LOCUS       NM_001078287            2637 bp    mRNA    linear   INV 04-MAY-2019
DEFINITION  Ciona intestinalis LIM/homeobox protein Lhx3a type 1 (lhx3), mRNA.
ACCESSION   NM_001078287
VERSION     NM_001078287.1
KEYWORDS    RefSeq.
SOURCE      Ciona intestinalis (vase tunicate)
  ORGANISM  Ciona intestinalis
            Eukaryota; Metazoa; Chordata; Tunicata; Ascidiacea; Phlebobranchia;
            Cionidae; Ciona.
REFERENCE   1  (bases 1 to 2637)
  AUTHORS   Kobayashi M, Takatori N, Nakajima Y, Kumano G, Nishida H and Saiga
            H.
  TITLE     Spatial and temporal expression of two transcriptional isoforms of
            Lhx3, a LIM class homeobox gene, during embryogenesis of two
            phylogenetically remote ascidians, Halocynthia roretzi and Ciona
            intestinalis
  JOURNAL   Gene Expr. Patterns 10 (2-3), 98-104 (2010)
   PUBMED   20123132
  REMARK    GeneRIF: maternal expression of Lhx3a, but not Lhx3b, is evident.
            In C. intestinalis, variations in the 5' region have been
            identified among Lhx3a transcripts.
REFERENCE   2  (bases 1 to 2637)
  AUTHORS   Christiaen L, Stolfi A, Davidson B and Levine M.
  TITLE     Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac
            field through synergistic activation of Mesp
  JOURNAL   Dev. Biol. 328 (2), 552-560 (2009)
   PUBMED   19389354
  REMARK    GeneRIF: Misexpression of Lhx3b is sufficient to induce ectopic
            Mesp activation in cells expressing Tbx6b. Injection of antisense
            morpholino oligonucleotides showed that the Lhx3b isoform is
            required for endogenous Mesp expression.
REFERENCE   3  (bases 1 to 2637)
  AUTHORS   Imai KS, Hino K, Yagi K, Satoh N and Satou Y.
  TITLE     Gene expression profiles of transcription factors and signaling
            molecules in the ascidian embryo: towards a comprehensive
            understanding of gene networks
  JOURNAL   Development 131 (16), 4047-4058 (2004)
   PUBMED   15269171
REFERENCE   4  (bases 1 to 2637)
  AUTHORS   Satou Y and Satoh N.
  TITLE     Genomewide surveys of developmentally relevant genes in Ciona
            intestinalis
  JOURNAL   Dev. Genes Evol. 213 (5-6), 211-212 (2003)
   PUBMED   12736827
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AB210532.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB210532.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMD00028078, SAMD00028079
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2637
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
     gene            1..2637
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="LIM/homeobox protein Lhx3a type 1"
                     /db_xref="GeneID:778667"
     exon            1..573
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /inference="alignment:Splign:2.1.0"
     CDS             6..1796
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx3a type 1"
                     /protein_id="NP_001071755.1"
                     /db_xref="GeneID:778667"
                     /translation="

MQTGSEFHQNSAGSIRHQPDIAYHQDRKHLSTQQWDDNGKKSDVNQDDDFDQYVDDDVGYDVGDDFDDDDDDDGIVVDCDDDRDSLMDLDFSTSLLSGHSGDFQDRKHDFPTSSLQELFSMTQSVTSSSCDVTNLVTSSIQSHPDLNDSGIVTTVGESPQNPFLPQTSSKQTDSAGSLFALLSSDQRIQAKIPKCTGCDHHIFDRYILKVQDKPWHSQCLKCNDCGRQLTDKCFSRGSYVYCKEDFFKRFGTKCSGCELAIPPTQVVRRAQDNVYHLECFRCFMCSEQLGTGDQFYLLDDSRLVCKKDYEHAKSRDLDMDNGIKRPRTTITAKQLETLKIAYNQSPKPARHVREQLSSDTGLDMRVVQVWFQNRRAKEKRLKKDTGRQRWGELFRSGAPSSGPHCRPNPDSPPSGGKRRVGGHSNRKRPSSSPGGTRIAIPIPSSIQSPGRAPTNGQIESNFIASEHNAPPHDGIMMGESPCFAPGEVPYPQQSSNHAYLSPGSIPDMGGFPNLTRNYDYVDGPQILGPGMAPIMKPPTNNAIPNYYVTSPQMHHNQHQKNDCDVISESSGHSNLSDLSSSPRSWLGELDHVTHFQ"

