LOCUS       NM_001398297            3834 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus PBX/knotted 1 homeobox 2 (PKNOX2), transcript variant
            3, mRNA.
ACCESSION   NM_001398297 XM_015297936
VERSION     NM_001398297.1
KEYWORDS    RefSeq.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1  (bases 1 to 3834)
  AUTHORS   Tang H, Finn RD and Thomas PD.
  TITLE     TreeGrafter: phylogenetic tree-based annotation of proteins with
            Gene Ontology terms and other annotations
  JOURNAL   Bioinformatics 35 (3), 518-520 (2019)
   PUBMED   30032202
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000341.1.
            
            On Dec 13, 2021 this sequence version replaced XM_015297936.3.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13267652.25293.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA103992290,
                                           SAMEA103992323 [ECO:0006172]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-87                JAENSK010000341.1  257264-257350       c
            88-209              JAENSK010000341.1  255219-255340       c
            210-360             JAENSK010000341.1  219896-220046       c
            361-438             JAENSK010000341.1  219496-219573       c
            439-507             JAENSK010000341.1  216926-216994       c
            508-1042            JAENSK010000341.1  215398-215932       c
            1043-1151           JAENSK010000341.1  213248-213356       c
            1152-1288           JAENSK010000341.1  208735-208871       c
            1289-1460           JAENSK010000341.1  204704-204875       c
            1461-1649           JAENSK010000341.1  202108-202296       c
            1650-1782           JAENSK010000341.1  197642-197774       c
            1783-1880           JAENSK010000341.1  197471-197568       c
            1881-2000           JAENSK010000341.1  195544-195663       c
            2001-2077           JAENSK010000341.1  194277-194353       c
            2078-2256           JAENSK010000341.1  193578-193756       c
            2257-3834           JAENSK010000341.1  191209-192786       c
FEATURES             Location/Qualifiers
     source          1..3834
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="24"
                     /map="24"
     gene            1..3834
                     /gene="PKNOX2"
                     /note="PBX/knotted 1 homeobox 2"
                     /db_xref="CGNC:49030"
                     /db_xref="GeneID:374067"
     exon            1..87
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            88..209
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            210..360
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            361..438
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            439..507
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            508..1042
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1043..1151
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    1053..1055
                     /gene="PKNOX2"
                     /note="upstream in-frame stop codon"
     CDS             1068..2501
                     /gene="PKNOX2"
                     /codon_start=1
                     /product="homeobox protein PKNOX2"
                     /protein_id="NP_001385226.1"
                     /db_xref="CGNC:49030"
                     /db_xref="GeneID:374067"
                     /translation="

MHHVSPAPALTMMATQTVPPPPYQDSPQMTATAQQPSKAQPVHLSAAPAPTAAVPPAAGDPQAQLEADKRAVYRHPLFPLLTLLFEKCEQATQGSECITSASFDVDIENFVHQQEQEHKPFFSDDPELDNLMVKAIQVLRIHLLELEKVNELCKDFCNRYITCLKTKMHSDNLLRNDLGGPYSPNPSSISLHPQEMLQSSPAALPAASNPPPGIVVPAAALPPGNLAMGSGAGSPAVPGGALYQPVTMVTSQGQVLTQAIAPGALQIPNAQVNLDLTSLLDGEDKKSKNKRGVLPKHATNIMRSWLFQHLMHPYPTEDEKRQIAAQTNLTLLQVNNWFINARRRILQPMLDASNPDPAPKAKKIKSQHRPTQRFWPNSIAAGVLQQQGGNSGTNPDGSLAMDNLQPLSSATATMAMQQAMLAAHEDSLDGTEEDDDEEDEDEMEEEEEEEEELEEEPGGLPAAPGANLGLDHSDSLE"

