LOCUS       NM_001398296            3230 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus PBX/knotted 1 homeobox 2 (PKNOX2), transcript variant
            2, mRNA.
ACCESSION   NM_001398296 XM_015297934
VERSION     NM_001398296.1
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 3230)
  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_015297934.3.
            
            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 :: SRR13267654.144621.1,
                                           SRR13267649.105370.1 [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
            439-547             JAENSK010000341.1  213248-213356       c
            548-684             JAENSK010000341.1  208735-208871       c
            685-856             JAENSK010000341.1  204704-204875       c
            857-1045            JAENSK010000341.1  202108-202296       c
            1046-1178           JAENSK010000341.1  197642-197774       c
            1179-1276           JAENSK010000341.1  197471-197568       c
            1277-1396           JAENSK010000341.1  195544-195663       c
            1397-1473           JAENSK010000341.1  194277-194353       c
            1474-1652           JAENSK010000341.1  193578-193756       c
            1653-3230           JAENSK010000341.1  191209-192786       c
FEATURES             Location/Qualifiers
     source          1..3230
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="24"
                     /map="24"
     gene            1..3230
                     /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..547
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    449..451
                     /gene="PKNOX2"
                     /note="upstream in-frame stop codon"
     CDS             464..1897
                     /gene="PKNOX2"
                     /codon_start=1
                     /product="homeobox protein PKNOX2"
                     /protein_id="NP_001385225.1"
                     /db_xref="CGNC:49030"
                     /db_xref="GeneID:374067"
                     /translation="

MHHVSPAPALTMMATQTVPPPPYQDSPQMTATAQQPSKAQPVHLSAAPAPTAAVPPAAGDPQAQLEADKRAVYRHPLFPLLTLLFEKCEQATQGSECITSASFDVDIENFVHQQEQEHKPFFSDDPELDNLMVKAIQVLRIHLLELEKVNELCKDFCNRYITCLKTKMHSDNLLRNDLGGPYSPNPSSISLHPQEMLQSSPAALPAASNPPPGIVVPAAALPPGNLAMGSGAGSPAVPGGALYQPVTMVTSQGQVLTQAIAPGALQIPNAQVNLDLTSLLDGEDKKSKNKRGVLPKHATNIMRSWLFQHLMHPYPTEDEKRQIAAQTNLTLLQVNNWFINARRRILQPMLDASNPDPAPKAKKIKSQHRPTQRFWPNSIAAGVLQQQGGNSGTNPDGSLAMDNLQPLSSATATMAMQQAMLAAHEDSLDGTEEDDDEEDEDEMEEEEEEEEELEEEPGGLPAAPGANLGLDHSDSLE"

