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2024-07-23 22:39:50, GGRNA.v2 : RefSeq release 224 (May, 2024)

LOCUS       NM_001397959            5239 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus ALX homeobox 4 (ALX4), transcript variant 3, mRNA.
ACCESSION   NM_001397959
VERSION     NM_001397959.1
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 5239)
  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 5239)
  AUTHORS   Takahashi M, Tamura K, Buscher D, Masuya H, Yonei-Tamura S,
            Matsumoto K, Naitoh-Matsuo M, Takeuchi J, Ogura K, Shiroishi T,
            Ogura T and Izpisua Belmonte JC.
  TITLE     The role of Alx-4 in the establishment of anteroposterior polarity
            during vertebrate limb development
  JOURNAL   Development 125 (22), 4417-4425 (1998)
   PUBMED   9778501
  REMARK    Erratum:[Development 1998 Dec;125(23):preceding 4595]
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000214.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13267655.245657.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN02738227 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-218               JAENSK010000214.1  15391299-15391516   c
            219-529             JAENSK010000214.1  15374961-15375271   c
            530-658             JAENSK010000214.1  15371154-15371282   c
            659-5239            JAENSK010000214.1  15366237-15370817   c
FEATURES             Location/Qualifiers
     source          1..5239
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="5"
                     /map="5"
     gene            1..5239
                     /gene="ALX4"
                     /note="ALX homeobox 4"
                     /db_xref="CGNC:48987"
                     /db_xref="GeneID:373976"
     exon            1..218
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    92..94
                     /gene="ALX4"
                     /note="upstream in-frame stop codon"
     exon            219..529
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     CDS             275..982
                     /gene="ALX4"
                     /note="isoform 2 is encoded by transcript variant 3;
                     aristaless-like homeobox 4; homeobox protein
                     aristaless-like 4"
                     /codon_start=1
                     /product="homeobox protein aristaless-like 4 isoform 2"
                     /protein_id="NP_001384888.1"
                     /db_xref="CGNC:48987"
                     /db_xref="GeneID:373976"
                     /translation="
MDSSYLSVKEAGVKVPQDRASTDLPSPMDKADSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQMQQVRTHFSTAYELPLLTRAENYAQIQNPSWIGNNGAASPVPACVVPCEPVPSCMSPHAHPHAAGGVSDFLGVSSTGGHVGQTHVGGLFGTAGIGPSLNGYELNSEPDRKSSSIAALRMKAKEHSAAISWAT"
     misc_feature    395..565
                     /gene="ALX4"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    905..961
                     /gene="ALX4"
                     /note="OAR motif; Region: OAR; pfam03826"
                     /db_xref="CDD:461067"
     exon            530..658
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     exon            659..5239
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
gcggcgccagcggagcggggacggaggaaggaggacggaacctcggggaggagaagggcgagcggccgcgccggcgctctccttccctcaatagggtcaacggatccgccgcgcagggagaggagggagctcccgccgggagtcgggccgaggcgctcggcggtgcggggcctcctccgcgggagctgcgggaccccctcgggcagcggcacgccaaggtaaggagagcagcttgggagaggctgacttgcagcccaacgccgacccctcgggcatggacagcagctacctcagcgtgaaggaggctggagtgaaagtccctcaggacagggccagcacggacctccccagccccatggacaaggcggactcggagagcaacaagggcaaaaaacggaggaaccgcaccaccttcaccagctaccagctggaggagctggagaaggtcttccagaagacccactacccagatgtctatgccagggagcagctagccatgaggacagacctcaccgaggcccgagtacaggtctggttccagaatcgacgagccaaatggcgcaagcgggagcggtttggccagatgcagcaggtccggacccacttctccactgcctacgagttgcctctgctcactcgtgctgagaactatgcccaaatccagaacccctcttggattggcaacaatggagccgcctcccctgtgcctgcttgtgttgtcccctgcgagccggtgccctcctgcatgtccccccacgcgcatccccacgcggctggtggtgtctccgacttcctcggtgtctctagcactggcggccacgtgggccagactcacgtgggtggcctctttggtacggccggcattggccccagcctcaacggctacgagctgaacagcgagccggaccgcaagagctccagcatcgcggccctgcggatgaaggcgaaggagcacagcgccgcgatctcctgggcgacatgacagggctgccgcccagcgcctcggcacaccacgagagccagtggggaagctgggagaccgtcctgccgggactccagccagcccttgcctcctcggggatgtgaacgcagcactttgagctaccctaggtgtatagaggacgtgtgttaacgtaagtggcgtgtgcccagcatggacgtgggaggtcctggcctcctggcactgggtcagggctgtggggcagcactgctgccacctgctctgggggtgtcctctgctatcgccactgcctcccctgggacttggatgcctttcctccccacgcctttttctgacaccagatctgccttcccggagagtaagagcccccccagcatctccagctcttccctcctcagaacccatctgccttgggcaggggacaggacggggactctggcaccagcaaagagacgctcttcaggttgctcctgcctcgtgggagccatggctgaacggggtgaggggatacccgaggccagaacggtggcagtgctatcccacctccttccacccagcaggaggtgaagcacggagcttaggggcctcttgtgtgggcacagtgcaaccacactgctgtccttgatggttctccagccatccagctcaagatatgcatatgaaatgatggctgcctggccctactgccaccttgcagaaggtcacaaccatatgggcactcggagtttgctctgttacagttgtagctgttgtgctgtagcaaaacatgttccctgtcttttacagggccaggagtcaccaccctcaggtcccccagggaccccaaagaggaacagcttgagtggagcacagagccagggctgtatgagggcatcctcacataacctatcattccctgcttccccaaaaccacctacccacaagaggaaggggagagctagggagtggggatagtagcatggtcccatctctgcatgttccactcctcccctcacctagcacagagaaggaaacaccaaaacttgttttctctcctgaagtcccacccatggttttccccccacatgctcccacttgcacagctgtgttaagtacagtctcctctacaaggccaaacctctctcaagccattcaatggtgtcatggcatcaaggataattgcagagtttccttttgccccaccaaaggtcaccagcagccatagcacacatgctgagttccaccttggtaagcaagagaagtgcagggttttgccccttacagccatcccctcacaccccatccactcaaggtgcagggagatctagcggccctgtaatgggctgcaaacaggctacaaccaaatgtcacgatgcaggtgaactgcataccatataaaaatatttctacagtgcctaaacattgccatacacaacacagatgattacatcaatgctagatcaaatgtaacacatacttattggaatatgggaagacccgtggtgctgtatcttgtctctctgtaaatacaccgagatgcctggctcagtgcacctcgcaacaacatgcagtcaagcagactatgcggatgacctgggcttttccacagaagcaaaccagactcacgttccagcctgaacgttcagctgagttatcagactaaaatgtgcttcaggtgctaaaaatgatgccgattaccgaatagctctggatcactgccctaatctctctcttctgcatgcactggcaataatgttaccgtttaaattgcagtgaataccaccatttaccttaccccagacttcctcgcccaaagctcttttcccacaatgcagagggaaaggcgcttttccaccacggcgctcagcctcccagaactcagcagtgcagcaggttgagagggtgcatgggatggatgcagcaagggcgtgagtactgctggctgtcccactgggtggccatggccatgctggggctttgctgcactctactgaagctgaagggcgttccttcctccactctcacagggccaggatttcacccaggctgcataacggctcacgagatgaagagctgcatcctctcctcctcatgcattggcctctgacaaccctaatcactgccagatgtgcccagtgctgagctgctgggtgcactgcaagtgcagagctctgctcccatgccccactctgctgccattcaccagcatagcccttctgcatctgccgtcctgctgcatcgtcctgccagcaacagcctgggcatgcagcgatgcaggcaggtcttcagctgtgtgcatctgcagttacacacatttttaaaattaatttaatagttaaaaaaacaaaaacaaacaagctagttgttaaattaacaagaaaagctgtataaatatatatatatatatacacacacttagatatatatgcgtgtgtgtgtgtatatatatatatacatatacatatatatatatatacacacataaatatatgtgtgtgtatatatatatatatatatatatacatatcttaacctagccaacctgcagctactgcatttttaagggtcacagggtcagtgctgttcttgcaatttcaagctaccacaaggatgcctttttaaataagaattattattattattttaatacttttcaattctatttatgtctttcttctctatttatttcttctttagtatttcactcctgtccatacatggtgttgcagttccctggctgggatttagatgcctgtgaagctgcaagtttcgcacctccccccccccagccgtgctgtatcctgcatggtgcagcacagcagccccagcaccctgagctcccttgctcccaagatgccctttccagccttgcagagggagcaaaggaggctgtcttgcattacccagggctggaaacacacaagacatcccagattttggggctaggaaaggcaagcagggagagcagcacagttcctaatgggggctgaccggtagccgggtgctgcttgctgccaagtgctcagagcagctgtgcatgcattggcagcatctgcaaaccagcggtgaacatcccacggctcccccggttgctgtcccctcagccctttaactcctccgagcatctcctgctgtgcgtgctggagcacagctggcctgagatacgggcaggggcaccgcagtaaaaacacccgcacggacacccactgtgcatgaagcggcagagctgctgcacacgtgcgtggcaccccctgcagcactcccctggggagcgggatgtgggggccctttggctgcagagggtggggaggccgggtcccatcgcacagagcagagcagcgccttgtcaaacgttctccaaacaaacaaaagccaaaaaggtagtttcctggaaaaggatttaaaaaacaatcaggcagacacagagatctgtgtttattttgctgcactgactgacacaacagaaagcaaacagaccgaattagaaattaaacccaaatgggaacagggggaggaatcgggctgaaagtcatccccagcccttgctgggcccgaggaggcagcccagcgcagcctggcaccccgctagctctttgctggtgccccactcactcccccatcgctaggtaggtaggtagagctaggacttttgtactactgattttttgaaggacagttttcaatgtgtaataatatatcggtttaggtgtgcagtgtttgaaagagagactgggagaaagaaagaaaacaaacctcaatcaatagtattgtttttgttgtaagatattgtaaccttgtataaacgcaaacattttcttttcctttagcttaaaggcctggggtagaacgtattcaaacaaacgaaaaaggttttaaaagttcaggaaattaaaaaaaaaaaaaagaattaaaaaaaaaatcatttaaaacattgccacgtgaggtttgtgccatgcaatgttaatgcctatgcagccatgtattagcagttcattacagtggaacattaaaaaaaaacaaaagaacaaacagacttgcagcttggtcctttccatgtttttttcaaagtaagttattgcacttgcagcttcctttcttttgtttgttcgtttgtttgtttggggggaggggagggctgggatttctgggcactactttttctttttccagttttttaaaggggtgcaattgctgggaaggccccccgctcccgaggccccgtggccacggaggtacaagcactgttgttgttgttttggtttgcaataaactccttctcttctctcctctcaactggaa
//

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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]