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2024-07-24 00:25:39, GGRNA.v2 : RefSeq release 224 (May, 2024)

LOCUS       NM_204162               5479 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus ALX homeobox 4 (ALX4), transcript variant 1, mRNA.
ACCESSION   NM_204162
VERSION     NM_204162.2
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 5479)
  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 5479)
  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.
            
            On Dec 6, 2021 this sequence version replaced NM_204162.1.
            
            ##Evidence-Data-START##
            CDS exon combination :: SRR13267655.181035.1, AF092538.1
                                    [ECO:0000331]
            RNAseq introns       :: mixed sample support SAMEA103992393,
                                    SAMEA103992470 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            inferred exon combination :: based on alignments, homology
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-56                JAENSK010000214.1  15395947-15396002   c
            57-458              JAENSK010000214.1  15394464-15394865   c
            459-769             JAENSK010000214.1  15374961-15375271   c
            770-898             JAENSK010000214.1  15371154-15371282   c
            899-5479            JAENSK010000214.1  15366237-15370817   c
FEATURES             Location/Qualifiers
     source          1..5479
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="5"
                     /map="5"
     gene            1..5479
                     /gene="ALX4"
                     /note="ALX homeobox 4"
                     /db_xref="CGNC:48987"
                     /db_xref="GeneID:373976"
     exon            1..56
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    29..31
                     /gene="ALX4"
                     /note="upstream in-frame stop codon"
     exon            57..458
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     CDS             59..1222
                     /gene="ALX4"
                     /note="isoform 1 is encoded by transcript variant 1;
                     aristaless-like homeobox 4; homeobox protein
                     aristaless-like 4"
                     /codon_start=1
                     /product="homeobox protein aristaless-like 4 isoform 1"
                     /protein_id="NP_989493.1"
                     /db_xref="CGNC:48987"
                     /db_xref="GeneID:373976"
                     /translation="
MNADTCVSYCDPAAMDSYYNAASQGADGSSPFRAFQASDKFGPAFLAAKGQSFGDSGAKCRSRYSPQECPSLDGSGQAPGPAAPPPAFSKYPQPQQQPPHLYMQRGPCKTPPESNLKLQESGGHNGALQVSCYGKESSLGEADLQPNADPSGMDSSYLSVKEAGVKVPQDRASTDLPSPMDKADSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQMQQVRTHFSTAYELPLLTRAENYAQIQNPSWIGNNGAASPVPACVVPCEPVPSCMSPHAHPHAAGGVSDFLGVSSTGGHVGQTHVGGLFGTAGIGPSLNGYELNSEPDRKSSSIAALRMKAKEHSAAISWAT"
     misc_feature    635..805
                     /gene="ALX4"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    1145..1201
                     /gene="ALX4"
                     /note="OAR motif; Region: OAR; pfam03826"
                     /db_xref="CDD:461067"
     exon            459..769
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     exon            770..898
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
     exon            899..5479
                     /gene="ALX4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
