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2024-03-29 21:07:38, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_020204               2515 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens LIM homeobox 9 (LHX9), transcript variant 1, mRNA.
ACCESSION   NM_020204
VERSION     NM_020204.2  GI:33569215
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 2515)
  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 2515)
  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 2515)
  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 2515)
  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 2515)
  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 2515)
  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 AY273889.2.
            On Aug 11, 2003 this sequence version replaced gi:30725888.
            
            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 (1) encodes the longer isoform
            (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY273889.2, BC131622.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025085, ERS025086 [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2515
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q31.1"
     gene            1..2515
                     /gene="LHX9"
                     /note="LIM homeobox 9"
                     /db_xref="GeneID:56956"
                     /db_xref="HGNC:14222"
                     /db_xref="HPRD:07299"
                     /db_xref="MIM:606066"
     exon            1..611
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       29
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:72744982"
     variation       120
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:112571220"
     variation       142
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:188941900"
     variation       167
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:78792205"
     variation       186
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:79137350"
     variation       226
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:111613412"
     variation       249
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:143233310"
     variation       281
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:193100591"
     variation       390
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:202051786"
     variation       400
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:184278663"
     misc_feature    411..413
                     /gene="LHX9"
                     /note="upstream in-frame stop codon"
     variation       428
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:150716946"
     variation       434
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:201902208"
     CDS             438..1631
                     /gene="LHX9"
                     /note="isoform 1 is encoded by transcript variant 1;
                     LIM/homeobox protein Lhx9; LIM homeobox protein 9"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx9 isoform 1"
                     /protein_id="NP_064589.2"
                     /db_xref="GI:33569216"
                     /db_xref="CCDS:CCDS1393.1"
                     /db_xref="GeneID:56956"
                     /db_xref="HGNC:14222"
                     /db_xref="HPRD:07299"
                     /db_xref="MIM:606066"
                     /translation="
MEIVGCRAEDNSCPFRPPAMLFHGISGGHIQGIMEEMERRSKTEARLAKGAQLNGRDAGMPPLSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYRRFSVQRCARCHLGISASEMVMRARDSVYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPPQLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRKSPALGVDIVNYNSGCNENEADHLDRDQQPYPPSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGVDKADGTSLPAPPSADSGALTPPGTATTLTDLTNPTITVVTSVTSNMDSHESGSPSQTTLTNLF
"
     misc_feature    618..809
                     /gene="LHX9"
                     /note="The first LIM domain of Lhx2; Region: LIM1_Lhx2;
                     cd09469"
                     /db_xref="CDD:188853"
     misc_feature    order(648..650,657..659,711..713,720..722,729..731,
                     738..740,795..797,804..806)
                     /gene="LHX9"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188853"
     misc_feature    822..998
                     /gene="LHX9"
                     /note="The second LIM domain of Lhx2 and Lhx9 family;
                     Region: LIM2_Lhx2_Lhx9; cd09377"
                     /db_xref="CDD:188763"
     misc_feature    order(834..836,843..845,900..902,909..911,918..920,
                     927..929,984..986,993..995)
                     /gene="LHX9"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188763"
     misc_feature    1239..1412
                     /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(1239..1253,1257..1259,1308..1310,1326..1328,
                     1365..1367,1371..1376,1383..1388,1392..1400,1404..1409)
                     /gene="LHX9"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1245..1247,1254..1256,1374..1376,1383..1388,
                     1395..1397)
                     /gene="LHX9"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     variation       439
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201066309"
     variation       485
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:148027167"
     variation       492
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:12091190"
     variation       536
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201760984"
     variation       575
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374479359"
     variation       579
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:113693840"
     variation       587
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201746672"
     variation       589
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:147454219"
     variation       604
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:144348823"
     exon            612..814
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       683
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:139510839"
     variation       744
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:377269488"
     exon            815..1170
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       947
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:146659273"
     variation       961
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:74638981"
     variation       963
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:143996891"
     variation       1002
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200641597"
