LOCUS       XM_078637537            2585 bp    mRNA    linear   INV 21-JAN-2026
DEFINITION  PREDICTED: Ciona intestinalis LIM/homeobox protein Lhx3a type 1
            (lhx3), transcript variant X1, mRNA.
ACCESSION   XM_078637537
VERSION     XM_078637537.1
DBLINK      BioProject: PRJNA1397229
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
            (NC_136105) annotated using gene prediction method: Gnomon.
            Also see:
                Documentation of NCBI's Annotation Process
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Full annotation
            Annotation Name             :: GCF_018327825.1-RS_2026_01
            Annotation Pipeline         :: NCBI Eukaryotic Genome Annotation
                                           Pipeline (EGAP)
            Annotation Software Version :: 10.5
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 01/16/2026
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..2585
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="13"
                     /geo_loc_name="France:Roscoff"
                     /collection_date="2018-11-26"
     gene            1..2585
                     /gene="lhx3"
                     /note="LIM/homeobox protein Lhx3a type 1; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 8 long SRA reads, 24 Proteins, and 84% coverage of the
                     annotated genomic feature by RNAseq alignments, including
                     48 samples with support for all annotated introns"
                     /db_xref="GeneID:778667"
     CDS             29..1822
                     /gene="lhx3"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx3a type 1 isoform X1"
                     /protein_id="XP_078493663.1"
                     /db_xref="GeneID:778667"
                     /translation="

MQTGSEFHQNSAGSLRRQPDIAYHQDRKHLSTQQWEDNNGKKSDENQDDDFDQYVDDDVGYDVGDEFDDDDDDDGIVVDCDDDRDSLMDLDFSTSLLSGHSGDFQDRKHDFPTSSLQELFSMTQSVTSSSCDVTNLVTSSIQSHHDLNDSGIVTTVGESPQPPFLPQTSSKQTDSAGSLFALLSSDQRIQAKIPKCTGCDHHIFDRYILKVQDKPWHSQCLKCNDCGRQLTDKCFSRGSYVYCKEDFFKRFGTKCSGCELAIPPTQVVRRAQDNVYHLECFRCFMCSDQLGTGDQFYLLDDSRLVCKKDYEHAKSRDLDMDNGIKRPRTTITAKQLETLKIAYNQSPKPARHVREQLSSDTGLDMRVVQVWFQNRRAKEKRLKKDTGRQRWGELFRSGAPSSGPHCRPNPDSPPSGGKRRVGGHSNRKRPSSSPGGTRIAIPIPSSIQSPGRAPTNGQIESNFIAPEHNAPPNDGIMMGESPCFAPGEVPYPQQSSNHAYLSPGSIPDIGGFPNLTRNYDYVDGPQLMGLGMPPIMKPPTNNAIPNYYVTNPQMHHNQLPKNDCDVISESSGHSNLSDLSSSPRSWLGELDHVTHFQ"

     polyA_site      2585
                     /gene="lhx3"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      

acgtcataatatcgcaggaacgtagacaatgcagaccggaagtgagtttcaccaaaattcagccggaagtttacgtcgccaaccggatattgcgtaccatcaagacagaaagcatttatcgacgcaacaatgggaagataataatggtaaaaaatccgacgagaatcaagatgacgatttcgaccaatacgtggacgatgacgtaggttatgacgtaggcgatgaatttgatgacgacgacgacgatgacggcatagtggttgattgtgacgacgacagagactcgctgatggatttagatttttcaacttccctactttccggacacagcggggactttcaggatcgaaaacacgactttcctacgtcatcgctgcaagaattattctctatgacgcaatcggtgacatcatcaagttgtgacgtcaccaacctcgtgaccagctccatccaatcgcaccacgacctcaacgactcggggatcgttaccacagtaggggaatcaccgcagcccccttttttaccccaaacctcgtcgaaacaaacggacagtgctgggtcgctgttcgcgcttctatcgtcggatcagcgaatacaagctaagataccgaaatgcactggatgtgaccaccatatatttgatcgttatatactcaaagtacaagataaaccatggcattcacaatgcttgaaatgcaacgattgtgggcgccaactgaccgataaatgtttttctcggggcagctacgtttattgcaaagaagattttttcaagaggttcggcaccaaatgctccggttgtgaactggccattcccccaacgcaagtggtgaggagggcacaggacaacgtgtatcatctagaatgcttcagatgttttatgtgtagcgaccagttaggcaccggtgatcaattctatttacttgatgatagtcggctcgtgtgcaagaaagattatgagcatgcaaagtctagagatcttgacatggacaacggtataaagcgaccccgtaccactatcaccgctaaacaactggaaacactgaagatcgcttacaaccaaagcccgaaacctgcccgccacgtgagggagcagctgagttcggatactgggttggatatgagagtagttcaggtatggtttcaaaacagaagagcgaaagaaaaacgtttaaagaaagacacaggccgacaacggtggggagagctgttccgctcaggggcgccgtctagcggccctcattgtcggccaaaccccgactcccctcccagcggtggtaagcggcgtgttggtggccatagcaaccgtaagcgtccctctagctcccctggtggtacacgtatagctatcccgattccctcgtccattcaaagcccgggtagagcgcccactaacggacaaattgaatccaacttcattgctcccgagcacaatgcgccacccaacgacggtatcatgatgggggaatccccttgctttgcacctggggaagtcccatacccgcaacaatcttccaaccatgcttatctttcccctggtagtattcccgacataggtggtttccctaacctgacacgaaactacgattacgtggatggtccccaattaatgggactaggaatgccgcctattatgaaaccccccaccaacaacgcgatcccgaattattacgtcacaaacccacaaatgcatcacaatcaactgccgaagaacgattgtgacgtcatatccgaaagtagcgggcactcgaacctaagcgatttatcttcaagtccaaggtcatggttgggtgaacttgaccacgtgacacatttccaataactcgttcccctagaaaagttttcactgtgatttctaagccgcccgtacaaattattaggttgggtgtatattatagaacgtatccgctattcagaaaatatcaagagttttttaccccgacccctctcctcttactccgacctcgaacacttaacccctaatttttgacccattgcccattacccctaacccctaacccctaacccctattctttaaccccaaagtttcgcaaattctgatgattgaaacctataatattcgcgttaaattaacttggaaatatcttgcaaagcaactttcttaaacacgcataactttatatagcaaatttctcaaagcggatgcgttttatgatatatatctcactaaattctcgtcgtatttggtacttttacacaccccctaaaagttacaatgggtattttaccaatatctaaaatacagactctattacgcatcagccatccccgtttataaccaatcaaatcgctctgttattcagtgacaacgtatttctataagacgcacatccaagcactattccaatcaagtcgcattaatcaattttgattagttataaaaggggatggctgcgtaacagtctgttttttaaaaacgcccctacagtgaaggtatatacccactatatatggcgtgtttatcatttccacatacctatataactacaaggggttgtgttatagttcccttcactccatctcgcttcaatccgccgctacaacgcaccttgtgccaaaataa

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