DR EMBL; AJ277919; CAB98128.1; JOINED; Genomic_DNA.
DR EMBL; AJ277920; CAB98128.1; JOINED; Genomic_DNA.
DR EMBL; AJ296272; CAC33174.1; -; mRNA.
DR EMBL; AY273889; AAP32471.2; -; mRNA.
DR EMBL; AL590115; CAH71760.1; -; Genomic_DNA.
DR EMBL; AL590115; CAH71761.1; -; Genomic_DNA.
DR EMBL; AL590115; CAH71763.1; -; Genomic_DNA.
DR EMBL; AL590115; CAH71764.1; -; Genomic_DNA.
DR EMBL; CH471067; EAW91290.1; -; Genomic_DNA.
DR EMBL; CH471067; EAW91292.1; -; Genomic_DNA.
DR EMBL; BC131622; AAI31623.1; -; mRNA.
DR CCDS; CCDS1393.1; -. [Q9NQ69-1]
DR CCDS; CCDS30962.1; -. [Q9NQ69-2]
DR RefSeq; NP_001014434.1; NM_001014434.1. [Q9NQ69-2]
DR RefSeq; NP_064589.2; NM_020204.2. [Q9NQ69-1]
DR PDB; 2DMQ; NMR; -; A=268-334.
DR PDBsum; 2DMQ; -.
DR AlphaFoldDB; Q9NQ69; -.
DR SMR; Q9NQ69; -.
DR BioGRID; 121280; 13.
DR IntAct; Q9NQ69; 9.
DR STRING; 9606.ENSP00000356357; -.
DR iPTMnet; Q9NQ69; -.
DR PhosphoSitePlus; Q9NQ69; -.
DR BioMuta; LHX9; -.
DR DMDM; 224471883; -.
DR MassIVE; Q9NQ69; -.
DR PaxDb; Q9NQ69; -.
DR PeptideAtlas; Q9NQ69; -.
DR PRIDE; Q9NQ69; -.
DR ProteomicsDB; 82089; -. [Q9NQ69-1]
DR ProteomicsDB; 82090; -. [Q9NQ69-2]
DR ProteomicsDB; 82091; -. [Q9NQ69-3]
DR ProteomicsDB; 82092; -. [Q9NQ69-4]
DR Antibodypedia; 1450; 94 antibodies from 18 providers.
DR DNASU; 56956; -.
DR Ensembl; ENST00000367387.6; ENSP00000356357.4; ENSG00000143355.16. [Q9NQ69-1]
DR Ensembl; ENST00000367390.7; ENSP00000356360.3; ENSG00000143355.16. [Q9NQ69-2]
DR Ensembl; ENST00000367391.5; ENSP00000356361.1; ENSG00000143355.16. [Q9NQ69-3]
DR GeneID; 56956; -.
DR KEGG; hsa:56956; -.
DR MANE-Select; ENST00000367387.6; ENSP00000356357.4; NM_020204.3; NP_064589.2.
DR UCSC; uc001gui.2; human. [Q9NQ69-1]
DR CTD; 56956; -.
DR DisGeNET; 56956; -.
DR GeneCards; LHX9; -.
DR HGNC; HGNC:14222; LHX9.
DR HPA; ENSG00000143355; Tissue enhanced (brain, ovary).
DR MIM; 606066; gene.
DR neXtProt; NX_Q9NQ69; -.
DR OpenTargets; ENSG00000143355; -.
DR PharmGKB; PA30368; -.
DR VEuPathDB; HostDB:ENSG00000143355; -.
DR eggNOG; KOG0490; Eukaryota.
DR GeneTree; ENSGT00940000158821; -.
DR HOGENOM; CLU_027802_4_1_1; -.
DR InParanoid; Q9NQ69; -.
DR OMA; MQINGRE; -.
DR OrthoDB; 1174930at2759; -.
DR PhylomeDB; Q9NQ69; -.
DR TreeFam; TF315442; -.
DR PathwayCommons; Q9NQ69; -.
DR Reactome; R-HSA-9010553; Regulation of expression of SLITs and ROBOs.
DR SignaLink; Q9NQ69; -.
DR BioGRID-ORCS; 56956; 8 hits in 1090 CRISPR screens.
DR EvolutionaryTrace; Q9NQ69; -.
DR GenomeRNAi; 56956; -.
DR Pharos; Q9NQ69; Tbio.
DR PRO; PR:Q9NQ69; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; Q9NQ69; protein.
DR Bgee; ENSG00000143355; Expressed in germinal epithelium of ovary and 54 other tissues.
DR ExpressionAtlas; Q9NQ69; baseline and differential.
DR Genevisible; Q9NQ69; HS.
DR GO; GO:0000785; C:chromatin; ISA:NTNU_SB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; ISA:NTNU_SB.
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; IDA:ARUK-UCL.
DR GO; GO:0008283; P:cell population proliferation; IEA:Ensembl.
DR GO; GO:0097380; P:dorsal spinal cord interneuron anterior axon guidance; ISS:UniProtKB.
DR GO; GO:0008585; P:female gonad development; IEA:Ensembl.
DR GO; GO:0035262; P:gonad morphogenesis; IEA:Ensembl.
DR GO; GO:0008584; P:male gonad development; IEA:Ensembl.
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 3D-structure; Alternative splicing; DNA-binding; Homeobox; LIM domain;
KW Metal-binding; Nucleus; Reference proteome; Repeat; Zinc.
FT CHAIN 1..397
FT /note="LIM/homeobox protein Lhx9"
FT /id="PRO_0000075798"
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..364
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="MEIVGCRAEDNSCPFRPP -> MLNGTTLEA (in isoform 2 and
FT isoform 3)"
FT /evidence="ECO:0000303|PubMed:11397841"
FT /id="VSP_036428"
FT VAR_SEQ 313..397
FT /note="VWFQNARAKFRRNLLRQENGGVDKADGTSLPAPPSADSGALTPPGTATTLTD
FT LTNPTITVVTSVTSNMDSHESGSPSQTTLTNLF -> GEQILGHYSQTSRRLKIP (in
FT isoform 3 and isoform 4)"
FT /evidence="ECO:0000305"
FT /id="VSP_036429"
FT HELIX 276..288
FT /evidence="ECO:0007829|PDB:2DMQ"
FT HELIX 294..303
FT /evidence="ECO:0007829|PDB:2DMQ"
FT HELIX 308..327
FT /evidence="ECO:0007829|PDB:2DMQ"
SQ SEQUENCE 397 AA; 43976 MW; FA8BBB550A5FCE03 CRC64;
MEIVGCRAED NSCPFRPPAM LFHGISGGHI QGIMEEMERR SKTEARLAKG AQLNGRDAGM
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
TLTDLTNPTI TVVTSVTSNM DSHESGSPSQ TTLTNLF
