LOCUS       XM_009861448            2366 bp    mRNA    linear   INV 22-OCT-2018
DEFINITION  PREDICTED: Ciona intestinalis LIM/homeobox protein Lhx3a type 1
            (lhx3), transcript variant X3, mRNA.
ACCESSION   XM_009861448
VERSION     XM_009861448.2
DBLINK      BioProject: PRJNA187185
KEYWORDS    RefSeq.
SOURCE      Ciona intestinalis (vase tunicate)
  ORGANISM  Ciona intestinalis
            Eukaryota; Metazoa; Chordata; Tunicata; Ascidiacea; Phlebobranchia;
            Cionidae; Ciona.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NW_004191144.1) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Oct 22, 2018 this sequence version replaced XM_009861448.1.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI
            Annotation Status           :: Full annotation
            Annotation Name             :: Ciona intestinalis Annotation
                                           Release 104
            Annotation Version          :: 104
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 8.1
            Annotation Method           :: Best-placed RefSeq; Gnomon
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..2366
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="Unknown"
     gene            1..2366
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="LIM/homeobox protein Lhx3a type 1; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 7 ESTs, 12 Proteins, and 95% coverage of the annotated
                     genomic feature by RNAseq alignments, including 44 samples
                     with support for all annotated introns"
                     /db_xref="GeneID:778667"
     CDS             63..1544
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx3a type 1 isoform X3"
                     /protein_id="XP_009859750.1"
                     /db_xref="GeneID:778667"
                     /translation="

MILDTKALDELTNLPSPGNGMTSRIMTSRFHPYAKVSKTSGMKSPTCGDSGAVVPPILASRPEVVGWQMEVETHVTEDYSDVLLVLSKIPKCTGCDHHIFDRYILKVQDKPWHSQCLKCNDCGRQLTDKCFSRGSYVYCKEDFFKRFGTKCSGCELAIPPTQVVRRAQDNVYHLECFRCFMCSEQLGTGDQFYLLDDSRLVCKKDYEHAKSRDLDMDNGIKRPRTTITAKQLETLKIAYNQSPKPARHVREQLSSDTGLDMRVVQVWFQNRRAKEKRLKKDTGRQRWGELFRSGAPSSGPHCRPNPDSPPSGGKRRVGGHSNRKRPSSSPGGTRIAIPIPSSIQSPGRAPTNGQIESNFIAPEHNAPPHDGIMMGESPCFAPGEVPYPQQSSNHAYLSPGSIPDMGGFPNLTRNYDYVDGPQILGPGMAPIMKPPTNNAIPNYYVTSPQMHHNQHQKNDCDVISESSGHSNLSDLSSSPRSWLGELDHVTHFQ"

     misc_feature    327..494
                     /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(336..338,345..347,399..401,408..410,417..419,
                     426..428,477..479,486..488)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188850"
     misc_feature    513..680
                     /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(513..515,522..524,579..581,588..590,597..599,
                     606..608,666..668,675..677)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(549..551,624..626)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Isl binding site; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(723..737,741..743,792..794,810..812,849..851,
                     855..860,867..872,876..884,888..893)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    729..890
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(729..731,738..740,858..860,867..872,879..881)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    <936..1283
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="EBNA-3B; Provisional; Region: PHA03378"
                     /db_xref="CDD:223065"
ORIGIN      

gcgattgtattccattgttaagaacaatcgatcaatttgttacagttaattctacaattaaaatgattctcgatactaaagcgctcgatgaacttacgaacctgccgtcgccaggtaacggtatgacgtcaagaatcatgacgtcgcgatttcacccgtacgcgaaagtttcgaaaacatcgggtatgaaatctcccacctgcggggattcgggggccgttgtcccgccgatattggcttcgcgacctgaggtcgtcggttggcaaatggaagtcgaaacgcacgtcacagaagattatagtgacgttttgttagttctttccaagataccaaaatgcaccggatgcgaccaccatatattcgaccggtatattctcaaagtacaggacaaaccttggcattcacaatgtttaaaatgcaacgactgtgggcgacaactgaccgataaatgtttttctcgcggtagttacgtttactgcaaggaagatttcttcaagaggttcggcaccaaatgctccggttgcgaactcgccattccccccacacaagtggttaggagggcacaggacaacgtgtaccatctagaatgcttcagatgtttcatgtgtagtgagcaattgggcaccggggaccaattctatttgctggatgatagtcggcttgtgtgtaagaaagattacgaacatgcaaagtcaagagatcttgacatggacaacggtataaagcgaccccgcaccactatcacagctaagcaactggaaacactgaagatcgcttacaatcaaagcccgaaacctgctcgccacgtgagggagcagctgagctcggacaccgggttagacatgagagtagttcaggtatggtttcaaaacagaagggcgaaagaaaaacgtttaaagaaagacacaggccgacaacgttggggagagctattccgatcaggggcgccgtctagtggccctcattgtcgaccaaacccagactccccgcccagcggtggtaagcgtcgtgttggtggccatagcaaccgtaagcggccctctagctctcctggtggcacacgtatagctatcccgataccatcgtcgattcaaagccctggtagggcgcccactaacggacaaattgaatccaactttattgctcccgagcacaatgcgccacctcacgacggtatcatgatgggtgaatccccttgctttgcacctggggaagtcccgtacccgcaacaatcttccaaccatgcttatctatcccctggtagtattcccgacatggggggtttccccaacctgacacgaaactacgattacgtagacggcccccaaatattgggaccaggaatggcgcctatcatgaaaccccccaccaacaacgcgataccgaattattacgtcacaagcccacaaatgcatcacaatcaacaccagaaaaacgattgtgacgtcatatccgaaagtagcggtcactcgaacctgagcgatctatcttcaagtccaaggtcatggctgggtgaacttgaccacgtgacacatttccaataactcgttcccctagaaaagttttcactgtgatttctatgccgcccgtacaattattagggttgggttaattattattgaaggtatccgctattgagaaaatatccagagtttttgaccccaacttcccttctccaaccttcaacccccaatttctgacctgttacccgttacctattacccctaactcctattcctaaccccaattgcaaagtttcgcaattccgatgattgagaccaaatattcgcggtaatttgaccccgaaatatctggcaaagtaactttcttctatgcacgcatgactttattgcaaaacggattttcttaaagcgggtgcgttctatgatatatatctcgctaaattctcgtcgtatttgggacttttacacccccattaaagttacaatgggtatttatacagatatctacaaactattacgcatccatccccgctgttaaccaatcaaatcgctctgttatacgcttcggtgacaacgtatttctgtaagacgcattatacgccaatcaagtcgctttaacccctaactaaccgaagcgaaacatagcggtttgattggttgtaaaagggatggttgtgtagtagtctgtatttgaaaaacccttttagtgaaggtatatatgcccactatatatgacgcgtttatcgtcgccacatacccgtataactacagggggttgtgttatagttcccttcattccatctcgcttcaatccgccgctaaaacgcaccctgtgccaaattaatgcggaactgtgtttcaccatgttgcaatattagttgtgtgagtacgcgaataaatatt

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