LOCUS       NM_205293               1404 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus homeobox B4 (HOXB4), mRNA.
ACCESSION   NM_205293 XM_001235893
VERSION     NM_205293.3
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 1404)
  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 1404)
  AUTHORS   Attia L, Yelin R and Schultheiss TM.
  TITLE     Analysis of nephric duct specification in the avian embryo
  JOURNAL   Development 139 (22), 4143-4151 (2012)
   PUBMED   23034630
  REMARK    GeneRIF: In the primitive streak, expression of the gene HoxB4 is
            associated with prospective duct IM, whereas expression of the more
            posterior Hox gene HoxA6 is associated with more posterior,
            non-duct-forming IM.
REFERENCE   3  (bases 1 to 1404)
  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   4  (bases 1 to 1404)
  AUTHORS   Amirthalingam GS, Howard S, Alvarez S, de Lera AR and Itasaki N.
  TITLE     Regulation of Hoxb4 induction after neurulation by somite signal
            and neural competence
  JOURNAL   BMC Dev Biol 9, 17 (2009)
   PUBMED   19243620
  REMARK    GeneRIF: Study shows that somites are required for the
            up-regulation of Hoxb4 in the neural tube at the level of somites 1
            to 5, the anterior-most domain of expression.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1404)
  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.
            
            On Dec 3, 2021 this sequence version replaced NM_205293.2.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BU334053.1, SRR13267655.5054.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992323
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-705               JAENSK010000364.1  756527-757231
            706-1404            JAENSK010000364.1  758015-758713
FEATURES             Location/Qualifiers
     source          1..1404
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="27"
                     /map="27"
     gene            1..1404
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /note="homeobox B4"
                     /db_xref="CGNC:15553"
                     /db_xref="GeneID:396230"
     exon            1..705
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    174..176
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /note="upstream in-frame stop codon"
     CDS             285..1022
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /note="homeo box B4; homeobox protein Hox-Z"
                     /codon_start=1
                     /product="homeobox protein Hox-B4"
                     /protein_id="NP_990624.1"
                     /db_xref="CGNC:15553"
                     /db_xref="GeneID:396230"
                     /translation="

MAMSSFLINSNYVDPKFPPCEEYSHSDYLPNHSPEYYSSQRRESTFQHEAMYQPRSACSEQLYPSCQSSGHQAAVLSPRGHVHPPAGLQSHLSEPNHPCEPGTPSPPPSCSQNSLNQSPSNSSCKEPVVYPWMKKVHVSTVNPNYSGGEPKRSRTAYTRQQVLELEKEFHYNRYLTRRRRVEIAHSLCLSERQIKIWFQNRRMKWKKDHKLPNTKIRSNPSSSSASLQIPPAASQSRSSGPASSL"

     misc_feature    order(735..749,753..755,804..806,822..824,861..863,
                     867..872,879..884,888..896,900..905)
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    741..902
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(741..743,750..752,870..872,879..884,891..893)
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            706..1404
                     /gene="HOXB4"
                     /gene_synonym="Chox-Z"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcggggcccggggaacggggccggaggggagcgggcgcccccggccgcctccccggggatgctccgggccccgggagagcccgtgccgggcagatttccttatccggggatcgcaggccacctcgccattggcccgcgctgtcacatggactccaactttgttcacttgacagtaagtaggagggtttcacgaaacaggaaaacgagtaaagggggggacaggaataaattttaggaaatatatatatatatatatttttcgtgtgtgcaattctaagaaattaatggccatgagctcgtttttgatcaactccaactatgtggaccccaagttcccaccctgtgaagagtattcccacagcgattaccttcccaatcactcgccggaatattacagcagccagaggcgagagagcactttccaacatgaagcgatgtaccagccgcggtcagcatgcagcgagcagctctacccgtcctgtcagagctccgggcaccaagcagcggtgttatccccccggggtcatgtccatcctccggccggactgcagagccatctctctgagccaaaccatccctgcgagccgggcacccccagccctccaccctcctgcagccaaaactctctgaaccaaagcccttccaattcctcttgcaaagagccggtagtttacccctggatgaaaaaagtccatgtaagcacggtaaaccccaattattcaggaggggaaccgaaacgttcgcgcacagcctacaccaggcagcaggtcctggagctggagaaggaattccactataaccgctatctcacccggaggcggagggtcgaaatcgcccattctctgtgcctctccgagcgccagatcaaaatctggttccagaacaggaggatgaaatggaagaaagaccacaagttacccaacaccaagatcaggtccaacccttccagctcctccgccagcctgcagatcccaccggcagcttctcaaagccgatccagcggaccagccagcagcctataactattccctgtatggacggggtgtgcgtgctcgtgggtgtgattgtgagtgtgagtgtgtgtagggaacacgggagaatagtggggtttttttaatgctccgagaagcgaaggaaggaggggggctttttttatttataaggggcaacagggagaggctcagctccaacaaagcagagccgtgctgctgtgcccctcttccattagaagaaggctgtaggtagtagttttcagatttggctaagatggatccttgtttcatctttaatcacgccaagctctgccccatttgtcatgtttactctcccgtacaaaggatggaccttatgtctgctattacctcgacaaccagcgttcactttaataaatgaggctcagtttct

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