LOCUS       NM_001301787            2614 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus cone-rod homeobox (CRX), mRNA.
ACCESSION   NM_001301787
VERSION     NM_001301787.2
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 2614)
  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 2614)
  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 2614)
  AUTHORS   Plouhinec JL, Leconte L, Sauka-Spengler T, Bovolenta P, Mazan S and
            Saule S.
  TITLE     Comparative analysis of gnathostome Otx gene expression patterns in
            the developing eye: implications for the functional evolution of
            the multigene family
  JOURNAL   Dev Biol 278 (2), 560-575 (2005)
   PUBMED   15680370
REFERENCE   4  (bases 1 to 2614)
  AUTHORS   Plouhinec JL, Sauka-Spengler T, Germot A, Le Mentec C, Cabana T,
            Harrison G, Pieau C, Sire JY, Veron G and Mazan S.
  TITLE     The mammalian Crx genes are highly divergent representatives of the
            Otx5 gene family, a gnathostome orthology class of
            orthodenticle-related homeogenes involved in the differentiation of
            retinal photoreceptors and circadian entrainment
  JOURNAL   Mol Biol Evol 20 (4), 513-521 (2003)
   PUBMED   12654938
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000454.1.
            
            On Dec 15, 2021 this sequence version replaced NM_001301787.1.
            
            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 :: DR424779.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992428
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-147               JAENSK010000454.1  92603-92749
            148-252             JAENSK010000454.1  93456-93560
            253-404             JAENSK010000454.1  94208-94359
            405-2614            JAENSK010000454.1  95921-98130
FEATURES             Location/Qualifiers
     source          1..2614
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="38"
                     /map="38"
     gene            1..2614
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /note="cone-rod homeobox"
                     /db_xref="CGNC:71991"
                     /db_xref="GeneID:103875463"
     exon            1..147
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /inference="alignment:Splign:2.1.0"
     exon            148..252
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /inference="alignment:Splign:2.1.0"
     CDS             156..1019
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /note="transcription factor Crx"
                     /codon_start=1
                     /product="cone-rod homeobox protein"
                     /protein_id="NP_001288716.1"
                     /db_xref="CGNC:71991"
                     /db_xref="GeneID:103875463"
                     /translation="

MMSYIKQPHYAVNGLTLAGPGMDLLHSAVGYPATPRKQRRERTTFTRAQLDILEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQSSGQPKARPAKKKPTPPREAPNDAGGAGPYSPTQPGPAGTPGSAAPVSIWSPASISPVPDPLAAGSAPGLPRSAPFSAAPYNQTAPYGQSYGGSAAYFGGLDCGAYLSPMHPPLGAPGAALSPLGAPMGAHLTPSPAALSGQSFGAGLGFGAVDCLEYKEQAGAWKLNFNAADCLDYKEQSSWKFQVL"

     misc_feature    270..437
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    <423..710
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /note="large tegument protein UL36; Provisional; Region:
                     PHA03247"
                     /db_xref="CDD:223021"
     misc_feature    603..857
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:427350"
     exon            253..404
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /inference="alignment:Splign:2.1.0"
     exon            405..2614
                     /gene="CRX"
                     /gene_synonym="OTX5"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

attgccggcggcggcggattaagccccgtccggggcccaatgtcaccccggggattaacgggggcggtgacatcacgcgggggctctacttaaagctccccccggcgcggggacgccttcccactgccagcccggaccccagcacagcccagagcatgatgtcctacatcaagcagccccactacgctgtcaatgggctgacgctggccgggccaggcatggatttgctgcattctgctgtggggtaccccgccaccccccggaagcagcgccgtgagcgcaccacgttcacgcgggcgcagttggacatcctggaggctctgtttgccaaaacgaggtaccccgacatcttcatgagggaggaggtggccctgaagatcaacctgcctgagtcccgcgtgcaggtgtggttcaagaaccgccgcgccaagtgccgccagcagcagcagcagagcagcgggcagcccaaggcgcgcccggccaagaagaagccgacgccgccccgagaagccccgaacgacgccgggggggccgggccgtacagccccacgcagcccggccccgcggggacccccggctccgccgcccccgtctccatttggagcccggcctccatctctcccgtgccggacccgttggccgccggcagcgctccgggtttgccgcgttccgctccgttctccgccgctccgtacaaccaaacggcgccctacgggcagagctacggcgggtcggccgcctacttcgggggcctggactgcggggcgtacctctcccccatgcaccctccgctgggggctcccggcgctgctctcagccccctgggggcacccatgggcgctcacctgacgccctcccccgccgctctgtccgggcagagcttcggggcggggttgggcttcggggcggtggattgcttggagtacaaagagcaggcgggagcgtggaagctcaacttcaacgcggccgattgcctggactacaaggagcagagctcctggaagttccaggtgttgtgaggggggaggagagacggggggtgggtgtgtgtgtgtggggggggggtgaattggggaggtgggcggccccgggggtcggggtggctctgcatggactggagttggggtgcgcagagtgcatggagcggccccgggggtgcagcagccccaaaggatgcggcatccctgcatggagcgttgctaagaaacagagcatccctgcatggagcgttgctaagaaacagagcatccctgcatggagcatcccctggggacacagcatccctgcatggagcatccccgggacatgcaacatccctgcatggagcatccctaagggtcacagtatccctgcgtggagcatccctgcatggagcacccccaggacgtgcaatatccctgcatggagcacccccaggacttgcagcgtccctgcgtggagcgttgctaagaaacagcatccctgcacggagcgtcactgtggaacacagcactgctgcatggagcattcctgcgtggggcatccccaaagaatgcagcattgctgcgtggagcatcattgcatggagcatctccaggacacacagcatccctgcgcggggcgtctctaaggagtgcagcatccctgtgtggggtttccctgcatgcatcacccgcagggggtggaggatctctgcatgcagcgcccttgcttggagcagccctaaggaacacagcacccctgcatggagcacccccaggacgtgcagcacctccgcatggagcatccccaaagaatgcagcacccctgcatggagcacctttgaatgcagcatcccgaaggagtgcagcatccccgcacgggctgtccctgcatgcatcgccctcagggtgtggaggacctttgcatgcagcgtccctgcttggagcggccctgcacggcgcatccccaggacgtgcagcgtctctgcatggtgcatccctaaggaacgcagcgtccctgcagagcattcccagtggttgcagcatcgctgcacggcgcatccctcaggactgcagcagccttgcaatccctgcatccctgcactctgcaccccagcttggagcatcccccccgcggcgcatccctgcagcacagcccatccctgcgcgctgcagctctgcgtggaccacccttgtggtgttgagcgctgcacctgcagcatgcagcgcccttgcaacacattgtgacgccttttgcaccgctgagcacctttgcagctggttggtatggatgcacctctgcagcacagagcgtgcacccagcacagagcatccttgcaacgtgttgcaacgcacccttgcggcacagagcaccgttgcagcatggagcacctttgcagctgcttggcatgcagctctgcagggtggagcacgcatccagcacggagcagccttgcaagctgttgcactgcacccttgcagcacagagcatcgttgcagtgcagtgcatcgctgcacaaactgacgttgccccccttcttcccccccccccccattgcagctccgcagcggaggagagcgcagaggagaggaaaaggctttaaaaacaaacaaacaaaaggaattaatcataattaaaacaaagtgcaaacgaa

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