LOCUS       NM_001014434            2078 bp    mRNA    linear   PRI 18-APR-2013
DEFINITION  Homo sapiens LIM homeobox 9 (LHX9), transcript variant 2, mRNA.
ACCESSION   NM_001014434
VERSION     NM_001014434.1  GI:62241032
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2078)
  AUTHORS   Vladimirova,V., Mikeska,T., Waha,A., Soerensen,N., Xu,J.,
            Reynolds,P.C. and Pietsch,T.
  TITLE     Aberrant methylation and reduced expression of LHX9 in malignant
            gliomas of childhood
  JOURNAL   Neoplasia 11 (7), 700-711 (2009)
   PUBMED   19568415
  REMARK    GeneRIF: LHX9 gene is frequently silenced in pediatric malignant
            astrocytomas
REFERENCE   2  (bases 1 to 2078)
  AUTHORS   Avraham,O., Hadas,Y., Vald,L., Zisman,S., Schejter,A., Visel,A. and
            Klar,A.
  TITLE     Transcriptional control of axonal guidance and sorting in dorsal
            interneurons by the Lim-HD proteins Lhx9 and Lhx1
  JOURNAL   Neural Dev 4, 21 (2009)
   PUBMED   19545367
  REMARK    GeneRIF: Lhx9 and Lhx1 serve as a binary switch in controlling the
            rostral versus caudal longitudinal turning of the caudal
            commissural axons. Lhx1 determines caudal turning and Lhx9 triggers
            rostral turning.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2078)
  AUTHORS   Barrios-Rodiles,M., Brown,K.R., Ozdamar,B., Bose,R., Liu,Z.,
            Donovan,R.S., Shinjo,F., Liu,Y., Dembowy,J., Taylor,I.W., Luga,V.,
            Przulj,N., Robinson,M., Suzuki,H., Hayashizaki,Y., Jurisica,I. and
            Wrana,J.L.
  TITLE     High-throughput mapping of a dynamic signaling network in mammalian
            cells
  JOURNAL   Science 307 (5715), 1621-1625 (2005)
   PUBMED   15761153
REFERENCE   4  (bases 1 to 2078)
  AUTHORS   Ottolenghi,C., Moreira-Filho,C., Mendonca,B.B., Barbieri,M.,
            Fellous,M., Berkovitz,G.D. and McElreavey,K.
  TITLE     Absence of mutations involving the LIM homeobox domain gene LHX9 in
            46,XY gonadal agenesis and dysgenesis
  JOURNAL   J. Clin. Endocrinol. Metab. 86 (6), 2465-2469 (2001)
   PUBMED   11397841
REFERENCE   5  (bases 1 to 2078)
  AUTHORS   Retaux,S., Rogard,M., Bach,I., Failli,V. and Besson,M.J.
  TITLE     Lhx9: a novel LIM-homeodomain gene expressed in the developing
            forebrain
  JOURNAL   J. Neurosci. 19 (2), 783-793 (1999)
   PUBMED   9880598
REFERENCE   6  (bases 1 to 2078)
  AUTHORS   Adams,M.D., Kerlavage,A.R., Fleischmann,R.D., Fuldner,R.A.,
            Bult,C.J., Lee,N.H., Kirkness,E.F., Weinstock,K.G., Gocayne,J.D.,
            White,O. et al.
  TITLE     Initial assessment of human gene diversity and expression patterns
            based upon 83 million nucleotides of cDNA sequence
  JOURNAL   Nature 377 (6547 SUPPL), 3-174 (1995)
   PUBMED   7566098
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AA316988.1, AJ277915.1 and
            AY273889.2.
            
