GGRNA | NM_001242334.1

LOCUS       NM_001242334            3394 bp    mRNA    linear   PRI 08-JUL-2013
DEFINITION  Homo sapiens LIM homeobox 6 (LHX6), transcript variant 4, mRNA.
ACCESSION   NM_001242334
VERSION     NM_001242334.1  GI:334191690
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 3394)
  AUTHORS   Zhang,Z., Gutierrez,D., Li,X., Bidlack,F., Cao,H., Wang,J.,
            Andrade,K., Margolis,H.C. and Amendt,B.A.
  TITLE     The LIM homeodomain transcription factor LHX6: a transcriptional
            repressor that interacts with pituitary homeobox 2 (PITX2) to
            regulate odontogenesis
  JOURNAL   J. Biol. Chem. 288 (4), 2485-2500 (2013)
   PUBMED   23229549
  REMARK    GeneRIF: LHX6 is a transcriptional repressor that interacts with
            pituitary homeobox 2 (PITX2) to regulate odontogenesis
REFERENCE   2  (bases 1 to 3394)
  AUTHORS   Paschou P, Stylianopoulou E, Karagiannidis I, Rizzo R, Tarnok Z,
            Wolanczyk T, Hebebrand J, Nothen MM, Lehmkuhl G, Farkas L, Nagy P,
            Szymanska U, Lykidis D, Androutsos C, Tsironi V, Koumoula A, Barta
            C, Klidonas S, Ypsilantis P, Simopoulos C, Skavdis G and Grigoriou
            M.
  CONSRTM   TSGeneSEE Consortium
  TITLE     Evaluation of the LIM homeobox genes LHX6 and LHX8 as candidates
            for Tourette syndrome
  JOURNAL   Genes Brain Behav. 11 (4), 444-451 (2012)
   PUBMED   22435649
  REMARK    GeneRIF: found positive association of LHX6 with Tourette syndrome
            in some European populations, not others. LHX6 demonstrates a high
            degree of population differentiation and is correlated with the
            North to South axis of European genetic variation.
REFERENCE   3  (bases 1 to 3394)
  AUTHORS   Jung,S., Jeong,D., Kim,J., Yi,L., Koo,K., Lee,J., Kim,C.J.,
            Kim,C.H., An,S., Yang,Y., Lim,J.S., Kim,K.I. and Lee,M.S.
  TITLE     Epigenetic regulation of the potential tumor suppressor gene,
            hLHX6.1, in human cervical cancer
  JOURNAL   Int. J. Oncol. 38 (3), 859-869 (2011)
   PUBMED   21240459
  REMARK    GeneRIF: hLHX6.1 could be a new tumor suppressor gene in the
            cervix.
REFERENCE   4  (bases 1 to 3394)
  AUTHORS   Jung,S., Jeong,D., Kim,J., Yi,L., Koo,K., Lee,J., Lee,S.D.,
            Park,J.W., Chang,B., Kim,C.H., Kim,C.J. and Lee,M.S.
  TITLE     The role of hLHX6-HMR as a methylation biomarker for early
            diagnosis of cervical cancer
  JOURNAL   Oncol. Rep. 23 (6), 1675-1682 (2010)
   PUBMED   20428825
  REMARK    GeneRIF: Hypermethylation of LHX6 is associated with cervical
            cancer.
REFERENCE   5  (bases 1 to 3394)
  AUTHORS   Joslyn,G., Ravindranathan,A., Brush,G., Schuckit,M. and White,R.L.
  TITLE     Human variation in alcohol response is influenced by variation in
            neuronal signaling genes
  JOURNAL   Alcohol. Clin. Exp. Res. 34 (5), 800-812 (2010)
   PUBMED   20201926
  REMARK    GeneRIF: Observational study and genome-wide association study of
            gene-disease association. (HuGE Navigator)
REFERENCE   6  (bases 1 to 3394)
  AUTHORS   Estecio,M.R., Youssef,E.M., Rahal,P., Fukuyama,E.E.,
            Gois-Filho,J.F., Maniglia,J.V., Goloni-Bertollo,E.M., Issa,J.P. and
            Tajara,E.H.
