LOCUS       XM_026839732            3581 bp    mRNA    linear   INV 22-OCT-2018
DEFINITION  PREDICTED: Ciona intestinalis LIM/homeobox protein Lhx3a type 1
            (lhx3), transcript variant X2, mRNA.
ACCESSION   XM_026839732
VERSION     XM_026839732.1
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 mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            ##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..3581
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="Unknown"
     gene            1..3581
                     /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: 1 mRNA, 4 ESTs, 11 Proteins, and 96% coverage of the
                     annotated genomic feature by RNAseq alignments, including
                     27 samples with support for all annotated introns"
                     /db_xref="GeneID:778667"
     CDS             1029..2759
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx3a type 1 isoform X2"
                     /protein_id="XP_026695533.1"
                     /db_xref="GeneID:778667"
                     /translation="

MQTGSEFHQNSAGSIRHQPDIAYHQDRKHLSTQQWDDNGYDVGDDFDDDDDDDGIVVDCDDDRDSLMDLDFSTSLLSGHSGDFQDRKHDFPTSSLQELFSMTQSVTSSSCDVTNLVTSSIQSHPDLNDSGIVTTVGESPQNPFLPQTSSKQTDSAGSLFALLSSDQRIQAKIPKCTGCDHHIFDRYILKVQDKPWHSQCLKCNDCGRQLTDKCFSRGSYVYCKEDFFKRFGTKCSGCELAIPPTQVVRRAQDNVYHLECFRCFMCSEQLGTGDQFYLLDDSRLVCKKDYEHAKSRDLDMDNGIKRPRTTITAKQLETLKIAYNQSPKPARHVREQLSSDTGLDMRVVQVWFQNRRAKEKRLKKDTGRQRWGELFRSGAPSSGPHCRPNPDSPPSGGKRRVGGHSNRKRPSSSPGGTRIAIPIPSSIQSPGRAPTNGQIESNFIAPEHNAPPHDGIMMGESPCFAPGEVPYPQQSSNHAYLSPGSIPDMGGFPNLTRNYDYVDGPQILGPGMAPIMKPPTNNAIPNYYVTSPQMHHNQHQKNDCDVISESSGHSNLSDLSSSPRSWLGELDHVTHFQ"

     misc_feature    1542..1709
                     /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(1551..1553,1560..1562,1614..1616,1623..1625,
                     1632..1634,1641..1643,1692..1694,1701..1703)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188850"
     misc_feature    1728..1895
                     /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(1728..1730,1737..1739,1794..1796,1803..1805,
                     1812..1814,1821..1823,1881..1883,1890..1892)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(1764..1766,1839..1841)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Isl binding site; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(1938..1952,1956..1958,2007..2009,2025..2027,
                     2064..2066,2070..2075,2082..2087,2091..2099,2103..2108)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    1944..2105
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(1944..1946,1953..1955,2073..2075,2082..2087,
                     2094..2096)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    <2151..2498
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="EBNA-3B; Provisional; Region: PHA03378"
                     /db_xref="CDD:223065"
ORIGIN      

