LOCUS       NM_153654               2586 bp    mRNA    linear   VRT 16-SEP-2024
DEFINITION  Danio rerio pbx/knotted 1 homeobox 2 (pknox2), mRNA.
ACCESSION   NM_153654
VERSION     NM_153654.2
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
REFERENCE   1  (bases 1 to 2586)
  AUTHORS   Trigila,A.P., Castagna,V.C., Berasain,L., Montini,D.,
            Rubinstein,M., Gomez-Casati,M.E. and Franchini,L.F.
  TITLE     Accelerated Evolution Analysis Uncovers PKNOX2 as a Key
            Transcription Factor in the Mammalian Cochlea
  JOURNAL   Mol Biol Evol 40 (7) (2023)
   PUBMED   37247388
REFERENCE   2  (bases 1 to 2586)
  AUTHORS   Pasquier,J., Cabau,C., Nguyen,T., Jouanno,E., Severac,D.,
            Braasch,I., Journot,L., Pontarotti,P., Klopp,C., Postlethwait,J.H.,
            Guiguen,Y. and Bobe,J.
  TITLE     Gene evolution and gene expression after whole genome duplication
            in fish: the PhyloFish database
  JOURNAL   BMC Genomics 17, 368 (2016)
   PUBMED   27189481
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2586)
  AUTHORS   Elkon,R., Milon,B., Morrison,L., Shah,M., Vijayakumar,S.,
            Racherla,M., Leitch,C.C., Silipino,L., Hadi,S., Weiss-Gayet,M.,
            Barras,E., Schmid,C.D., Ait-Lounis,A., Barnes,A., Song,Y.,
            Eisenman,D.J., Eliyahu,E., Frolenkov,G.I., Strome,S.E., Durand,B.,
            Zaghloul,N.A., Jones,S.M., Reith,W. and Hertzano,R.
  TITLE     RFX transcription factors are essential for hearing in mice
  JOURNAL   Nat Commun 6, 8549 (2015)
   PUBMED   26469318
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2586)
  AUTHORS   Kudoh,T., Tsang,M., Hukriede,N.A., Chen,X., Dedekian,M.,
            Clarke,C.J., Kiang,A., Schultz,S., Epstein,J.A., Toyama,R. and
            Dawid,I.B.
  TITLE     A gene expression screen in zebrafish embryogenesis
  JOURNAL   Genome Res 11 (12), 1979-1987 (2001)
   PUBMED   11731487
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC117639.1.
            
            On Jun 18, 2006 this sequence version replaced NM_153654.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC117639.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA3505370,
                                           SAMEA3505371 [ECO:0006172]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2586
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="10"
                     /map="10"
     gene            1..2586
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="pbx/knotted 1 homeobox 2"
                     /db_xref="GeneID:386959"
                     /db_xref="ZFIN:ZDB-GENE-031118-112"
     exon            1..61
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            62..170
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    72..74
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="upstream in-frame stop codon"
     CDS             84..1508
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /codon_start=1
                     /product="homeobox protein PKNOX2"
                     /protein_id="NP_705940.1"
                     /db_xref="GeneID:386959"
                     /db_xref="ZFIN:ZDB-GENE-031118-112"
                     /translation="

MMQHVSPAPALTMMATQSVPPPSYQESQQMTGTTQQNSKGQHVHLSAASAGGAAPVSVTLDPQAQLESDKRAVYRHPLFPLLALLFEKCEQATQGSECITSASFDVDIENFVHQQEQDHKPFFSEDPELDNLMVKAIQVLRIHLLELEKVNELCKDFCNRYITCLKTKMHSDNLLRNDLGGPYSPSQTSLGLQQDLLQSSSPSLTSVSSTVNSSGIVVPAGPLQQNNISMTTINSQVVSGGTLYQPVAMVTSQGQVLTQGLPQGTIQIQNNQVNLDLSSLLDGDDKKSKNKRGVLPKHATNIMRSWLFQHLMHPYPTEDEKRQIAAQTNLTLLQVNNWFINARRRILQPMLDASNPDPAPKAKKMKSQHRPTQRFWPDSIVAGVLQTHGTNNSDNSLGMDGLQPLSSDSATLAMQQAMLGGTDDSMDGTEEEDEEEEEDEGLDEDDDEEDDEEHEASRQMIRRDLGLNHNEGLE"