  TITLE     LHX6 is a sensitive methylation marker in head and neck carcinomas
  JOURNAL   Oncogene 25 (36), 5018-5026 (2006)
   PUBMED   16732332
  REMARK    GeneRIF: differentially methylated hypermethylation of LHX6 is a
            good cancer marker in HNSCC as well as in other kinds of neoplasias
            and confirm the importance of searching for markers of epigenetic
            dysregulation in cancer
REFERENCE   7  (bases 1 to 3394)
  AUTHORS   Humphray,S.J., Oliver,K., Hunt,A.R., Plumb,R.W., Loveland,J.E.,
            Howe,K.L., Andrews,T.D., Searle,S., Hunt,S.E., Scott,C.E.,
            Jones,M.C., Ainscough,R., Almeida,J.P., Ambrose,K.D., Ashwell,R.I.,
            Babbage,A.K., Babbage,S., Bagguley,C.L., Bailey,J., Banerjee,R.,
            Barker,D.J., Barlow,K.F., Bates,K., Beasley,H., Beasley,O.,
            Bird,C.P., Bray-Allen,S., Brown,A.J., Brown,J.Y., Burford,D.,
            Burrill,W., Burton,J., Carder,C., Carter,N.P., Chapman,J.C.,
            Chen,Y., Clarke,G., Clark,S.Y., Clee,C.M., Clegg,S., Collier,R.E.,
            Corby,N., Crosier,M., Cummings,A.T., Davies,J., Dhami,P., Dunn,M.,
            Dutta,I., Dyer,L.W., Earthrowl,M.E., Faulkner,L., Fleming,C.J.,
            Frankish,A., Frankland,J.A., French,L., Fricker,D.G., Garner,P.,
            Garnett,J., Ghori,J., Gilbert,J.G., Glison,C., Grafham,D.V.,
            Gribble,S., Griffiths,C., Griffiths-Jones,S., Grocock,R., Guy,J.,
            Hall,R.E., Hammond,S., Harley,J.L., Harrison,E.S., Hart,E.A.,
            Heath,P.D., Henderson,C.D., Hopkins,B.L., Howard,P.J., Howden,P.J.,
            Huckle,E., Johnson,C., Johnson,D., Joy,A.A., Kay,M., Keenan,S.,
            Kershaw,J.K., Kimberley,A.M., King,A., Knights,A., Laird,G.K.,
            Langford,C., Lawlor,S., Leongamornlert,D.A., Leversha,M., Lloyd,C.,
            Lloyd,D.M., Lovell,J., Martin,S., Mashreghi-Mohammadi,M.,
            Matthews,L., McLaren,S., McLay,K.E., McMurray,A., Milne,S.,
            Nickerson,T., Nisbett,J., Nordsiek,G., Pearce,A.V., Peck,A.I.,
            Porter,K.M., Pandian,R., Pelan,S., Phillimore,B., Povey,S.,
            Ramsey,Y., Rand,V., Scharfe,M., Sehra,H.K., Shownkeen,R.,
            Sims,S.K., Skuce,C.D., Smith,M., Steward,C.A., Swarbreck,D.,
            Sycamore,N., Tester,J., Thorpe,A., Tracey,A., Tromans,A.,
            Thomas,D.W., Wall,M., Wallis,J.M., West,A.P., Whitehead,S.L.,
            Willey,D.L., Williams,S.A., Wilming,L., Wray,P.W., Young,L.,
            Ashurst,J.L., Coulson,A., Blocker,H., Durbin,R., Sulston,J.E.,
            Hubbard,T., Jackson,M.J., Bentley,D.R., Beck,S., Rogers,J. and
            Dunham,I.
  TITLE     DNA sequence and analysis of human chromosome 9
  JOURNAL   Nature 429 (6990), 369-374 (2004)
   PUBMED   15164053
REFERENCE   8  (bases 1 to 3394)
  AUTHORS   Simpson,J.C., Wellenreuther,R., Poustka,A., Pepperkok,R. and
            Wiemann,S.
  TITLE     Systematic subcellular localization of novel proteins identified by
            large-scale cDNA sequencing
  JOURNAL   EMBO Rep. 1 (3), 287-292 (2000)
   PUBMED   11256614
REFERENCE   9  (bases 1 to 3394)
  AUTHORS   Kimura,N., Ueno,M., Nakashima,K. and Taga,T.
  TITLE     A brain region-specific gene product Lhx6.1 interacts with Ldb1
            through tandem LIM-domains
  JOURNAL   J. Biochem. 126 (1), 180-187 (1999)
   PUBMED   10393337
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK289827.1, BC103936.1,
            AK126982.1 and AI265821.1.