     misc_feature    743..1000
                     /gene="PKNOX2"
                     /note="N-terminal of Homeobox Meis and PKNOX1; Region:
                     Meis_PKNOX_N; pfam16493"
                     /db_xref="CDD:465140"
     misc_feature    order(1325..1339,1343..1345,1403..1405,1421..1423,
                     1460..1462,1466..1471,1478..1483,1487..1495)
                     /gene="PKNOX2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1331..1333,1340..1342,1469..1471,1478..1483,
                     1490..1492)
                     /gene="PKNOX2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1379..1495
                     /gene="PKNOX2"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            548..684
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            685..856
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            857..1045
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1046..1178
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1179..1276
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1277..1396
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1397..1473
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1474..1652
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1653..3230
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gggcggggctctgcgcggcggggccgggcgggcggcagcggcggcgcgctgtcaggccggtgccggtgtgatgaagattggcggcagggaaccttctgatggctgagcagtccctgccgcgccgcccgcctgcacctcccgtcccaacccccggagacctgcaggaattcggcgtccgacccccagccgtggccgatgcgcaggtgtagacccaaactgtaccaataaccactgtgagagcctgtgctggggagctgtcatcgttgaggagcagaagggagcaggacgagatacagctgtggatttccctttgtggatatactggcaacgagcgcatcttcatattgcagacatatctcggctgtgacccatactcagaagttttgcttttgtggctgtgaacgtttcgtgcagcggctcctcgagcacccgcagacggttctcaatgtgactcctgcccaggatgcaccatgtctccccggcgccggctctgacgatgatggccacccagacggtgccccctcctccctaccaagacagcccacagatgacggctacagcccagcagcccagcaaggctcagcccgtgcacctctccgccgcgccggctcccactgcagccgtaccccccgcagccggcgacccgcaggcgcagctggaggccgacaagcgagccgtctacaggcacccactgttcccgctgcttacgctgctctttgagaagtgtgagcaggcaacccaaggctctgagtgcatcacctcagccagcttcgacgtcgacattgaaaactttgtccaccagcaggagcaggagcacaaacctttcttcagtgatgaccctgagctggacaacctgatggtgaaggcaatccaggtgctgcgcatccacctcctggagctggagaaggtcaacgaattgtgcaaggacttttgcaaccgctacatcacctgcctcaaaaccaagatgcacagtgacaacctactcaggaacgacctggggggcccctactcccccaacccctcctccatcagcctccaccctcaggagatgctgcagagctcacccgcggcactaccagccgcctccaaccccccaccgggcatcgtggtgcctgcagccgcactgcccccaggcaacctggccatgggcagcggggctggatcgcccgccgtgccaggtggagccctgtaccagcccgtgacgatggtgacatctcagggccaggtcctcacccaagccatcgcccctggtgccctgcagatccccaacgcccaggttaacctggatctcacctcactccttgacggcgaggacaagaagtccaagaacaagcggggcgttctgcccaaacacgccaccaacatcatgcgctcctggctcttccagcacctcatgcacccctatcccacagaggatgagaagaggcaaatcgctgcccaaaccaacctgaccctcttacaagtcaataactggttcatcaacgcccgccggcgcatcctgcaaccgatgctcgatgccagcaacccagacccagcccctaaagccaagaaaatcaaatctcagcaccggcccacccagcggttctggcccaactccatcgctgctggagtccttcagcagcagggtggcaattcagggacaaatcctgatggctccctcgccatggacaacctgcagcccctctcatcagccacggccaccatggccatgcagcaggccatgcttgcagctcacgaggactccctagatggcactgaggaggacgacgatgaggaggatgaggacgagatggaggaggaggaagaggaggaggaggagctggaggaagagcccggtggcctcccggctgcgcctggtgctaaccttggtttggaccacagtgactcactggagtagctcatcctgcgcgctccccaaatcgtggatggcaccggaagcgacctctcccagaatggcaaaaacacagcaagaataacaacagattggtgaggacaaagctaactgtggaggcactgacagatgccccatccgcctgtgggccaccggggccaccacatcagcacatggcagtgaaggacacatgtttacaaggcacatattgtggccggatttttttgaggttttctttcaggttttctttgttttctcccttttcccttcatttttggtaaggaaagcgtttataggggaggctattttccccaccgtgctcggatgccaccatgggctgttgcatcctcttggatttcttggtgcaaaaaaaaccccaaccaaaacaggattgatgtatttctggggtaagcttccacaaaaaaaggtcattcacataaatattggcatgtgggaaagaattgccaagttgccaattctgcttcctatcagattggaggaaagtttcatgctcttgacccacaggattgctcgaatctccctgttttggcctcagtgctgtggccatttggtgactctacacacgactttcaggaaaagggaggaagctccccaaactctttaatttatgtgctaaaaacccatcaaatctcagccttgtccttcagggctgagactggatgccaagttgggctggatgccaggctgagcaagacctttccagggtgttttggtaccaaataggaataaaatagcagcctttcatcccaaattggatagtgatttgcccaggaggaaagaaattcagaaagattctatctccccaacgtcatccacctgcgcaggaaaacattgggtttctcacccccaagtgccacaagcgagctgtcagggggcagctgtacaaaaacactgtgtttgggggctttgagtggtagcaaaaaggcgaattctgccttaaaacacgagaataaaggcagcccaggtaacacagggcatcttctcagttccatgggggttaaaaaaaaaaaaaaggatttttttctgcaagttcttccccatcagttggggtttgttcttctgtaataaggaaggattttggcggctgcatgaattgccatttttgaccttcttttggctcttgaagagttgagaagaaacagcagccgcagccaaacgggccgcagcaacaaagcgatgcaatgggcaacaaagcctatttttcagtactgatctggcgtgaatgtaatctgtaatttcataaaggattcattgtaatttagtattaattcatgtccatttattataaagtgctacgagatgaggttttgcagctgta

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