LOCUS       NM_204226               3299 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus PBX/knotted 1 homeobox 2 (PKNOX2), transcript variant
            1, mRNA.
ACCESSION   NM_204226 XM_015297933
VERSION     NM_204226.2
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 3299)
  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 or before Dec 13, 2021 this sequence version replaced
            XM_015297933.3, NM_204226.1.
            
            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 :: SRR13267654.233022.1,
                                           SRR13267652.4945.1 [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
            508-616             JAENSK010000341.1  213248-213356       c
            617-753             JAENSK010000341.1  208735-208871       c
            754-925             JAENSK010000341.1  204704-204875       c
            926-1114            JAENSK010000341.1  202108-202296       c
            1115-1247           JAENSK010000341.1  197642-197774       c
            1248-1345           JAENSK010000341.1  197471-197568       c
            1346-1465           JAENSK010000341.1  195544-195663       c
            1466-1542           JAENSK010000341.1  194277-194353       c
            1543-1721           JAENSK010000341.1  193578-193756       c
            1722-3299           JAENSK010000341.1  191209-192786       c
FEATURES             Location/Qualifiers
     source          1..3299
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="24"
                     /map="24"
     gene            1..3299
                     /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..616
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    518..520
                     /gene="PKNOX2"
                     /note="upstream in-frame stop codon"
     CDS             533..1966
                     /gene="PKNOX2"
                     /codon_start=1
                     /product="homeobox protein PKNOX2"
                     /protein_id="NP_989557.1"
                     /db_xref="CGNC:49030"
                     /db_xref="GeneID:374067"
                     /translation="

MHHVSPAPALTMMATQTVPPPPYQDSPQMTATAQQPSKAQPVHLSAAPAPTAAVPPAAGDPQAQLEADKRAVYRHPLFPLLTLLFEKCEQATQGSECITSASFDVDIENFVHQQEQEHKPFFSDDPELDNLMVKAIQVLRIHLLELEKVNELCKDFCNRYITCLKTKMHSDNLLRNDLGGPYSPNPSSISLHPQEMLQSSPAALPAASNPPPGIVVPAAALPPGNLAMGSGAGSPAVPGGALYQPVTMVTSQGQVLTQAIAPGALQIPNAQVNLDLTSLLDGEDKKSKNKRGVLPKHATNIMRSWLFQHLMHPYPTEDEKRQIAAQTNLTLLQVNNWFINARRRILQPMLDASNPDPAPKAKKIKSQHRPTQRFWPNSIAAGVLQQQGGNSGTNPDGSLAMDNLQPLSSATATMAMQQAMLAAHEDSLDGTEEDDDEEDEDEMEEEEEEEEELEEEPGGLPAAPGANLGLDHSDSLE"