            
            Summary: This gene encodes a member of a large protein family that
            contains the LIM domain, a unique cysteine-rich zinc-binding
            domain. The encoded protein may function as a transcriptional
            regulator and may be involved in the control of differentiation and
            development of neural and lymphoid cells. Two alternatively spliced
            transcript variants encoding distinct isoforms have been described
            for this gene. Alternatively spliced transcript variants have been
            identified, but their biological validity has not been determined.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (4) differs in the 5' UTR and
            coding sequence compared to variant 1. The resulting isoform (4) is
            shorter at the N-terminus compared to isoform 1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK289827.1, AB031041.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025081, ERS025085 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1446              AK289827.1         1-1446
            1447-1703           BC103936.1         1252-1508
            1704-3378           AK126982.1         1913-3587
            3379-3394           AI265821.1         1-16                c
FEATURES             Location/Qualifiers
     source          1..3394
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="9"
                     /map="9q33.2"
     gene            1..3394
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="LIM homeobox 6"
                     /db_xref="GeneID:26468"
                     /db_xref="HGNC:21735"
                     /db_xref="MIM:608215"
     exon            1..178
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     CDS             110..1201
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="isoform 4 is encoded by transcript variant 4; LIM
                     homeodomain protein 6.1; LIM/homeobox protein Lhx6.1"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx6 isoform 4"
                     /protein_id="NP_001229263.1"
                     /db_xref="GI:334191691"
                     /db_xref="CCDS:CCDS56583.1"
                     /db_xref="GeneID:26468"
                     /db_xref="HGNC:21735"
                     /db_xref="MIM:608215"
                     /translation="

MAQPGSGCKATTRCLEGTAPPAMAQSDAEALAGALDKDEGQASPCTPSTPSVCSPPSAASSVPSAGKNICSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQQNSCYIKNKEIFCKMDYFSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHYDTMIENLKRAAENGNGLTLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNNPDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKHTPQHPVPPSGAPPSRLPSALSDDIHYTPFSSPERARMVTLHGYIESQVQCGQVHCRLPYTAPPVHLKADMDGPLSNRGEKVILFQY

"
     misc_feature    272..691
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9UPM6.2);
                     Region: Required for interaction with LDB1 (By
                     similarity)"
     misc_feature    317..478
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="The first LIM domain of Lhx6; Region: LIM1_Lhx6;
                     cd09380"
                     /db_xref="CDD:188766"
     misc_feature    order(317..319,326..328,380..382,389..391,398..400,
                     407..409,464..466,473..475)
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188766"
     misc_feature    500..664
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="The second LIM domain of Lhx6; Region: LIM2_Lhx6;
                     cd09382"
                     /db_xref="CDD:188768"
     misc_feature    order(500..502,509..511,566..568,575..577,584..586,
                     593..595,650..652,659..661)
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188768"
     misc_feature    767..940
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /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:28970"
     misc_feature    order(767..781,785..787,836..838,854..856,893..895,
                     899..904,911..916,920..928,932..937)
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(773..775,782..784,902..904,911..916,923..925)
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     exon            179..361
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            362..483
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            484..704
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            705..805