     misc_feature    579..746
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="The first LIM domain of Lhx3a; Region: LIM1_Lhx3a;
                     cd09466"
                     /db_xref="CDD:188850"
     misc_feature    order(588..590,597..599,651..653,660..662,669..671,
                     678..680,729..731,738..740)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188850"
     misc_feature    765..932
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="The second LIM domain of Lhx3-Lhx4 family; Region:
                     LIM2_Lhx3_Lhx4; cd09376"
                     /db_xref="CDD:188762"
     misc_feature    order(765..767,774..776,831..833,840..842,849..851,
                     858..860,918..920,927..929)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(801..803,876..878)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Isl binding site; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(975..989,993..995,1044..1046,1062..1064,1101..1103,
                     1107..1112,1119..1124,1128..1136,1140..1145)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    981..1142
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(981..983,990..992,1110..1112,1119..1124,1131..1133)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            574..748
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            749..951
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            952..1109
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            1110..1380
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            1381..2620
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agacaatgcagaccggaagtgagtttcatcaaaattcagccggaagtatacgtcaccaaccggatattgcgtaccaccaagacagaaagcatttatcgacgcaacaatgggatgacaatggtaaaaaatccgacgtgaatcaagatgacgattttgaccaatacgtggacgatgacgtaggttatgacgtaggcgatgattttgatgatgacgacgacgatgacggcatagtggtcgattgtgatgacgacagagactcgctgatggatttagatttttcaacatccttgctttccggtcacagtggggatttccaggatcgaaaacacgactttcctacgtcatcgctgcaagaactattctctatgacgcaatcggtgacgtcatcaagttgtgacgtcaccaacctcgtgaccagctccatccaatcacatcccgacctcaacgactcggggatcgttaccacagtaggggaatccccgcagaacccctttttaccccaaacctcttcgaaacaaacggacagcgctgggtcgctgttcgcgcttctatcgtccgatcaacgaatacaagccaagataccaaaatgcaccggatgcgatcaccatatattcgaccggtatattctcaaagtacaggacaaaccttggcattcacaatgtttaaaatgcaacgactgtgggcgacaactgaccgataaatgtttttctcgcggtagttacgtttactgcaaagaagatttcttcaagaggttcggcaccaaatgctccggttgcgaactcgccattccccccacacaagtggttaggagggcacaggacaacgtgtaccatctagaatgcttcagatgtttcatgtgtagtgagcaattgggcaccggggaccaattctatttgctggatgatagtcggcttgtgtgtaagaaagattacgaacatgcaaagtcaagagatcttgacatggacaacggtataaagcgaccccgcaccactattacagctaagcaactggaaacactgaagatcgcttacaatcaaagcccgaaacctgctcgccacgtgagggagcagctgagctcggacaccgggttagacatgagagtagttcaggtatggtttcaaaacagaagggcgaaagaaaaacgtttaaagaaagacacaggccgacaacgttggggagagctattccgatcaggggcgccgtctagtggccctcattgtcgaccaaacccagactccccgcccagcggtggtaagcgtcgtgttggtggccatagcaaccgtaagcggccctctagctctcctggtggcacacgtatagctatcccgataccatcgtcgattcaaagccctggtagggcgcccactaacggacaaattgaatccaactttattgcttccgagcacaatgcgccacctcacgacggtatcatgatgggtgaatccccttgctttgcacctggggaagtcccgtacccgcaacaatcttccaaccatgcttatctatcccctggtagtattcccgacatggggggtttccccaacctgacacgaaactacgattacgtagacggcccccaaatattgggaccaggaatggcgcctatcatgaaaccccccaccaacaacgcgataccgaattattacgtcacaagcccacaaatgcatcacaatcaacaccagaaaaacgattgtgacgtcatatccgaaagtagcggtcactcgaacctgagcgatctatcttcaagtccaaggtcatggctgggtgaacttgaccacgtgacacatttccaataactcgttcccctagaaaagttttcactgtgatttctatgccgcccgtacaattattagggttgggttaattattattgaaggtatccgctattgagaaaatatccagagtttttgaccccaacttcccttctccaaccttcaacccccaatttctgacctgttacccgttacctattacccctaactcctattcctaaccccaattgcaaagtttcgcaattccgatgattgagaccaaatattcgcggtaatttgaccccgaaatatctggcaaagtaactttcttctatgcacgcatgactttattgcaaaacggattttcttaaagcgggtgcgttctatgatatatatctcgctaaattctcgtcgtatttgggacttttacacccccattaaagttacaatgggtatttatacagatatctacaaactattacgcatccatccccgctgttaaccaatcaaatcgctctgttatacgcttcggtgacaacgtatttctgtaagacgcattatacgccaatcaagtcgctttaacccctaactaaccgaagcgaaacatagcggtttgattggttgtaaaagggatggttgtgtagtagtctgtatttgaaaaacccttttagtgaaggtatatatgcccactatatatgacgcgtttatcgtcgccacatacccgtataactacagggggttgtgttatagttcccttcattccatctcgcttcaatccgccgctaaaacgcaccctgtgccaaattaatgcggaactgtgtttcaccatgttgcaatattagttgtgtgagtacgcgaataaatattcaaaaaaaaaaaaaaaaaa

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