LOCUS       NM_001080859            2163 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus homeobox B1 (HOXB1), transcript variant 1, mRNA.
ACCESSION   NM_001080859 XM_001234950
VERSION     NM_001080859.5
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 2163)
  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 2163)
  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 2163)
  AUTHORS   Peale FV Jr, Mason K, Hunter AW and Bothwell M.
  TITLE     Multiplex display polymerase chain reaction amplifies and resolves
            related sequences sharing a single moderately conserved domain
  JOURNAL   Anal Biochem 256 (2), 158-168 (1998)
   PUBMED   9473273
REFERENCE   4  (bases 1 to 2163)
  AUTHORS   Sundin OH, Busse HG, Rogers MB, Gudas LJ and Eichele G.
  TITLE     Region-specific expression in early chick and mouse embryos of
            Ghox-lab and Hox 1.6, vertebrate homeobox-containing genes related
            to Drosophila labial
  JOURNAL   Development 108 (1), 47-58 (1990)
   PUBMED   1693558
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000364.1.
            
            On Dec 14, 2021 this sequence version replaced NM_001080859.4.
            
            Transcript Variant: This variant (1) has the long intron. The
            encoded protein is conserved in birds.
            
            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 :: SRR13267655.158692.1,
                                           SRR13267653.16507.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992440, SAMEA3109051
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-723               JAENSK010000364.1  800940-801662
            724-2163            JAENSK010000364.1  802368-803807
FEATURES             Location/Qualifiers
     source          1..2163
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="27"
                     /map="27"
     gene            1..2163
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /note="homeobox B1"
                     /db_xref="CGNC:10116"
                     /db_xref="GeneID:395900"
     exon            1..723
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    63..65
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /note="upstream in-frame stop codon"
     CDS             117..1049
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     homeobox-containing transcription factor Hoxb-1; homeobox
                     protein Hox-B1"
                     /codon_start=1
                     /product="homeobox protein Hox-B1 isoform 1"
                     /protein_id="NP_001074328.2"
                     /db_xref="CGNC:10116"
                     /db_xref="GeneID:395900"
                     /translation="

MDNTRMNSFLEYAICNRGTGAYHHLEQSSPSFPSCSGSPSSDTFHGEGRYGAGGSAVAAAHLPPQSPGFFPAASGRSVPFAAAAPSAGYPTQNCSPGYGHHQLYLGQQDADGVYFQAAGYSSSTGPHLGSLAEGYCGAVGQYQQQQHLYGQEQPGYLPGVYGNLSPSLNEDKDPACPSEPCPNASAARTFDWMKVKRNPPKTAKVSEYGLLGQPNTIRTNFTTKQLTELEKEFHFNKYLTRARRVEIAATLELNETQVKIWFQNRRMKQKKREKEGLAPPAASRSAKEASEASDQSNCTSPEASPSSVSS"

     misc_feature    order(768..773,777..779,828..830,846..848,885..887,
                     891..896,903..908,912..920,924..929)
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    768..926
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(774..776,894..896,903..908,915..917)
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            724..2163
                     /gene="HOXB1"
                     /gene_synonym="Ghox-lab; HOXB-1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gttcgagggccagcgatgcatggaaggaagttttacagctttgacatactatctaaaggttgtagggcaggcggaatcccccccaaaacaggctgaccctcctccatcagtggcagatggacaatactaggatgaactccttcttagagtatgcaatttgtaaccgtgggacgggcgcctaccaccatttagagcaaagctccccttccttcccctcttgctcaggtagcccctccagtgacacttttcatggagaagggcgctacggtgcggggggcagcgcggtcgcggccgcccatctccccccgcagagccccggcttcttccccgccgcctccgggcgctccgtgcccttcgcggccgctgccccgagcgccgggtacccaacccaaaattgcagccccggctacgggcaccaccagctctacctcggccagcaggacgcggacggcgtgtacttccaggcggccgggtactcctccagcaccggaccccacctcggctccctggcagagggctattgtggggccgtagggcagtaccagcagcagcagcacctttacgggcaggagcagcccggttacttgcccggggtttacggcaacctctcgccttccctaaatgaggacaaagaccccgcgtgtccctccgagccgtgccccaatgccagcgcggcgcggaccttcgattggatgaaagtgaagaggaaccctcccaagacagccaaagtgtcggaatacgggctgctgggccagcccaacaccattcgcaccaacttcaccaccaagcagctgacggagctggagaaggagtttcactttaacaagtacctcacccgggcccggagggtggagatcgccgctacactggagctcaacgaaacccaagtcaagatctggttccagaacaggcggatgaaacagaagaagagggaaaaggaaggtctcgcccctcctgctgcctccaggtccgcgaaggaagcgagtgaagcctcggatcagtccaactgcacctcacctgaggcctcccccagctccgtgtcctcctgagccgcggttccgcggggcacaacgaccggatcggggctgccttcgagggccgctgctccccgccgctccccgcagcccgacccgcactgccccgcacagccccggccgcacacgcttccctccgagccgccccttcggctccggccgcctccacgcgtgcggtgcccattccccgtttgccttcctctcttaatttatagaccctccgtcaaacgttggactccaaaggagcggccgtgtcctcgtttatccttagcaataggcgtttgtctcagggacgtttctcccttctcccctcccccgataggaactgcactttcaactacagaaacttgaaaacgaatttagttctctcccgctttaaagatgtgcacaacgacttttgtccgcacgcaccctgagtttgctgtgttattcctcccctcgagacggctaaaacagaaaagtttggggtgctttttttttgtttcccttttacatttactctgtgtatctcggaaagagcccaaggcgctgaaggcctctgggaagacccgaaaaagaaaagaaacgaagcaaaaacgcaactcctctgctgccattttgcactatcgtcgctttacagggtttcctacacgctctccgcctgtattaccgatcctgggggtgggagcgttgtgctatcagataaaacgagataaggggaaggctgagcccggggtgctttgggcaacggtcattgccgcaccgagtgtgaacgtgcatgggacgaaggccgggggggtccgcactgcgctcccccaaccgcgatgcactgactgctatttattgtacgtctcgatagcctcacgtcttggggcgaagctgcacggctcctcgtatccccaccccctcaggcttatcggagtccgagaaaaacataattaaccacggccagttgctaccctttaccaccagaagctttagcgcagggcgaagtgaaaaccacggcgagtttcgttaaaggttgttttaaagagataaagggtcatcctgaaaagcctgtggtttcttaatcggaatctgttttccctctactcccttccctgtttttcgaaatgaaactacctcagtctaataaagtttactttttcca

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