aaaaaacaaaatttgtgatgatggtagtttatgttcgtgtatgtatatatggtgaaatgtgggtgttgggttatatgggtattaagggtcataaagttttggggtttttgaaacacccatgttatttgtggactgttgttttataagaagcaaaatttcgaataaaattatctccgccccgcttgcgatgtgtatcgtgtacgtgtggataaataatgtaataggggaagtgaatgaatgaaaatgtatgcaaaaatactaaccaaaaactacatgcgaggctggttagtaatgaataatgtaataggcgatttgctcccgagatcttaacgccaattgcccgttttaaagtttgctgacgaattattatttattttgcgtttaaggcggttttatgttacatttcatacttcggaaaaattcggaatttttcggagaaattttgggagttgaattttcggttcgggtgttttcgtaaagtttcgttaaatttcggaagtatttcgaaaatgattttaaatccaatacactgaaggtttttgaaagcaaaccatcgttttcaatttacataatgcaatctcgtcgccgtgccaactgcgtcacaatcgccgccattttgcatccattgttttcgacgcgaacgacaatggcagctttgacgattggaatcgcggccgcgaaaggaaacttagggtgtgtttcgtaacataaggtgttatgatgtaattctattctataagggtgaagtacttatcgaggtttaggggtttagaccattttgcccattacccgatcaagtcgatcaagtcgtgccaaaaatagtagatattttgttacttctgctaccaggcctaacaatgcaatataaactttctataaaaaatgttaatcctattgctcgaatgtcggacgaaacatccgattaaaatgtctacaacacgttatgcctggtagcagaagtaacaacgttatagttacaacattattacgtcacattaatacgtcatactatcgcaggaacgtagacaatgcagaccggaagtgagtttcatcaaaattcagccggaagtatacgtcaccaaccggatattgcgtaccaccaagacagaaagcatttatcgacgcaacaatgggatgacaatggttatgacgtaggcgatgattttgatgatgacgacgacgatgacggcatagtggtcgattgtgatgacgacagagactcgctgatggatttagatttttcaacatccttgctttccggtcacagtggggatttccaggatcgaaaacacgactttcctacgtcatcgctgcaagaactattctctatgacgcaatcggtgacgtcatcaagttgtgacgtcaccaacctcgtgaccagctccatccaatcacatcccgacctcaacgactcggggatcgttaccacagtaggggaatccccgcagaacccctttttaccccaaacctcttcgaaacaaacggacagcgctgggtcgctgttcgcgcttctatcgtccgatcaacgaatacaagccaagataccaaaatgcaccggatgcgaccaccatatattcgaccggtatattctcaaagtacaggacaaaccttggcattcacaatgtttaaaatgcaacgactgtgggcgacaactgaccgataaatgtttttctcgcggtagttacgtttactgcaaggaagatttcttcaagaggttcggcaccaaatgctccggttgcgaactcgccattccccccacacaagtggttaggagggcacaggacaacgtgtaccatctagaatgcttcagatgtttcatgtgtagtgagcaattgggcaccggggaccaattctatttgctggatgatagtcggcttgtgtgtaagaaagattacgaacatgcaaagtcaagagatcttgacatggacaacggtataaagcgaccccgcaccactatcacagctaagcaactggaaacactgaagatcgcttacaatcaaagcccgaaacctgctcgccacgtgagggagcagctgagctcggacaccgggttagacatgagagtagttcaggtatggtttcaaaacagaagggcgaaagaaaaacgtttaaagaaagacacaggccgacaacgttggggagagctattccgatcaggggcgccgtctagtggccctcattgtcgaccaaacccagactccccgcccagcggtggtaagcgtcgtgttggtggccatagcaaccgtaagcggccctctagctctcctggtggcacacgtatagctatcccgataccatcgtcgattcaaagccctggtagggcgcccactaacggacaaattgaatccaactttattgctcccgagcacaatgcgccacctcacgacggtatcatgatgggtgaatccccttgctttgcacctggggaagtcccgtacccgcaacaatcttccaaccatgcttatctatcccctggtagtattcccgacatggggggtttccccaacctgacacgaaactacgattacgtagacggcccccaaatattgggaccaggaatggcgcctatcatgaaaccccccaccaacaacgcgataccgaattattacgtcacaagcccacaaatgcatcacaatcaacaccagaaaaacgattgtgacgtcatatccgaaagtagcggtcactcgaacctgagcgatctatcttcaagtccaaggtcatggctgggtgaacttgaccacgtgacacatttccaataactcgttcccctagaaaagttttcactgtgatttctatgccgcccgtacaattattagggttgggttaattattattgaaggtatccgctattgagaaaatatccagagtttttgaccccaacttcccttctccaaccttcaacccccaatttctgacctgttacccgttacctattacccctaactcctattcctaaccccaattgcaaagtttcgcaattccgatgattgagaccaaatattcgcggtaatttgaccccgaaatatctggcaaagtaactttcttctatgcacgcatgactttattgcaaaacggattttcttaaagcgggtgcgttctatgatatatatctcgctaaattctcgtcgtatttgggacttttacacccccattaaagttacaatgggtatttatacagatatctacaaactattacgcatccatccccgctgttaaccaatcaaatcgctctgttatacgcttcggtgacaacgtatttctgtaagacgcattatacgccaatcaagtcgctttaacccctaactaaccgaagcgaaacatagcggtttgattggttgtaaaagggatggttgtgtagtagtctgtatttgaaaaacccttttagtgaaggtatatatgcccactatatatgacgcgtttatcgtcgccacatacccgtataactacagggggttgtgttatagttcccttcattccatctcgcttcaatccgccgctaaaacgcaccctgtgccaaattaatgcggaactgtgtttcaccatgttgcaatattagttgtgtgagtacgcgaataaatatt

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