LOCUS       NM_001397895            3373 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus homeobox B3 (HOXB3), mRNA.
ACCESSION   NM_001397895
VERSION     NM_001397895.1
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 3373)
  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
REFERENCE   2  (bases 1 to 3373)
  AUTHORS   Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C,
            Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N and Hunter S.
  TITLE     Manual GO annotation of predictive protein signatures: the InterPro
            approach to GO curation
  JOURNAL   Database (Oxford) 2012, bar068 (2012)
   PUBMED   22301074
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3373)
  AUTHORS   Carre W, Wang X, Porter TE, Nys Y, Tang J, Bernberg E, Morgan R,
            Burnside J, Aggrey SE, Simon J and Cogburn LA.
  TITLE     Chicken genomics resource: sequencing and annotation of 35,407 ESTs
            from single and multiple tissue cDNA libraries and CAP3 assembly of
            a chicken gene index
  JOURNAL   Physiol Genomics 25 (3), 514-524 (2006)
   PUBMED   16554550
REFERENCE   4  (bases 1 to 3373)
  AUTHORS   Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong
            WT, Tickle C, Brown WR, Wilson SA and Hubbard SJ.
  TITLE     A comprehensive collection of chicken cDNAs
  JOURNAL   Curr Biol 12 (22), 1965-1969 (2002)
   PUBMED   12445392
REFERENCE   5  (bases 1 to 3373)
  AUTHORS   Rex M and Scotting PJ.
  TITLE     Chick HoxB3: deduced amino-acid sequence and embryonic gene
            expression
  JOURNAL   Gene 149 (2), 381-382 (1994)
   PUBMED   7959024
REFERENCE   6  (bases 1 to 3373)
  AUTHORS   Gaunt SJ.
  TITLE     Conservation in the Hox code during morphological evolution
  JOURNAL   Int J Dev Biol 38 (3), 549-552 (1994)
   PUBMED   7848839
REFERENCE   7  (bases 1 to 3373)
  AUTHORS   Scotting PJ, Hewitt M and Keynes RJ.
  TITLE     Isolation and analysis of chick homeobox cDNA clones
  JOURNAL   Nucleic Acids Res 18 (13), 3999 (1990)
   PUBMED   1973835
REFERENCE   8  (bases 1 to 3373)
  AUTHORS   Sasaki H and Kuroiwa A.
  TITLE     The nucleotide sequence of the cDNA encoding a chicken Deformed
            family homeobox gene, Chox-Z
  JOURNAL   Nucleic Acids Res 18 (1), 184 (1990)
   PUBMED   1968620
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000364.1, BU202463.1, X52749.1, BI065824.1, X80113.1 and
            CR391614.1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            CDS exon combination :: SRR13267659.146668.1 [ECO:0000331]
            RNAseq introns       :: single sample supports all introns
                                    SAMEA103992428, SAMEA103992432
                                    [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-31                JAENSK010000364.1  743390-743420
            32-390              BU202463.1         1-359
            391-393             JAENSK010000364.1  773845-773847
            394-714             BU202463.1         363-683
            715-974             JAENSK010000364.1  782717-782976
            975-1040            X52749.1           1-66
            1041-1593           BI065824.1         15-567
            1594-1735           X80113.1           473-614
            1736-2433           CR391614.1         1-698
            2434-3373           JAENSK010000364.1  785485-786424
FEATURES             Location/Qualifiers
     source          1..3373
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="27"
                     /map="27"
     gene            1..3373
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="homeobox B3"
                     /db_xref="CGNC:49352"
                     /db_xref="GeneID:395502"
     exon            1..48
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
     exon            49..111
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
     exon            112..352
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
     exon            353..409
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
     exon            410..472
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
     exon            473..1026
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    558..560
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="upstream in-frame stop codon"
     CDS             591..1790
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="homeo box B3; chox-2.7; homeobox protein Hox-2.7;
                     Homeobox protein Hox-B4; Homeobox protein Hox-Z"
                     /codon_start=1
                     /product="homeobox protein Hox-B3"
                     /protein_id="NP_001384824.1"
                     /db_xref="CGNC:49352"
                     /db_xref="GeneID:395502"
                     /translation="

MQKTTYYESSTLFGGYSYGSTNGFGYEGPQQPFQPGSHVENDFQRSACSLQSLGNTTQHAKSKDLNGSCMRPSLPQEHHPPPTVSPPPNPTTNSTSSNSNNQSGSSKSAPSKANLSANASLTKQIFPWMKESRQNSKQKSSSPSTETCSGEKSPPGSSASKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKKDQKSKGMGSSSGGPSPTGSPPQPMQSSAGFMNALHTMSSNYDAPSPPSFNKPHQNAYAMSTNYQNPIKGCPSQQKYTNTAPEYDPHVLQGNGVAYGTPSMQGSPVYVGGNYVDSLPTSGPSLYGLNHLPHHQAANMDYSGPPQMPPSQHHGPCEPHPTYTDLSSHHASSQGRIQEAPKLTHL"

