LOCUS       XM_009861895            2225 bp    mRNA    linear   INV 21-JAN-2026
DEFINITION  PREDICTED: Ciona intestinalis homeobox transcription factor Pax1/9
            (pax1/9), transcript variant X2, mRNA.
ACCESSION   XM_009861895
VERSION     XM_009861895.4
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_136103) annotated using gene prediction method: Gnomon.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Jan 21, 2026 this sequence version replaced XM_009861895.3.
            
            ##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..2225
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="11"
                     /geo_loc_name="France:Roscoff"
                     /collection_date="2018-11-26"
     gene            1..2225
                     /gene="pax1/9"
                     /note="homeobox transcription factor Pax1/9; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 27 long SRA reads, 15 Proteins, and 99% coverage of
                     the annotated genomic feature by RNAseq alignments,
                     including 51 samples with support for all annotated
                     introns"
                     /db_xref="GeneID:445592"
     CDS             557..1915
                     /gene="pax1/9"
                     /codon_start=1
                     /product="homeobox transcription factor Pax1/9 isoform X2"
                     /protein_id="XP_009860197.2"
                     /db_xref="GeneID:445592"
                     /translation="

MLSCLPQSFESKLSPDELKKLHEKQKEFLDQTFGEVNQLGGVFVNGRPLPNALRLRIIELAQLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPGVVNAIKDYKVRDPGIFAWEIRDRLLSDAVCDKYNVPSVSSISRILRNKIGNVLHPNNPLNPNYVPISNIENSTPPQSANMRPTYNSPIYNHYMVPPTGKPNMPNAPPSIRGSPMPCHPFYSHSVTEILRGSRFDQPHLQGTAPNNVMTSESISVAQPNGSYHHQLLPVSVPSVIPKLEEWNNMTPYGVPPPTQVTTVHLNGGEKSSPVSRDITSLQQSPTSEENRSSHPLSTLYVTPPANTPYVTSAPQMANNSHHYVTPAYIPTYGHPGWQQQSLPMNGVDPGLTGNPAPQRSVHSLQNGGLQHGYPKLAVSAPQTGDGKNPGNQKLDRPPIHSNGQTSST"

     polyA_site      2225
                     /gene="pax1/9"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      

catcaaaagttatgaattatgacgtcataaaggtaacttcgtgtatatgaatgtgacgtcacaatacaacattgtccaaacatacagatactggttatgacatcataaacgagcacgcgacctgtcccattgttacgttcgtttatattgagcggataatcgcgaatttacgcggtggccgcgaatcggttaaacacacaaaccgttggtgtcttgatcgaatgttgggagcttctggatcgagaatcgtttctaccattgtcctaggatcggtgtcaaatgggttaggaacaatggtcgggctggctcggatatttgataagatttggacaaaacacacgcacttgtatgggaggcgcagacacctcacagcaccgcccataacttgttgggggttgtttaaaccagttgttgagaaaactttaatttttagttgaaacaaattaattaatgagatcaaaataaatattgtcagccgttgtaatggtatggtttcttagattgctatgtaaggttgtatatgttgatatatattgttgaatgttagttgtaaggaatgttgtcgtgtttaccacaaagttttgaatccaaactcagtccagacgaactcaagaaacttcacgaaaaacaaaaagaatttttagatcaaactttcggggaagtgaaccaactcggcggggtatttgtgaacggacgaccgctgcccaacgctctgcgactccgaataatcgagttagctcaactagggattcgaccttgtgatataagtcgacaactacgggtgtcacatggttgtgtgagcaagatacttgcccgttataatgaaacaggatcaatcttaccaggagcaattggtggtagcaaaccaagagttacaacaccgggtgtagtgaacgcgataaaggattacaaagttagggaccctggaatatttgcatgggagatcagggaccgccttctaagcgacgcagtttgcgataaatacaatgtcccttcagtgagttctatcagccgaatattaaggaacaagatcgggaacgtccttcatccaaacaaccctcttaaccccaactacgtccctatcagcaacatcgagaattccacccccccacaaagcgctaacatgaggccaacgtacaacagtccaatatacaatcattatatggtcccaccaacagggaaaccaaacatgccaaacgccccaccatccataagagggtctccaatgccttgccatccgttctattctcattcagtgacagaaatactgagaggttctcgattcgatcaaccacacttacaaggaaccgcacccaacaacgtgatgacgtcagaatcaatttccgtggcgcaacctaacggtagttaccaccaccagttgctaccagtgtcggtaccaagtgtcattcccaaacttgaggaatggaataacatgacaccgtacggtgtaccacccccgacacaagttacaaccgtacacttgaacgggggggagaaatcgtcgcccgtatcacgtgatattacgtcactgcaacaatcacctacgtcagaggagaaccgatcgtcacatccgctttccactctctacgtcacaccacctgccaacaccccatacgtcacttccgctccacaaatggcgaataattcccaccattacgtgacaccggcctacattccaacgtacggccatccaggctggcagcaacaatctttaccgatgaacggagtggatcccggcttaacaggaaacccagcaccccagaggagtgtacacagcttacaaaatggtggcttacaacatggataccccaaactcgctgtctcggctccccaaacaggagacggaaaaaatcccgggaatcaaaaactcgaccgccctccgatccattctaatggtcaaacgtcatcaacgtgatgtcatatagatatattatgacgtcataatacttaatgaatgaggattgtttccattcgcgaattgaatcactgccgccattgctgcctttggtttattatgcatctcagtgaagccactattgtacctactcactaactagtagataaacaactaacaatataccgccatcttttttgtagttttcactttttcatttttctgaaacatttttttgaaactaaattttgattccacacaaatttgaaatttaaacagtttttgcactgaagccataatatttgtaataataaacaaaaaatgttaagaa

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