     misc_feature    1347..1604
                     /gene="PKNOX2"
                     /note="N-terminal of Homeobox Meis and PKNOX1; Region:
                     Meis_PKNOX_N; pfam16493"
                     /db_xref="CDD:465140"
     misc_feature    order(1929..1943,1947..1949,2007..2009,2025..2027,
                     2064..2066,2070..2075,2082..2087,2091..2099)
                     /gene="PKNOX2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1935..1937,1944..1946,2073..2075,2082..2087,
                     2094..2096)
                     /gene="PKNOX2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1983..2099
                     /gene="PKNOX2"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            1152..1288
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1289..1460
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1461..1649
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1650..1782
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1783..1880
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1881..2000
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            2001..2077
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            2078..2256
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            2257..3834
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gggcggggctctgcgcggcggggccgggcgggcggcagcggcggcgcgctgtcaggccggtgccggtgtgatgaagattggcggcagggaaccttctgatggctgagcagtccctgccgcgccgcccgcctgcacctcccgtcccaacccccggagacctgcaggaattcggcgtccgacccccagccgtggccgatgcgcaggtgtagacccaaactgtaccaataaccactgtgagagcctgtgctggggagctgtcatcgttgaggagcagaagggagcaggacgagatacagctgtggatttccctttgtggatatactggcaacgagcgcatcttcatattgcagacatatctcggctgtgacccatactcagaagttttgcttttgtggctgtgaacgtttcgtgcagcggctcctcgagcacccgcagacgagacatccctggagcattgtagtcggcagcggggatgggcatcttcggagagaagagaaatatttagcgcgtgcaggagccctctgtggagacagcagtgctgagctctggcagcccgctgtgagcagagcgagaccagcgccgtcctcgtgtgaggaaacaccctttggaaggctgaaatcccctcctgtggcagatccacactcccaaccgcctcaaataatcgtgcgacgtcaggaggaaaatgggaaatgcatgaaaacctgtctgcatggcttccacgtggaatcctgggttatccaccacgcgctgcgaggagaagctgttgaattagctgggaaaaatgatccccattttccactggtttggaagcagcagctgcagcttgcaaagccaacattaatgtcatctgcacaaaatggtgacgtggagtccaacgcggtgattttttggcatgcagggttacttccaatgcagtttcacagcagttttgctaatcgtgcaggtcagagattatttcccctttgcctccaggatggcggtgactgctgctgacacttggatttttgtaacgttttgaagcatcggtgaccaccctgaaaaggttctcaatgtgactcctgcccaggatgcaccatgtctccccggcgccggctctgacgatgatggccacccagacggtgccccctcctccctaccaagacagcccacagatgacggctacagcccagcagcccagcaaggctcagcccgtgcacctctccgccgcgccggctcccactgcagccgtaccccccgcagccggcgacccgcaggcgcagctggaggccgacaagcgagccgtctacaggcacccactgttcccgctgcttacgctgctctttgagaagtgtgagcaggcaacccaaggctctgagtgcatcacctcagccagcttcgacgtcgacattgaaaactttgtccaccagcaggagcaggagcacaaacctttcttcagtgatgaccctgagctggacaacctgatggtgaaggcaatccaggtgctgcgcatccacctcctggagctggagaaggtcaacgaattgtgcaaggacttttgcaaccgctacatcacctgcctcaaaaccaagatgcacagtgacaacctactcaggaacgacctggggggcccctactcccccaacccctcctccatcagcctccaccctcaggagatgctgcagagctcacccgcggcactaccagccgcctccaaccccccaccgggcatcgtggtgcctgcagccgcactgcccccaggcaacctggccatgggcagcggggctggatcgcccgccgtgccaggtggagccctgtaccagcccgtgacgatggtgacatctcagggccaggtcctcacccaagccatcgcccctggtgccctgcagatccccaacgcccaggttaacctggatctcacctcactccttgacggcgaggacaagaagtccaagaacaagcggggcgttctgcccaaacacgccaccaacatcatgcgctcctggctcttccagcacctcatgcacccctatcccacagaggatgagaagaggcaaatcgctgcccaaaccaacctgaccctcttacaagtcaataactggttcatcaacgcccgccggcgcatcctgcaaccgatgctcgatgccagcaacccagacccagcccctaaagccaagaaaatcaaatctcagcaccggcccacccagcggttctggcccaactccatcgctgctggagtccttcagcagcagggtggcaattcagggacaaatcctgatggctccctcgccatggacaacctgcagcccctctcatcagccacggccaccatggccatgcagcaggccatgcttgcagctcacgaggactccctagatggcactgaggaggacgacgatgaggaggatgaggacgagatggaggaggaggaagaggaggaggaggagctggaggaagagcccggtggcctcccggctgcgcctggtgctaaccttggtttggaccacagtgactcactggagtagctcatcctgcgcgctccccaaatcgtggatggcaccggaagcgacctctcccagaatggcaaaaacacagcaagaataacaacagattggtgaggacaaagctaactgtggaggcactgacagatgccccatccgcctgtgggccaccggggccaccacatcagcacatggcagtgaaggacacatgtttacaaggcacatattgtggccggatttttttgaggttttctttcaggttttctttgttttctcccttttcccttcatttttggtaaggaaagcgtttataggggaggctattttccccaccgtgctcggatgccaccatgggctgttgcatcctcttggatttcttggtgcaaaaaaaaccccaaccaaaacaggattgatgtatttctggggtaagcttccacaaaaaaaggtcattcacataaatattggcatgtgggaaagaattgccaagttgccaattctgcttcctatcagattggaggaaagtttcatgctcttgacccacaggattgctcgaatctccctgttttggcctcagtgctgtggccatttggtgactctacacacgactttcaggaaaagggaggaagctccccaaactctttaatttatgtgctaaaaacccatcaaatctcagccttgtccttcagggctgagactggatgccaagttgggctggatgccaggctgagcaagacctttccagggtgttttggtaccaaataggaataaaatagcagcctttcatcccaaattggatagtgatttgcccaggaggaaagaaattcagaaagattctatctccccaacgtcatccacctgcgcaggaaaacattgggtttctcacccccaagtgccacaagcgagctgtcagggggcagctgtacaaaaacactgtgtttgggggctttgagtggtagcaaaaaggcgaattctgccttaaaacacgagaataaaggcagcccaggtaacacagggcatcttctcagttccatgggggttaaaaaaaaaaaaaaggatttttttctgcaagttcttccccatcagttggggtttgttcttctgtaataaggaaggattttggcggctgcatgaattgccatttttgaccttcttttggctcttgaagagttgagaagaaacagcagccgcagccaaacgggccgcagcaacaaagcgatgcaatgggcaacaaagcctatttttcagtactgatctggcgtgaatgtaatctgtaatttcataaaggattcattgtaatttagtattaattcatgtccatttattataaagtgctacgagatgaggttttgcagctgta

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