     variation       1015
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372071986"
     variation       1026
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:145525454"
     variation       1044
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:149074150"
     variation       1064..1065
                     /gene="LHX9"
                     /replace=""
                     /replace="g"
                     /db_xref="dbSNP:375826024"
     variation       1065
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200168581"
     variation       1090
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:374656570"
     variation       1093
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:374017815"
     variation       1100
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:148334914"
     variation       1124
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:368047494"
     variation       1135
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:147043102"
     variation       1149
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:371329562"
     variation       1153
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:183473436"
     variation       1154
                     /gene="LHX9"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:201684330"
     exon            1171..1373
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       1178
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:12046958"
     STS             1209..1443
                     /gene="LHX9"
                     /standard_name="Lhx9"
                     /db_xref="UniSTS:525919"
     variation       1213
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372121857"
     variation       1222
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:192831993"
     variation       1244
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:115445561"
     variation       1249
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:184403189"
     variation       1313
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200789883"
     exon            1374..2515
                     /gene="LHX9"
                     /inference="alignment:Splign:1.39.8"
     variation       1429
                     /gene="LHX9"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:139884549"
     variation       1470
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372714030"
     variation       1491
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:376004736"
     variation       1506
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:369709160"
     variation       1562
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:202120884"
     variation       1598
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:74697737"
     variation       1623
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:375493889"
     variation       1637..1638
                     /gene="LHX9"
                     /replace=""
                     /replace="t"
                     /db_xref="dbSNP:111260868"
     variation       1639
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:369694327"
     variation       1666
                     /gene="LHX9"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:373458786"
     variation       1711
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:189939240"
     variation       2098
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:181449909"
     variation       2249
                     /gene="LHX9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199896763"
     variation       2264
                     /gene="LHX9"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:186139205"
     variation       2283
                     /gene="LHX9"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:142625651"
     variation       2300
                     /gene="LHX9"
                     /replace=""
                     /replace="t"
                     /db_xref="dbSNP:200169822"
ORIGIN      
ctacaggcactgggaacttgcaagcagccagggaacgctgaaaatagcacgtctttttctttctttgtgttcaaaactattttctttcttcaccagattttgttttcctccccccgctgcagttgtttcccattagtaactcgatctctcagagcagtaagattcgccttctacgcctctttttccctccgcccgaattgtttgttttctgcacatctccttcagggagccgctgaggcttccccccaactcttcccagttctttttgcttcccctcggccccccaagcagaccgatttccactccatctgtttcttctcctcctttctctccctctttccctccatcctcgagcgtctctgcgctcctacagggcagccctctctggtcccttgcctccttcactcggatgagctgaaagccccgggcgtgtgtatatggaaatagtggggtgccgagcagaagacaactcgtgtcctttccgccccccagccatgctctttcacgggatctccggaggccacatccaaggcatcatggaggagatggagcgcagatccaagactgaggcccgtctggccaaaggcgcccagctcaacggccgcgacgcgggcatgcccccgctcagcccggagaagcccgccctgtgcgccggctgcgggggcaagatctcggacaggtactatctgctggctgtggacaaacagtggcatctgagatgcctgaagtgctgtgaatgtaagctggccctcgagtccgagctcacctgctttgccaaggacggtagcatttactgcaaggaggattactacagaaggttctctgtgcagagatgtgcccgctgccaccttggcatttccgcctcggagatggtcatgcgcgcccgagactctgtctaccacctgagctgcttcacctgctccacttgcaacaagactctgaccacgggcgaccatttcggcatgaaggacagcctggtgtactgccgcgcccacttcgagaccctcttgcaaggagagtatccaccgcagctgagctacacggagctggcggccaagagcggcggcctggccctgccttacttcaacggtacgggcaccgtgcagaaagggcggccccggaagcggaagagcccagcgctgggagtggacatcgtcaattacaactcaggttgtaatgagaatgaggcagaccacttggaccgggaccagcagccttatccaccctcgcagaagaccaagcgcatgcgaacctctttcaagcatcaccagctccggaccatgaaatcctactttgccatcaaccacaacccggatgccaaggacctcaagcagcttgcccagaaaacaggtctgaccaaaagagttttgcaggtttggttccaaaacgcacgagccaaattcagaaggaaccttttgcggcaggagaatgggggtgttgataaagctgacggcacgtcgcttccggccccgccctcagcagacagcggagctctcactccacccggcactgcgaccactttaacagacctgaccaatcccactatcactgtagtgacatccgtgacctctaacatggacagccacgaatccggaagcccctcacaaactaccttaacaaaccttttctaacattggttttttttttttagtttttaaattcttcctcttctttttattattattctaattattattattttattatttacaagactttttttttcttctaacccacaagatatttggggaataaaaataacagcttggtgtgtagcatctgcagccacttggcaaatgagtttacagtattgtctcctttaagtgaatatattttgtctacaaagtgtatttggatttaaaaaaattaattaggtctttcagttggtaaggagagtttttgaataattctaataagtgcctcttaaaattgtatgttacttatttccagaatctcgaagaaaaaagaaaaaagagtggtattattatgggcaaataatcatattcccacttaaatgattaggttaataaagaaccagataattaattagttactttttaaatcttgcaattgtatgtgtgattatggagttttgaaaacgttacattttttaaatcttaaaactgaaaacttgtttttagtatttctatttcttacctgaactgttaattcaagtgaggaatatgatgaaataaaagcattaactacagacattttaaatagtaatgattaattaggtgagaaatctattacaggaatgtgacttttccttctcttaggggtgtacaactctaaaaactttttacttggttatttgtttttcaacatttgaaaaatacttaagctccctatgtatccatgaaaattccgcattgattttgacattccatacttttaacctcctaaagctaaaaacaatagctcggaaaccattctttctagttactttttttcccagggaaaatggaaataagcaaaatataatgttttaagaagtaaaaaaatcaatataatt
//

Annotations:

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

by @meso_cacase at DBCLS
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