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            806..901
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            902..1076
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            1077..1180
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     exon            1181..3384
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /inference="alignment:Splign:1.39.8"
     variation       1203
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:11540516"
     variation       1249
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:1065351"
     STS             3113..3323
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
                     /standard_name="RH36482"
                     /db_xref="UniSTS:76578"
     polyA_signal    3339..3344
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
     polyA_site      3393
                     /gene="LHX6"
                     /gene_synonym="LHX6.1"
ORIGIN

gttcggcgccggtttatataacaggcgcggggaggcgctgggctcaggctgtgcggagccagttcagcagccgccgccgcctgcgttccctccccccctcccccaggtgatggcccagccagggtccggctgcaaagcgaccacccgctgtcttgaagggaccgcgccgcccgccatggctcagtctgacgccgaggccctggcaggagctctggacaaggacgagggtcaggcctccccatgtacgcccagcacgccatctgtctgctcaccgccctctgccgcctcctccgtgccgtctgcaggcaagaacatctgctccagctgcggcctcgagatcctggaccgatatctgctcaaggtcaacaacctcatctggcacgtgcggtgcctcgagtgctccgtgtgtcgcacgtcgctgaggcagcagaacagctgctacatcaagaacaaggagatcttctgcaagatggactacttcagccgattcgggaccaagtgtgcccggtgcggccgacagatctacgccagcgactgggtgcggagagctcgcggcaacgcctaccacctggcctgcttcgcctgcttctcgtgcaagcgccagctgtccactggtgaggagttcggcctggtcgaggagaaggtgctctgccgcatccactacgacaccatgattgagaacctcaagagggccgccgagaacgggaacggcctcacgttggagggggcagtgccctcggaacaggacagtcaacccaagccggccaagcgcgcgcggacgtccttcaccgcggaacagctgcaggttatgcaggcgcagttcgcgcaggacaacaaccccgacgctcagacgctgcagaagctggcggacatgacgggcctcagccggagagtcatccaggtgtggtttcaaaactgccgggcgcgtcataaaaagcacacgccgcaacacccagtgccgccctcgggggcgcccccgtcccgccttccctccgccctgtccgacgacatccactacaccccgttcagcagccccgagcgggcgcgcatggtcaccctgcacggctacattgagagtcaggtacagtgcgggcaggtgcactgccggctgccttacaccgcaccccccgtccacctcaaagccgatatggatgggccgctctccaaccggggtgagaaggtcatcctttttcagtactaacgctgccggcacttccgcatctgcccgtgggcgccccacagctgcccctcagccgctgagatccagtgtccaagctgcggccaggagtccacccacctccgcatccacccccgtccgccatcctgcccaccaccaggtcggttcccgaggcctggcctttccctctcctgctgagaaccagaacccaccaggagcaccacagagtcctcctcttggaaggcagaactccctgaaatctggaatcagggtggaaacagcctgtttttcccatttaaacaggagtcctcttcaacttcagctgattacaataacaaaaggcggaattgaattgtgcgatgccaacggccttctcatttacaggtttttttcccccacattggcctttatttactacttccttggaaccatctctgaattctgaatagctgacaacccccaatgttatccactctgttgcttttgtctggaaaactctacagtgtttgtgggatgtccccaaaggaaagctatgttctaattttatcatttccatctgtctggttatgtcaagttaattcagaaagagaagagacagtgaccaaccctgagaggcctaatagggcagagatggaggcctgcccagactaggaggcagcggggatagacagggaatggggagaagaaagacccccattggtttggaaatcaaggagagggcggtgacatattggaccagaagaggcactagccattttaaggagaggaaagagaaaactctggggtcagggagagaccctacccccacctaattatccagcatatatgtaagaaacatagcagcgatggtattcgatctgtgccatgactcttctgaatgtttggacaggttagagttggggacccctgttggccacttgttgacctctcatagtggtgcttgggccaggtcttctcaatggaaggggaatcccttataggggagagggaacagagcccagtgaaatggcagtcagaatgttaaccctggatccatctctaagtagagagagggtgcccattgcctaggtgagtgtgccaagctcaggattccaactggtgcctctgagcttcccaatcaatacttcctggagccagccccacccacccctgagaacagaggtcagacacagctgcgtaacatccatcctgctacaactcttccaccccaaacaaaagggctcaggctacacacgaccatgatttatgttttcaggggatgcccatttgtcccaagcttatcctgtaattctagaattacctggtgtcctgatgcattttccactagaggttgctaatcagcatgttttagcccaagtccgccttcctgctgtggttaacctgttatgttgcttttggaaggagactctaagacagggaaagcaagttcatggtacatacgcagccattgtctctgtttttacccatggcagacattgctaatcaatggcagctctatttcactgagtctggataaggtttcagagttcaaatgcttgacgttggcacttaacatgaaagcctataggtcattcttgctctgggatctacaggcagggtaggcacaggtgcagcctaagaagggaacctgcttcctctcccttccaaagacagtgacagctgactgagggcaaagagcaggcaccactcagaacgtggtgagtacagctcagctcagcactcagtcagtggtaacttgtgcccagccctgtgctaggcgctgacattaacaggagcaaccagggcccaattcctggccttggagctcaaatctttcctttgatttttgctcctgatcatcaaggccccagtggcaaccatgtggtaagtggccaaccaagccctacccagggtcacccaacacactctgccttgagcctctcctcagggtctattccttgcgtggattatgtggccgtagcatgttacagttcaaacatgtctccactaccctgttaagagcagcctgggaacgtacaggccatcaagactatttatttaaatacaaaaaaaggggaaaacacacacacggaaaaaaaattgtaagcactttttttgtaaaaccaatgtctgttttgttacatacctttcatgtcgtgctttgtaaatgtcttatttgtgtaataaagttaatgcaagtagaagtgctggcactgaaatccagaacaaaaaaaaaaa

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