LHX9_DANRE
ID LHX9_DANRE Reviewed; 396 AA.
AC Q1LWV4; Q3LHM3;
DT 03-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=LIM/homeobox protein Lhx9;
DE Short=LIM homeobox protein 9;
GN Name=lhx9;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=16226737; DOI=10.1016/j.ydbio.2005.09.023;
RA Ando H., Kobayashi M., Tsubokawa T., Uyemura K., Furuta T., Okamoto H.;
RT "Lhx2 mediates the activity of Six3 in zebrafish forebrain growth.";
RL Dev. Biol. 287:456-468(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: May be involved in gonadal development. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00108}.
CC -!- DEVELOPMENTAL STAGE: Expression starts 11 hours post-fertilization
CC (hpf) in the presumptive forebrain and becomes restricted to specific
CC clusters of cells in the telencephalon and diencephalon at 24 hpf.
CC Expressed in the neurons of the postoptic commissure at 30 hpf.
CC {ECO:0000269|PubMed:16226737}.
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DR EMBL; AB188254; BAE45355.1; -; mRNA.
DR EMBL; BX004971; CAP09368.1; -; Genomic_DNA.
DR EMBL; BX511183; CAK04966.1; -; Genomic_DNA.
DR EMBL; BC163023; AAI63023.1; -; mRNA.
DR EMBL; BC163060; AAI63060.1; -; mRNA.
DR EMBL; BC163073; AAI63073.1; -; mRNA.
DR RefSeq; NP_001032320.2; NM_001037243.2.
DR RefSeq; XP_017208628.1; XM_017353139.1.
DR AlphaFoldDB; Q1LWV4; -.
DR BMRB; Q1LWV4; -.
DR SMR; Q1LWV4; -.
DR STRING; 7955.ENSDARP00000054806; -.
DR PaxDb; Q1LWV4; -.
DR Ensembl; ENSDART00000054807; ENSDARP00000054806; ENSDARG00000056979.
DR GeneID; 550405; -.
DR KEGG; dre:550405; -.
DR CTD; 56956; -.
DR ZFIN; ZDB-GENE-050417-210; lhx9.
DR eggNOG; KOG0490; Eukaryota.
DR GeneTree; ENSGT00940000158821; -.
DR HOGENOM; CLU_027802_4_1_1; -.
DR InParanoid; Q1LWV4; -.
DR OMA; MQINGRE; -.
DR OrthoDB; 1174930at2759; -.
DR PhylomeDB; Q1LWV4; -.
DR TreeFam; TF315442; -.
DR PRO; PR:Q1LWV4; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 22.
DR Bgee; ENSDARG00000056979; Expressed in brain and 26 other tissues.
DR ExpressionAtlas; Q1LWV4; baseline.
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:0097380; P:dorsal spinal cord interneuron anterior axon guidance; ISS:UniProtKB.
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:0048665; P:neuron fate specification; IMP:ZFIN.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0021794; P:thalamus development; IGI:ZFIN.
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 2: Evidence at transcript level;
KW DNA-binding; Homeobox; LIM domain; Metal-binding; Nucleus;
KW Reference proteome; Repeat; Zinc.
FT CHAIN 1..396
FT /note="LIM/homeobox protein Lhx9"
FT /id="PRO_0000364231"
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 328..365
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 377..396
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 342..365
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 31
FT /note="Q -> E (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
FT CONFLICT 35
FT /note="E -> A (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
FT CONFLICT 85
FT /note="L -> H (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
FT CONFLICT 135
FT /note="R -> H (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
FT CONFLICT 208
FT /note="G -> A (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
FT CONFLICT 222..223
FT /note="VQ -> R (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
FT CONFLICT 341
FT /note="S -> L (in Ref. 1; BAE45355)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 396 AA; 44020 MW; DF20667727633EA0 CRC64;
MEVVGCKAKE SSCTLRPAAM LFHGISGDHI QGIMEEMERR SKSESRLAKT VQMNGRETTM
PSMSPEKPAL CAGCGGKISD RYYLLAVDKQ WHLRCLKCCE CKLALESELT CFAKDGSIYC
KEDYYRRFSV QRCARCHLGI SASEMVMRAR DSVYHLSCFT CTTCNKTLTT GDHFGMKDNL
VYCRVHFETL IQGEYHPQLN YAELAAKGGG LALPYFNGTG TVQKGRPRKR KSPAMGIDIG
SYSSGCNEND ADHLDRDQQP YPPSQKTKRM RTSFKHHQLR TMKSYFAINH NPDAKDLKQL
AQKTGLTKRV LQVWFQNARA KFRRNVLRQE NGGVDKADGT SLPPPSSDSG ALTPPSTATT
LTDLTNPSIT VVTSVTSSLD SHESGSPPQT TLTNLF