            Summary: This gene encodes a member of the LIM homeobox gene family
            of developmentally expressed transcription factors. The encoded
            protein contains a homeodomain and two cysteine-rich zinc-binding
            LIM domains involved in protein-protein interactions. The protein
            is highly similar to a mouse protein that causes gonadal agenesis
            when inactivated, suggesting a role in gonadal development.
            Alternative splicing results in multiple transcript variants.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) differs in the 5' UTR and
            coding region compared to variant 1, resulting in a protein that
            maintains the reading frame but has a shorter N-terminus.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AJ277915.1 [ECO:0000332]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-27                AA316988.1         1-27
            28-1191             AJ277915.1         1-1164
            1192-2078           AY273889.2         1629-2515
FEATURES             Location/Qualifiers
     source          1..2078
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q31.1"
     gene            1..2078
                     /gene="LHX9"
                     /note="LIM homeobox 9"
                     /db_xref="GeneID:56956"
                     /db_xref="HGNC:14222"
                     /db_xref="MIM:606066"
     exon            1..55
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    4..6
                     /gene="LHX9"
                     /note="upstream in-frame stop codon"
     variation       9
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:375387397"
     variation       14
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:200719762"
     variation       20
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:371771009"
     CDS             28..1194
                     /gene="LHX9"
                     /note="isoform 2 is encoded by transcript variant 2;
                     LIM/homeobox protein Lhx9; LIM homeobox protein 9"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx9 isoform 2"
                     /protein_id="NP_001014434.1"
                     /db_xref="GI:62241033"
                     /db_xref="CCDS:CCDS30962.1"
                     /db_xref="GeneID:56956"
                     /db_xref="HGNC:14222"
                     /db_xref="MIM:606066"
                     /translation="

MLNGTTLEAAMLFHGISGGHIQGIMEEMERRSKTEARLAKGAQLNGRDAGMPPLSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYRRFSVQRCARCHLGISASEMVMRARDSVYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPPQLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRKSPALGVDIVNYNSGCNENEADHLDRDQQPYPPSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGVDKADGTSLPAPPSADSGALTPPGTATTLTDLTNPTITVVTSVTSNMDSHESGSPSQTTLTNLF

"
     misc_feature    181..372
                     /gene="LHX9"
                     /note="The first LIM domain of Lhx2; Region: LIM1_Lhx2;
                     cd09469"
                     /db_xref="CDD:188853"
     misc_feature    order(211..213,220..222,274..276,283..285,292..294,
                     301..303,358..360,367..369)
                     /gene="LHX9"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188853"
     misc_feature    385..561
                     /gene="LHX9"
                     /note="The second LIM domain of Lhx2 and Lhx9 family;
                     Region: LIM2_Lhx2_Lhx9; cd09377"
                     /db_xref="CDD:188763"
     misc_feature    order(397..399,406..408,463..465,472..474,481..483,
                     490..492,547..549,556..558)
                     /gene="LHX9"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188763"
     misc_feature    802..975
                     /gene="LHX9"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:238039"
     misc_feature    order(802..816,820..822,871..873,889..891,928..930,
                     934..939,946..951,955..963,967..972)
                     /gene="LHX9"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(808..810,817..819,937..939,946..951,958..960)
                     /gene="LHX9"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            56..174
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       99
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201760984"
     variation       138
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374479359"
     variation       142
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:113693840"
     variation       150
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201746672"
     variation       152
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:147454219"
     variation       167
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:144348823"
     exon            175..377
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       246
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:139510839"
     variation       307
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:377269488"
     exon            378..733
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       510
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:146659273"
     variation       524
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:74638981"
     variation       526
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:143996891"
     variation       565
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200641597"
     variation       578
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372071986"
     variation       589
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:145525454"
     variation       607
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:149074150"
     variation       627..628
                     /gene="LHX9"
                     /replace=""
                     /replace="g"
                     /db_xref="dbSNP:375826024"
     variation       628
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200168581"
     variation       653
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:374656570"
     variation       656
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:374017815"
     variation       663
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:148334914"
     variation       687
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:368047494"
     variation       698
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:147043102"
     variation       712
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:371329562"
     variation       716
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:183473436"
     variation       717
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:201684330"
     exon            734..936
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       741
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:12046958"
     STS             772..1006
                     /gene="LHX9"
                     /standard_name="Lhx9"
                     /db_xref="UniSTS:525919"
     variation       776
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372121857"
     variation       785
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:192831993"
     variation       807
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:115445561"
     variation       812
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:184403189"
     variation       876
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200789883"
     exon            937..2078
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       992
                     /gene="LHX9"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:139884549"
     variation       1033
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372714030"
     variation       1054
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:376004736"
     variation       1069
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:369709160"
     variation       1125
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:202120884"
     variation       1161
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:74697737"
     variation       1186
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:375493889"
     variation       1200..1201
                     /gene="LHX9"
                     /replace=""
                     /replace="t"
                     /db_xref="dbSNP:111260868"
     variation       1202
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:369694327"
     variation       1229
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:373458786"
     variation       1274
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:189939240"
     variation       1661
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:181449909"
     variation       1812
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199896763"
     variation       1827
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:186139205"
     variation       1846
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:142625651"
     variation       1863
                     /gene="LHX9"
                     /replace=""
                     /replace="t"
                     /db_xref="dbSNP:200169822"
ORIGIN      

