LOCUS       NM_001032469            1930 bp    mRNA    linear   INV 04-MAY-2019
DEFINITION  Ciona intestinalis homeobox transcription factor Pax6 (pax6), mRNA.
ACCESSION   NM_001032469
VERSION     NM_001032469.1
KEYWORDS    RefSeq.
SOURCE      Ciona intestinalis (vase tunicate)
  ORGANISM  Ciona intestinalis
            Eukaryota; Metazoa; Chordata; Tunicata; Ascidiacea; Phlebobranchia;
            Cionidae; Ciona.
REFERENCE   1  (bases 1 to 1930)
  AUTHORS   Irvine SQ, Fonseca VC, Zompa MA and Antony R.
  TITLE     Cis-regulatory organization of the Pax6 gene in the ascidian Ciona
            intestinalis
  JOURNAL   Dev. Biol. 317 (2), 649-659 (2008)
   PUBMED   18342846
  REMARK    GeneRIF: Ci-Pax6 intronic elements drive gene expression in the
            eye, brain and nerve cord.
REFERENCE   2  (bases 1 to 1930)
  AUTHORS   Imai KS, Hino K, Yagi K, Satoh N and Satou Y.
  TITLE     Gene expression profiles of transcription factors and signaling
            molecules in the ascidian embryo: towards a comprehensive
            understanding of gene networks
  JOURNAL   Development 131 (16), 4047-4058 (2004)
   PUBMED   15269171
REFERENCE   3  (bases 1 to 1930)
  AUTHORS   Satou Y and Satoh N.
  TITLE     Genomewide surveys of developmentally relevant genes in Ciona
            intestinalis
  JOURNAL   Dev. Genes Evol. 213 (5-6), 211-212 (2003)
   PUBMED   12736827
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AB079883.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB079883.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMD00028081, SAMD00028082
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1930
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="9"
                     /map="9"
     gene            1..1930
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="homeobox transcription factor Pax6"
                     /db_xref="GeneID:445643"
     exon            1..141
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    63..65
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="upstream in-frame stop codon"
     CDS             66..1559
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /codon_start=1
                     /product="homeobox transcription factor Pax6"
                     /protein_id="NP_001027641.1"
                     /db_xref="GeneID:445643"
                     /translation="

MATYDSCRQASSMALCFNRESLPHKGHSGMNQLGGMFVNGRPLPDSIRQKIVEFAHNGARPCDISRILQVSNGCVSKILARYYETGTIRPRAIGGSKPRVATPEVVNKIASYKRECPSIFAWEIRDRLLNEGICNNDNIPSVSSINRVLRNLNGDHQTGGFIETNGRDPKSGSQLGLEWSLTCNGWLPQQTMCQEQIAAEGLMGLKGKESVVESEAKDGSSEARLQLKRKLQRNRTSFTQIQVEALEKEFERTHYPDVFARERLATKIDLPEARIQVWFSNRRAKWRREEKIRSQRSSAASDGSDVMRRTNDQQSIGQCGVYSSVTQQHAQANHQLPAYHMPPEPYTGMNGYQMTSLPQTMKVEHFPPMHRMHEAPYLYGLSSGGPSNLTPPPHYTSYDHDRRVEEPSHNTIPTPPSSANQPSPDHDHHGSHMQPLDGGIYQASLSGMHVGHQHHALVGAQATDQSASSMIVPPMTALQNPANFHTAEGYWQSGVQG"

     misc_feature    141..515
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="Paired Box domain; Region: PAX; smart00351"
                     /db_xref="CDD:128645"
     misc_feature    order(156..161,174..176,180..188,192..194,207..209,
                     243..245,249..251,276..278,285..287,291..296,306..308,
                     333..353,357..368,423..431,486..488,492..497,504..506,
                     513..515)
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238076"
     misc_feature    <657..1022
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(762..773,777..779,828..830,846..848,885..887,
                     891..896,903..908,912..920,924..929)
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(765..767,774..776,894..896,903..908,915..917)
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    768..926
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            142..307
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            308..488
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            489..684
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            685..810
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            811..893
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            894..1059
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            1060..1149
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            1150..1416
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
     exon            1417..1900
                     /gene="pax6"
                     /gene_synonym="Ci-Pax6"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggacttttctgatttaggaaaatttacattttctgtctctggacattttcggcgaaatattttaaatggcgacgtacgattcttgtaggcaagccagcagcatggcgttgtgttttaatagggaaagtcttccacataaaggtcatagcggaatgaatcaattaggcggaatgttcgtcaacggccgaccccttcctgacagtattcgccaaaaaatcgtcgaatttgcacataacggtgcgcgcccttgcgacatctcgcggatcctgcaagtatcgaacggatgtgtcagtaaaattttagcaagatattacgaaactggaacaatccgaccacgggcaatcggggggagcaagcctcgagtcgcaaccccggaagtcgtcaacaaaatcgcttcctacaagcgggagtgtcccagtatatttgcatgggagatcagggatcgtttgttaaacgaaggaatttgcaacaacgataatatcccgagtgtgtcttccataaaccgcgttcttcgaaacttaaacggtgaccaccaaaccggaggtttcattgagacgaatggtcgagatccaaaatcgggttcgcagttggggttagagtggtcattaacttgtaacggttggttgccccagcaaactatgtgccaggaacaaattgcggccgaaggtcttatgggactcaaaggcaaggaatcggttgtggaatcagaagccaaagacggtagtagtgaagcccgtcttcaattgaaacgtaaactccaacgaaaccgaacctctttcacacaaattcaagtcgaagctcttgaaaaagaatttgaaaggactcactacccggatgttttcgcacgggaaaggctggcaacaaaaattgatttacccgaagctcgaatacaggtttggttttcgaaccgtcgcgcaaaatggcgacgtgaagagaaaatacgtagccagcgcagcagcgccgctagtgacggctctgacgtaatgcgtagaacgaacgatcaacaaagtatcggccaatgcggcgtctactctagcgttacacaacagcatgcacaagccaaccaccagctcccagcttaccacatgccacccgaaccttacacgggaatgaacggataccagatgacgtcactccctcaaaccatgaaagtcgagcacttcccacccatgcacagaatgcacgaagctccatacttatacgggttatccagtggtggtccaagcaaccttacacccccaccacactacacatcgtatgatcatgaccgcagagttgaagaaccatcccacaacacaatacccacaccccctagctcagccaaccaaccatcgcccgatcacgaccaccacggctctcatatgcaaccgctagacggcggtatataccaagcatcgttgagtggtatgcacgtaggccatcaacaccatgcactagttggcgcccaagctactgaccaatcagcttcgtccatgatcgttcctccaatgactgccctgcagaatcctgccaacttccatactgccgagggttattggcagtcaggcgtccaaggctaaacaaccgcaaaagtgacgttcgatagttcagtcagtaggccatgtttgagttaacctacatattaaactcgggcacttgtgtgttgtgaatggtcacgcgatgatgtccaaactacctccctagtcaaagttaatttatgaacattgccgtaacgcccgtcgtgtattaatctttatatatataagcgcattgaggcgtttatgacttatttacttttgcttggcttgttctgcaaacaatattatacaatgtgctatataatgataattacgcggaactgtttcttgtactccgtaaatactgatttgtgttgaaataaatgtcccattcatgtttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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