     misc_feature    812..1069
                     /gene="PKNOX2"
                     /note="N-terminal of Homeobox Meis and PKNOX1; Region:
                     Meis_PKNOX_N; pfam16493"
                     /db_xref="CDD:465140"
     misc_feature    order(1394..1408,1412..1414,1472..1474,1490..1492,
                     1529..1531,1535..1540,1547..1552,1556..1564)
                     /gene="PKNOX2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1400..1402,1409..1411,1538..1540,1547..1552,
                     1559..1561)
                     /gene="PKNOX2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1448..1564
                     /gene="PKNOX2"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            617..753
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            754..925
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            926..1114
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1115..1247
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1248..1345
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1346..1465
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1466..1542
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1543..1721
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
     exon            1722..3299
                     /gene="PKNOX2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gggcggggctctgcgcggcggggccgggcgggcggcagcggcggcgcgctgtcaggccggtgccggtgtgatgaagattggcggcagggaaccttctgatggctgagcagtccctgccgcgccgcccgcctgcacctcccgtcccaacccccggagacctgcaggaattcggcgtccgacccccagccgtggccgatgcgcaggtgtagacccaaactgtaccaataaccactgtgagagcctgtgctggggagctgtcatcgttgaggagcagaagggagcaggacgagatacagctgtggatttccctttgtggatatactggcaacgagcgcatcttcatattgcagacatatctcggctgtgacccatactcagaagttttgcttttgtggctgtgaacgtttcgtgcagcggctcctcgagcacccgcagacgagacatccctggagcattgtagtcggcagcggggatgggcatcttcggagagaagagaaatatttagcggttctcaatgtgactcctgcccaggatgcaccatgtctccccggcgccggctctgacgatgatggccacccagacggtgccccctcctccctaccaagacagcccacagatgacggctacagcccagcagcccagcaaggctcagcccgtgcacctctccgccgcgccggctcccactgcagccgtaccccccgcagccggcgacccgcaggcgcagctggaggccgacaagcgagccgtctacaggcacccactgttcccgctgcttacgctgctctttgagaagtgtgagcaggcaacccaaggctctgagtgcatcacctcagccagcttcgacgtcgacattgaaaactttgtccaccagcaggagcaggagcacaaacctttcttcagtgatgaccctgagctggacaacctgatggtgaaggcaatccaggtgctgcgcatccacctcctggagctggagaaggtcaacgaattgtgcaaggacttttgcaaccgctacatcacctgcctcaaaaccaagatgcacagtgacaacctactcaggaacgacctggggggcccctactcccccaacccctcctccatcagcctccaccctcaggagatgctgcagagctcacccgcggcactaccagccgcctccaaccccccaccgggcatcgtggtgcctgcagccgcactgcccccaggcaacctggccatgggcagcggggctggatcgcccgccgtgccaggtggagccctgtaccagcccgtgacgatggtgacatctcagggccaggtcctcacccaagccatcgcccctggtgccctgcagatccccaacgcccaggttaacctggatctcacctcactccttgacggcgaggacaagaagtccaagaacaagcggggcgttctgcccaaacacgccaccaacatcatgcgctcctggctcttccagcacctcatgcacccctatcccacagaggatgagaagaggcaaatcgctgcccaaaccaacctgaccctcttacaagtcaataactggttcatcaacgcccgccggcgcatcctgcaaccgatgctcgatgccagcaacccagacccagcccctaaagccaagaaaatcaaatctcagcaccggcccacccagcggttctggcccaactccatcgctgctggagtccttcagcagcagggtggcaattcagggacaaatcctgatggctccctcgccatggacaacctgcagcccctctcatcagccacggccaccatggccatgcagcaggccatgcttgcagctcacgaggactccctagatggcactgaggaggacgacgatgaggaggatgaggacgagatggaggaggaggaagaggaggaggaggagctggaggaagagcccggtggcctcccggctgcgcctggtgctaaccttggtttggaccacagtgactcactggagtagctcatcctgcgcgctccccaaatcgtggatggcaccggaagcgacctctcccagaatggcaaaaacacagcaagaataacaacagattggtgaggacaaagctaactgtggaggcactgacagatgccccatccgcctgtgggccaccggggccaccacatcagcacatggcagtgaaggacacatgtttacaaggcacatattgtggccggatttttttgaggttttctttcaggttttctttgttttctcccttttcccttcatttttggtaaggaaagcgtttataggggaggctattttccccaccgtgctcggatgccaccatgggctgttgcatcctcttggatttcttggtgcaaaaaaaaccccaaccaaaacaggattgatgtatttctggggtaagcttccacaaaaaaaggtcattcacataaatattggcatgtgggaaagaattgccaagttgccaattctgcttcctatcagattggaggaaagtttcatgctcttgacccacaggattgctcgaatctccctgttttggcctcagtgctgtggccatttggtgactctacacacgactttcaggaaaagggaggaagctccccaaactctttaatttatgtgctaaaaacccatcaaatctcagccttgtccttcagggctgagactggatgccaagttgggctggatgccaggctgagcaagacctttccagggtgttttggtaccaaataggaataaaatagcagcctttcatcccaaattggatagtgatttgcccaggaggaaagaaattcagaaagattctatctccccaacgtcatccacctgcgcaggaaaacattgggtttctcacccccaagtgccacaagcgagctgtcagggggcagctgtacaaaaacactgtgtttgggggctttgagtggtagcaaaaaggcgaattctgccttaaaacacgagaataaaggcagcccaggtaacacagggcatcttctcagttccatgggggttaaaaaaaaaaaaaaggatttttttctgcaagttcttccccatcagttggggtttgttcttctgtaataaggaaggattttggcggctgcatgaattgccatttttgaccttcttttggctcttgaagagttgagaagaaacagcagccgcagccaaacgggccgcagcaacaaagcgatgcaatgggcaacaaagcctatttttcagtactgatctggcgtgaatgtaatctgtaatttcataaaggattcattgtaatttagtattaattcatgtccatttattataaagtgctacgagatgaggttttgcagctgta

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