gcgtgatccactccttttcctctaagaatgctgaacggtaccactctagaggcagccatgctctttcacgggatctccggaggccacatccaaggcatcatggaggagatggagcgcagatccaagactgaggcccgtctggccaaaggcgcccagctcaacggccgcgacgcgggcatgcccccgctcagcccggagaagcccgccctgtgcgccggctgcgggggcaagatctcggacaggtactatctgctggctgtggacaaacagtggcatctgagatgcctgaagtgctgtgaatgtaagctggccctcgagtccgagctcacctgctttgccaaggacggtagcatttactgcaaggaggattactacagaaggttctctgtgcagagatgtgcccgctgccaccttggcatttccgcctcggagatggtcatgcgcgcccgagactctgtctaccacctgagctgcttcacctgctccacttgcaacaagactctgaccacgggcgaccatttcggcatgaaggacagcctggtgtactgccgcgcccacttcgagaccctcttgcaaggagagtatccaccgcagctgagctacacggagctggcggccaagagcggcggcctggccctgccttacttcaacggtacgggcaccgtgcagaaagggcggccccggaagcggaagagcccagcgctgggagtggacatcgtcaattacaactcaggttgtaatgagaatgaggcagaccacttggaccgggaccagcagccttatccaccctcgcagaagaccaagcgcatgcgaacctctttcaagcatcaccagctccggaccatgaaatcctactttgccatcaaccacaacccggatgccaaggacctcaagcagcttgcccagaaaacaggtctgaccaaaagagttttgcaggtttggttccaaaacgcacgagccaaattcagaaggaaccttttgcggcaggagaatgggggtgttgataaagctgacggcacgtcgcttccggccccgccctcagcagacagcggagctctcactccacccggcactgcgaccactttaacagacctgaccaatcccactatcactgtagtgacatccgtgacctctaacatggacagccacgaatccggaagcccctcacaaactaccttaacaaaccttttctaacattggttttttttttttagtttttaaattcttcctcttctttttattattattctaattattattattttattatttacaagactttttttttcttctaacccacaagatatttggggaataaaaataacagcttggtgtgtagcatctgcagccacttggcaaatgagtttacagtattgtctcctttaagtgaatatattttgtctacaaagtgtatttggatttaaaaaaattaattaggtctttcagttggtaaggagagtttttgaataattctaataagtgcctcttaaaattgtatgttacttatttccagaatctcgaagaaaaaagaaaaaagagtggtattattatgggcaaataatcatattcccacttaaatgattaggttaataaagaaccagataattaattagttactttttaaatcttgcaattgtatgtgtgattatggagttttgaaaacgttacattttttaaatcttaaaactgaaaacttgtttttagtatttctatttcttacctgaactgttaattcaagtgaggaatatgatgaaataaaagcattaactacagacattttaaatagtaatgattaattaggtgagaaatctattacaggaatgtgacttttccttctcttaggggtgtacaactctaaaaactttttacttggttatttgtttttcaacatttgaaaaatacttaagctccctatgtatccatgaaaattccgcattgattttgacattccatacttttaacctcctaaagctaaaaacaatagctcggaaaccattctttctagttactttttttcccagggaaaatggaaataagcaaaatataatgttttaagaagtaaaaaaatcaatataatt

//

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:56956 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IEA
            GeneID:56956 -> Molecular function: GO:0003714 [transcription corepressor activity] evidence: ISS
            GeneID:56956 -> Molecular function: GO:0008270 [zinc ion binding] evidence: IEA
            GeneID:56956 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:56956 -> Biological process: GO:0008045 [motor neuron axon guidance] evidence: ISS
            GeneID:56956 -> Biological process: GO:0008283 [cell proliferation] evidence: IEA
            GeneID:56956 -> Biological process: GO:0008584 [male gonad development] evidence: IEA
            GeneID:56956 -> Biological process: GO:0008585 [female gonad development] evidence: IEA
            GeneID:56956 -> Biological process: GO:0035262 [gonad morphogenesis] evidence: IEA
            GeneID:56956 -> Biological process: GO:0045892 [negative regulation of transcription, DNA-dependent] evidence: ISS
            GeneID:56956 -> Cellular component: GO:0005634 [nucleus] evidence: IEA