     misc_feature    366..623
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="N-terminal of Homeobox Meis and PKNOX1; Region:
                     Meis_PKNOX_N; pfam16493"
                     /db_xref="CDD:465140"
     misc_feature    order(948..962,966..968,1026..1028,1044..1046,1083..1085,
                     1089..1094,1101..1106,1110..1118)
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(954..956,963..965,1092..1094,1101..1106,1113..1115)
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1002..1118
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            171..307
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            308..479
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            480..665
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            666..801
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            802..899
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            900..1019
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            1020..1096
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            1097..1266
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
     exon            1267..2563
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggcagcgcgccggcggacagactccaacatcagatgcgctgatgctgagaacaagcaaactggtctccatgtgaagctatcccatgatgcaacatgtgtccccagcaccagcattgaccatgatggccacacagagcgtccctccaccatcataccaggagagccaacagatgacaggcactactcagcaaaactcaaagggccagcatgtgcacctctctgcagcgtcagcaggaggagccgctccggtcagcgtgactcttgaccctcaagcccaactggagtctgacaaacgagccgtttacaggcatcctctttttcctcttctggcgttgctgtttgagaagtgtgaacaagccacgcagggctcagaatgcatcacatccgccagcttcgacgtcgacatcgaaaactttgtccaccagcaagagcaggaccacaagcctttcttcagcgaggatcctgaactagacaacctgatggtgaaggccatccaggtgttgcggatccacctgctggagctggagaaggtgaacgagctctgtaaagacttctgcaaccgctacatcacctgcctcaagaccaagatgcacagtgacaatctgctccgaaacgacctgggcggcccgtattctccatcccagaccagcctcggcctgcagcaggacctgcttcaaagctcatccccatcgctcacctccgtctccagcacagtgaactcctccgggatcgtagtcccagccggtcccctgcagcagaacaacatctccatgaccactatcaactctcaggtggtctcaggtgggacgctgtatcagccggtggcaatggttacctcacaggggcaggtgttaacacaggggttaccacagggaaccatccagatccaaaacaatcaggtgaatctggacttgtcctcactcttggatggcgatgacaagaaatcaaaaaacaaaagaggcgtccttcccaaacatgccacaaacattatgcgttcctggctcttccagcatctcatgcacccttatccaacagaagatgagaaaagacagattgcagcgcaaacaaaccttaccttattacaggtgaacaactggtttatcaatgcccgcaggcgtattctgcagcccatgctggatgccagtaatcctgaccctgctcccaaagccaagaagatgaaatctcagcacagacccacacagcgcttctggcccgattccattgtagctggagtcctgcagacacacggcacaaacaactcagacaactctcttggcatggacggcctgcagcctctgtcctcagactcggctacgctggccatgcagcaggccatgctgggcggaaccgacgactccatggacggcacagaggaggaggacgaggaggaggaggaagacgagggactcgatgaggacgacgacgaagaggacgacgaagaacacgaggcgagcagacagatgatcaggcgagatctgggcctcaatcacaatgaaggactcgaataaagaatgaaaaatagcataactgacttaactcttactcatcaccatgcaaaacatctcaacgccgcacaaatggctctcattggacactaagtgccatggagcacccaatcataatgaaggggaggggcctaccattctggactccaaaattgatggaacattgtatattgggccgctttacgcaaccggtcatgctactctcatgcatataatccatttaagccttactttctttaaatatgtctctttggttctcaggtgtcttagcatgacattatgtctaccctcatatttataaccatgcaatgagtggatgttttaggcatgtttttttattattattattattagtttcattttttgtagagttaacaaaatattcagtcttggaagttaaacaaacagaaaaaaagaaacaatctaaatgcctgacagcacaatgtatgtacatttgacagtgatgcattttccccccctcagacgcttcatatttattttgtaatctgtcagaaggctgtggcacaatcaacaaaggatgccgtccgcaaacgcatgtcgggagactcagagtgccaagcatctcttccatagcgaggaacaaaaaactctctccgaaatatgtttggacctacaaatgacgtttactgaagaacactgcaggaaaaacaaaaagacatatttacaggtgcgtatcacaccctgaaacgcccctgctttattttatgtgaaggacgaaactaaacaaaaaaaaaaaaaactgtgaagatatttctgagctgtatctacggatctacagaatcacctgtttctgatatgtgatgtttagagaagacagaggatgtttctgaatgttattacagttggtctttgtgaagtacatgtttctcattatccttttcttggttgttgttcttttttttaaatggttcttccagagcaagtgatgataggggagctttttaattatttgtttgtatacattgttgtcataatctattgtgtttcagtagaccattttgataattaaaaacgttgaaactttaaaaacttaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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