     misc_feature    order(1071..1085,1089..1091,1140..1142,1158..1160,
                     1197..1199,1203..1208,1215..1220,1224..1232,1236..1241)
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1077..1079,1086..1088,1206..1208,1215..1220,
                     1227..1229)
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1080..1238
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    1590..1781
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /note="Domain of unknown function (DUF4074); Region:
                     DUF4074; pfam13293"
                     /db_xref="CDD:433094"
     exon            1027..3373
                     /gene="HOXB3"
                     /gene_synonym="2.7; CHOX; CHOX-Z; HOXB-3; HOXB4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcgggtccagttttcagtccagagagccaatagactgcagtcctgaaaggaggatttcagggcccgttgtcgtatggcagtgccggaggtgggggtgaatttttgctgctgcaaatctccgcagaccgtctgttggggaaaaagcacccggagttcgaccagaatcttcaggggaaataataatactaataataaaatctggatcgtaaaggtgaaagctttatatttgggggagaaaacccaaaccctcacccaagccccccctcccccagacctctcactttggaagaaaccacccaaaccatgagggccgtctctggggcgttggaaaaaggatgtgggagcgaaccaggtcctttctcccccatgctcagaccgtccaacagcgcccatcgggtcccggattcagttcttctcctttctcaaactccaccgcagccccgtgtttgctggaccacacatccgggaaccggtcagcttccaatagacagctggaaacggcctgtcacgtggccttggggtgccaatgttctgccataggggtgtcaagaccctggtagctggaaaaatcattttggggaatcctggagatgcagaagacaacgtactacgaaagctccacgctctttgggggctattcctatgggagcaccaatgggtttggctacgagggtccccagcagcccttccaaccgggttcccacgtggagaacgacttccagaggtccgcctgctccctccagtctctcggcaacacaactcagcacgcaaaaagtaaagacctgaatgggagctgtatgaggccgagtttgccccaggagcaccatccgcctccgactgtctcaccacccccaaaccccaccaccaacagcaccagtagcaacagcaataaccagtcagggagcagcaaaagtgccccgagtaaagccaacctcagtgcaaacgccagtctcaccaagcagattttcccctggatgaaagaatcgaggcaaaactcgaaacagaaaagcagctcccctagcacagaaacctgcagcggcgagaaaagccctccaggctcctcggcctccaagagagcccgcacagcttacaccagcgcgcagctggtggagctggagaaggaattccacttcaaccgctacctgtgccggccccggcgcgtggagatggccaacctgctgaacctcagcgagaggcagatcaagatctggttccagaacaggaggatgaagtataagaaagatcagaagtcaaaagggatgggctcttcctctggagggccttcccccaccggcagccccccccaacccatgcaatcctccgccgggtttatgaacgccttgcacaccatgagcagtaactatgatgccccctccccaccttccttcaataagccccaccaaaatgcctacgccatgtcaactaactaccaaaaccccatcaaaggctgcccctcccaacagaagtacaccaacacggcccccgagtacgacccccatgtattacaagggaacggggtggcctacgggactcccagcatgcagggaagtcccgtctacgttggaggtaactatgtggactccctgcccacctctggcccatccctttacggcctcaatcacctcccacatcaccaggcggccaacatggactacagtgggcccccgcagatgcctccaagccaacaccacggaccatgcgagccccaccccacctacacagacctttcctcgcaccacgcatcttctcagggcagaatccaggaggcccccaagctgacccacctgtgatcgggagcagggatgggctcaagtgaactggatggcaaccaacacatgacttggatggggcacggggcaggacggccttcagaaacatttgtgttgagctgttttcttcctttcttctcttaggcaagttctaccaagctgttgagcttgccagtgttatttctgggttctgtttggcacagtttccaaggacttcagtatttaatgtcaaaagcatctctctctctgaaaagatgtacctcctgtgggtcaacacaaatgtttctgaagtggctttgggggtgtttaatgggaacctagtagacgtttagcagcaacaccctcaatttccaaacccagggcagattatcactgataattcttggccaatggaaagcagatggccagcctaacctttacagttgctgcctctgcatctacacctggctacacaggttagcacaagggatgcacaagaaaaccgccctccacttcagtcctaatcaagagcttcgtgctttcctccccaacctccagaggcagggcatccttcttcgctgagttacttcccaccaatcccgacacaaaaggcaaatatacacacctgccaacgcgtgggatccacgctcttcccctcccacccacacatcccctctcaaaaataatagtaagaaaaaagaaaagaaaatgagagaggtctaagaattgcaaaaaggtttaggaaacgagtttctaaattgccttgaaccccaccaacaggaacggcagtccaaagagaggaagaaaatgttgacaggtctgaatatttttccacctttgccactgatgatgtgaaatttccatttgatgatgccagggtttttgtttttttgggggggatttttcttagggttcattaatagaaaagcaatcttaagacttagaagtcctatgcttctttcctcctcttctcttgaccttacgtgaaaacagggtatatttgaacaaatggaatgtcctccaatggaagcagaagtgaatggatctctaggatttgctaatgctttattgtctggacatctttgttgcacttagagtttacatataatgggtataaaaacaactttgaagggcgttcattgaactcagtcgagacgtccttcaataggtgtgtgttctggtgaacattcatatatatttattggttatagccagtttaaaatattttcctttttgtattatttatccccaatattatgtatttatatgagggaaaaaaaaagaatcaaattgtacttttttagtatttacttgttataaaggacattgtgtttccttgtcattgtacaacaagcttattttagttactgtaatttagaaagacgagtagttttatgttaccttcgtacttatgaataatgtaattagttctactggaggcatgagagcagaaccagactgtaattgtatagtcctgaattagaagaactatagctaatccctccctcccatcttgcccctcctctttggagatctttctttgttcttatagtagttattttatttccttgcttaagggttgtctgttgaacaattcttgaataaactttctgttatcaatttca

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