LOCUS       XM_026839731            2708 bp    mRNA    linear   INV 22-OCT-2018
DEFINITION  PREDICTED: Ciona intestinalis LIM/homeobox protein Lhx3a type 1
            (lhx3), transcript variant X1, mRNA.
ACCESSION   XM_026839731
VERSION     XM_026839731.1
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..2708
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="Unknown"
     gene            1..2708
                     /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: 3 mRNAs, 6 ESTs, 12 Proteins, and 95% coverage of the
                     annotated genomic feature by RNAseq alignments, including
                     15 samples with support for all annotated introns"
                     /db_xref="GeneID:778667"
     CDS             94..1884
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx3a type 1 isoform X1"
                     /protein_id="XP_026695532.1"
                     /db_xref="GeneID:778667"
                     /translation="

MQTGSEFHQNSAGSIRHQPDIAYHQDRKHLSTQQWDDNGKKSDVNQDDDFDQYVDDDVGYDVGDDFDDDDDDDGIVVDCDDDRDSLMDLDFSTSLLSGHSGDFQDRKHDFPTSSLQELFSMTQSVTSSSCDVTNLVTSSIQSHPDLNDSGIVTTVGESPQNPFLPQTSSKQTDSAGSLFALLSSDQRIQAKIPKCTGCDHHIFDRYILKVQDKPWHSQCLKCNDCGRQLTDKCFSRGSYVYCKEDFFKRFGTKCSGCELAIPPTQVVRRAQDNVYHLECFRCFMCSEQLGTGDQFYLLDDSRLVCKKDYEHAKSRDLDMDNGIKRPRTTITAKQLETLKIAYNQSPKPARHVREQLSSDTGLDMRVVQVWFQNRRAKEKRLKKDTGRQRWGELFRSGAPSSGPHCRPNPDSPPSGGKRRVGGHSNRKRPSSSPGGTRIAIPIPSSIQSPGRAPTNGQIESNFIAPEHNAPPHDGIMMGESPCFAPGEVPYPQQSSNHAYLSPGSIPDMGGFPNLTRNYDYVDGPQILGPGMAPIMKPPTNNAIPNYYVTSPQMHHNQHQKNDCDVISESSGHSNLSDLSSSPRSWLGELDHVTHFQ"

     misc_feature    667..834
                     /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(676..678,685..687,739..741,748..750,757..759,
                     766..768,817..819,826..828)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188850"
     misc_feature    853..1020
                     /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(853..855,862..864,919..921,928..930,937..939,
                     946..948,1006..1008,1015..1017)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(889..891,964..966)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Isl binding site; other site"
                     /db_xref="CDD:188762"
     misc_feature    order(1063..1077,1081..1083,1132..1134,1150..1152,
                     1189..1191,1195..1200,1207..1212,1216..1224,1228..1233)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    1069..1230
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(1069..1071,1078..1080,1198..1200,1207..1212,
                     1219..1221)
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    <1276..1623
                     /gene="lhx3"
                     /gene_synonym="Ci-Lhx3a; Lhx4"
                     /note="EBNA-3B; Provisional; Region: PHA03378"
                     /db_xref="CDD:223065"
ORIGIN      

taacgctggtttcccccaacgtcatagagtagattcattgtttcgtaataaacgaccacatacgtcacacacgatgttacaggaacgtagacaatgcagaccggaagtgagtttcatcaaaattcagccggaagtatacgtcaccaaccggatattgcgtaccaccaagacagaaagcatttatcgacgcaacaatgggatgacaatggtaaaaaatccgacgtgaatcaagatgacgattttgaccaatacgtggacgatgacgtaggttatgacgtaggcgatgattttgatgatgacgacgacgatgacggcatagtggtcgattgtgatgacgacagagactcgctgatggatttagatttttcaacatccttgctttccggtcacagtggggatttccaggatcgaaaacacgactttcctacgtcatcgctgcaagaactattctctatgacgcaatcggtgacgtcatcaagttgtgacgtcaccaacctcgtgaccagctccatccaatcacatcccgacctcaacgactcggggatcgttaccacagtaggggaatccccgcagaacccctttttaccccaaacctcttcgaaacaaacggacagcgctgggtcgctgttcgcgcttctatcgtccgatcaacgaatacaagccaagataccaaaatgcaccggatgcgaccaccatatattcgaccggtatattctcaaagtacaggacaaaccttggcattcacaatgtttaaaatgcaacgactgtgggcgacaactgaccgataaatgtttttctcgcggtagttacgtttactgcaaggaagatttcttcaagaggttcggcaccaaatgctccggttgcgaactcgccattccccccacacaagtggttaggagggcacaggacaacgtgtaccatctagaatgcttcagatgtttcatgtgtagtgagcaattgggcaccggggaccaattctatttgctggatgatagtcggcttgtgtgtaagaaagattacgaacatgcaaagtcaagagatcttgacatggacaacggtataaagcgaccccgcaccactatcacagctaagcaactggaaacactgaagatcgcttacaatcaaagcccgaaacctgctcgccacgtgagggagcagctgagctcggacaccgggttagacatgagagtagttcaggtatggtttcaaaacagaagggcgaaagaaaaacgtttaaagaaagacacaggccgacaacgttggggagagctattccgatcaggggcgccgtctagtggccctcattgtcgaccaaacccagactccccgcccagcggtggtaagcgtcgtgttggtggccatagcaaccgtaagcggccctctagctctcctggtggcacacgtatagctatcccgataccatcgtcgattcaaagccctggtagggcgcccactaacggacaaattgaatccaactttattgctcccgagcacaatgcgccacctcacgacggtatcatgatgggtgaatccccttgctttgcacctggggaagtcccgtacccgcaacaatcttccaaccatgcttatctatcccctggtagtattcccgacatggggggtttccccaacctgacacgaaactacgattacgtagacggcccccaaatattgggaccaggaatggcgcctatcatgaaaccccccaccaacaacgcgataccgaattattacgtcacaagcccacaaatgcatcacaatcaacaccagaaaaacgattgtgacgtcatatccgaaagtagcggtcactcgaacctgagcgatctatcttcaagtccaaggtcatggctgggtgaacttgaccacgtgacacatttccaataactcgttcccctagaaaagttttcactgtgatttctatgccgcccgtacaattattagggttgggttaattattattgaaggtatccgctattgagaaaatatccagagtttttgaccccaacttcccttctccaaccttcaacccccaatttctgacctgttacccgttacctattacccctaactcctattcctaaccccaattgcaaagtttcgcaattccgatgattgagaccaaatattcgcggtaatttgaccccgaaatatctggcaaagtaactttcttctatgcacgcatgactttattgcaaaacggattttcttaaagcgggtgcgttctatgatatatatctcgctaaattctcgtcgtatttgggacttttacacccccattaaagttacaatgggtatttatacagatatctacaaactattacgcatccatccccgctgttaaccaatcaaatcgctctgttatacgcttcggtgacaacgtatttctgtaagacgcattatacgccaatcaagtcgctttaacccctaactaaccgaagcgaaacatagcggtttgattggttgtaaaagggatggttgtgtagtagtctgtatttgaaaaacccttttagtgaaggtatatatgcccactatatatgacgcgtttatcgtcgccacatacccgtataactacagggggttgtgttatagttcccttcattccatctcgcttcaatccgccgctaaaacgcaccctgtgccaaattaatgcggaactgtgtttcaccatgttgcaatattagttgtgtgagtacgcgaataaatattca

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