LOCUS       NM_153654               2597 bp    mRNA    linear   VRT 04-JAN-2026
DEFINITION  Danio rerio pbx/knotted 1 homeobox 2 (pknox2), transcript variant
            1, mRNA.
ACCESSION   NM_153654
VERSION     NM_153654.3
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 2597)
  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 2597)
  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 2597)
  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 2597)
  AUTHORS   Varshney,G.K., Lu,J., Gildea,D.E., Huang,H., Pei,W., Yang,Z.,
            Huang,S.C., Schoenfeld,D., Pho,N.H., Casero,D., Hirase,T.,
            Mosbrook-Davis,D., Zhang,S., Jao,L.E., Zhang,B., Woods,I.G.,
            Zimmerman,S., Schier,A.F., Wolfsberg,T.G., Pellegrini,M.,
            Burgess,S.M. and Lin,S.
  TITLE     A large-scale zebrafish gene knockout resource for the genome-wide
            study of gene function
  JOURNAL   Genome Res 23 (4), 727-735 (2013)
   PUBMED   23382537
REFERENCE   5  (bases 1 to 2597)
  AUTHORS   Wang,D., Jao,L.E., Zheng,N., Dolan,K., Ivey,J., Zonies,S., Wu,X.,
            Wu,K., Yang,H., Meng,Q., Zhu,Z., Zhang,B., Lin,S. and Burgess,S.M.
  TITLE     Efficient genome-wide mutagenesis of zebrafish genes by retroviral
            insertions
  JOURNAL   Proc Natl Acad Sci U S A 104 (30), 12428-12433 (2007)
   PUBMED   17640903
REFERENCE   6  (bases 1 to 2597)
  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     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JBMGRA010000010.1.
            
            On Jul 28, 2025 this sequence version replaced NM_153654.2.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26395028.617731.1, GFIL01030477.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA3505370,
                                           SAMEA3505371 [ECO:0006172]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-24                JBMGRA010000010.1  36213170-36213193   c
            25-96               JBMGRA010000010.1  36168183-36168254   c
            97-205              JBMGRA010000010.1  36096592-36096700   c
            206-342             JBMGRA010000010.1  36058754-36058890   c
            343-514             JBMGRA010000010.1  36032638-36032809   c
            515-700             JBMGRA010000010.1  36026944-36027129   c
            701-836             JBMGRA010000010.1  36023927-36024062   c
            837-934             JBMGRA010000010.1  36023416-36023513   c
            935-1054            JBMGRA010000010.1  36019046-36019165   c
            1055-1131           JBMGRA010000010.1  36015763-36015839   c
            1132-1301           JBMGRA010000010.1  36015421-36015590   c
            1302-2597           JBMGRA010000010.1  36012511-36013806   c
FEATURES             Location/Qualifiers
     source          1..2597
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="10"
                     /map="10"
     gene            1..2597
                     /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"
     misc_feature    107..109
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="upstream in-frame stop codon"
     CDS             119..1543
                     /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    401..658
                     /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(983..997,1001..1003,1061..1063,1079..1081,
                     1118..1120,1124..1129,1136..1141,1145..1153)
                     /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(989..991,998..1000,1127..1129,1136..1141,1148..1150)
                     /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    1037..1153
                     /gene="pknox2"
                     /gene_synonym="ft92g05; id:ibd2866; prep2; wu:ft92g05;
                     zgc:136733"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
ORIGIN      

agtctgatgaagattggcattcagactgtgtggagggcagcgcgccggcggacagactccaacatcagatgcgctgatgctgagaacaagcaaactggtctccatgtgaagctatcccatgatgcaacatgtgtccccagcaccagcattgaccatgatggccacacagagcgtccctccaccatcataccaggagagccaacagatgacaggcactactcagcaaaactcaaagggccagcatgtgcacctctctgcagcgtcagcaggaggagccgctccggtcagcgtgactcttgaccctcaagcccaactggagtctgacaaacgagccgtttacaggcatcctctttttcctcttctggcgttgctgtttgagaagtgtgaacaagccacgcagggctcagaatgcatcacatccgccagcttcgacgtcgacatcgaaaactttgtccaccagcaagagcaggaccacaagcctttcttcagcgaggatcctgaactagacaacctgatggtgaaggccatccaggtgttgcggatccacctgctggagctggagaaggtgaacgagctctgtaaagacttctgcaaccgctacatcacctgcctcaagaccaagatgcacagtgacaatctgctccgaaacgacctgggcggcccgtattctccatcccagaccagcctcggcctgcagcaggacctgcttcaaagctcatccccatcgctcacctccgtctccagcacagtgaactcctccgggatcgtagtcccagccggtcccctgcagcagaacaacatctccatgaccactatcaactctcaggtggtctcaggtgggacgctgtatcagccggtggcaatggttacctcacaggggcaggtgttaacacaggggttaccacagggaaccatccagatccaaaacaatcaggtgaatctggacttgtcctcactcttggatggcgatgacaagaaatcaaaaaacaaaagaggcgtccttcccaaacatgccacaaacattatgcgttcctggctcttccagcatctcatgcacccttatccaacagaagatgagaaaagacagattgcagcgcaaacaaaccttaccttattacaggtgaacaactggtttatcaatgcccgcaggcgtattctgcagcccatgctggatgccagtaatcctgaccctgctcccaaagccaagaagatgaaatctcagcacagacccacacagcgcttctggcccgattccattgtagctggagtcctgcagacacacggcacaaacaactcagacaactctcttggcatggacggcctgcagcctctgtcctcagactcggctacgctggccatgcagcaggccatgctgggcggaaccgacgactccatggacggcacagaggaggaggacgaggaggaggaggaagacgagggactcgatgaggacgacgacgaagaggacgacgaagaacacgaggcgagcagacagatgatcaggcgagatctgggcctcaatcacaatgaaggactcgaataaagaatgaaaaatagcataactgacttaactcttactcatcaccatgcaaaacatctcaacgccgcacaaatggctctcattggacactaagtgccatggagcacccaatcataatgaaggggaggggcctaccattctggactccaaaattgatggaacattgtatattgggccgctttacgcaaccggtcatgctactctcatgcatataatccatttaagccttactttctttaaatatgtctctttggttctcaggtgtcttagcatgacattatgtctaccctcatatttataaccatgcaatgagtggatgttttaggcatgtttttttattattattattattagtttcattttttgtagagttaacaaaatattcagtcttggaagttaaacaaacagaaaaaaagaaacaatctaaatgcctgacagcacaatgtatgtacatttgacagtgatgcattttccccccctcagacgcttcatatttattttgtaatctgtcagaaggctgtggcacaatcaacaaaggatgccgtccgcaaacgcatgtcgggagactcagagtgccaagcatctcttccatagcgaggaacaaaaaactctctccgaaatatgtttggacctacaaatgacgtttactgaagaacactgcaggaaaaacaaaaagacatatttacaggtgcgtatcacaccctgaaacgcccctgctttattttatgtgaaggacgaaactaaacaaaaaaaaaaaaactgtgaagatatttctgagctgtatctacggatctacagaatcacctgtttctgatatgtgatgtttagagaagacagaggatgtttctgaatgttattacagttggtctttgtgaagtacatgtttctcattatccttttcttggttgttgttcttttttttaaatggttcttccagagcaagtgatgataggggagctttttaattatttgtttgtatacattgttgtcataatctattgtgtttcagtagaccattttgataattaaaaacgttgaaactttaaaaacttaaaaa

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