gactgaagaactgtggatgcagtttgcgtaatatctttattaccgagaacttcaaggaatgaatgctgatacttgtgtttcttattgtgatccggctgccatggattcctactacaacgcagcctcccagggcgcagacggctcctcgccttttagggcatttcaagcgagtgacaagttcggccccgctttcctggccgccaaaggacagagcttcggtgacagcggcgcgaagtgccggagccgctacagcccgcaggaatgcccgtccctggacggcagcgggcaggcgccgggccccgccgcgcccccgcccgcctttagcaaatacccgcagccccagcagcagccgccgcacctctacatgcagcgcggcccctgcaagacccccccggagagcaacctcaagctgcaggagagcggcggccacaacggagccctgcaggtctcctgttacggtaaggagagcagcttgggagaggctgacttgcagcccaacgccgacccctcgggcatggacagcagctacctcagcgtgaaggaggctggagtgaaagtccctcaggacagggccagcacggacctccccagccccatggacaaggcggactcggagagcaacaagggcaaaaaacggaggaaccgcaccaccttcaccagctaccagctggaggagctggagaaggtcttccagaagacccactacccagatgtctatgccagggagcagctagccatgaggacagacctcaccgaggcccgagtacaggtctggttccagaatcgacgagccaaatggcgcaagcgggagcggtttggccagatgcagcaggtccggacccacttctccactgcctacgagttgcctctgctcactcgtgctgagaactatgcccaaatccagaacccctcttggattggcaacaatggagccgcctcccctgtgcctgcttgtgttgtcccctgcgagccggtgccctcctgcatgtccccccacgcgcatccccacgcggctggtggtgtctccgacttcctcggtgtctctagcactggcggccacgtgggccagactcacgtgggtggcctctttggtacggccggcattggccccagcctcaacggctacgagctgaacagcgagccggaccgcaagagctccagcatcgcggccctgcggatgaaggcgaaggagcacagcgccgcgatctcctgggcgacatgacagggctgccgcccagcgcctcggcacaccacgagagccagtggggaagctgggagaccgtcctgccgggactccagccagcccttgcctcctcggggatgtgaacgcagcactttgagctaccctaggtgtatagaggacgtgtgttaacgtaagtggcgtgtgcccagcatggacgtgggaggtcctggcctcctggcactgggtcagggctgtggggcagcactgctgccacctgctctgggggtgtcctctgctatcgccactgcctcccctgggacttggatgcctttcctccccacgcctttttctgacaccagatctgccttcccggagagtaagagcccccccagcatctccagctcttccctcctcagaacccatctgccttgggcaggggacaggacggggactctggcaccagcaaagagacgctcttcaggttgctcctgcctcgtgggagccatggctgaacggggtgaggggatacccgaggccagaacggtggcagtgctatcccacctccttccacccagcaggaggtgaagcacggagcttaggggcctcttgtgtgggcacagtgcaaccacactgctgtccttgatggttctccagccatccagctcaagatatgcatatgaaatgatggctgcctggccctactgccaccttgcagaaggtcacaaccatatgggcactcggagtttgctctgttacagttgtagctgttgtgctgtagcaaaacatgttccctgtcttttacagggccaggagtcaccaccctcaggtcccccagggaccccaaagaggaacagcttgagtggagcacagagccagggctgtatgagggcatcctcacataacctatcattccctgcttccccaaaaccacctacccacaagaggaaggggagagctagggagtggggatagtagcatggtcccatctctgcatgttccactcctcccctcacctagcacagagaaggaaacaccaaaacttgttttctctcctgaagtcccacccatggttttccccccacatgctcccacttgcacagctgtgttaagtacagtctcctctacaaggccaaacctctctcaagccattcaatggtgtcatggcatcaaggataattgcagagtttccttttgccccaccaaaggtcaccagcagccatagcacacatgctgagttccaccttggtaagcaagagaagtgcagggttttgccccttacagccatcccctcacaccccatccactcaaggtgcagggagatctagcggccctgtaatgggctgcaaacaggctacaaccaaatgtcacgatgcaggtgaactgcataccatataaaaatatttctacagtgcctaaacattgccatacacaacacagatgattacatcaatgctagatcaaatgtaacacatacttattggaatatgggaagacccgtggtgctgtatcttgtctctctgtaaatacaccgagatgcctggctcagtgcacctcgcaacaacatgcagtcaagcagactatgcggatgacctgggcttttccacagaagcaaaccagactcacgttccagcctgaacgttcagctgagttatcagactaaaatgtgcttcaggtgctaaaaatgatgccgattaccgaatagctctggatcactgccctaatctctctcttctgcatgcactggcaataatgttaccgtttaaattgcagtgaataccaccatttaccttaccccagacttcctcgcccaaagctcttttcccacaatgcagagggaaaggcgcttttccaccacggcgctcagcctcccagaactcagcagtgcagcaggttgagagggtgcatgggatggatgcagcaagggcgtgagtactgctggctgtcccactgggtggccatggccatgctggggctttgctgcactctactgaagctgaagggcgttccttcctccactctcacagggccaggatttcacccaggctgcataacggctcacgagatgaagagctgcatcctctcctcctcatgcattggcctctgacaaccctaatcactgccagatgtgcccagtgctgagctgctgggtgcactgcaagtgcagagctctgctcccatgccccactctgctgccattcaccagcatagcccttctgcatctgccgtcctgctgcatcgtcctgccagcaacagcctgggcatgcagcgatgcaggcaggtcttcagctgtgtgcatctgcagttacacacatttttaaaattaatttaatagttaaaaaaacaaaaacaaacaagctagttgttaaattaacaagaaaagctgtataaatatatatatatatatacacacacttagatatatatgcgtgtgtgtgtgtatatatatatatacatatacatatatatatatatacacacataaatatatgtgtgtgtatatatatatatatatatatatacatatcttaacctagccaacctgcagctactgcatttttaagggtcacagggtcagtgctgttcttgcaatttcaagctaccacaaggatgcctttttaaataagaattattattattattttaatacttttcaattctatttatgtctttcttctctatttatttcttctttagtatttcactcctgtccatacatggtgttgcagttccctggctgggatttagatgcctgtgaagctgcaagtttcgcacctccccccccccagccgtgctgtatcctgcatggtgcagcacagcagccccagcaccctgagctcccttgctcccaagatgccctttccagccttgcagagggagcaaaggaggctgtcttgcattacccagggctggaaacacacaagacatcccagattttggggctaggaaaggcaagcagggagagcagcacagttcctaatgggggctgaccggtagccgggtgctgcttgctgccaagtgctcagagcagctgtgcatgcattggcagcatctgcaaaccagcggtgaacatcccacggctcccccggttgctgtcccctcagccctttaactcctccgagcatctcctgctgtgcgtgctggagcacagctggcctgagatacgggcaggggcaccgcagtaaaaacacccgcacggacacccactgtgcatgaagcggcagagctgctgcacacgtgcgtggcaccccctgcagcactcccctggggagcgggatgtgggggccctttggctgcagagggtggggaggccgggtcccatcgcacagagcagagcagcgccttgtcaaacgttctccaaacaaacaaaagccaaaaaggtagtttcctggaaaaggatttaaaaaacaatcaggcagacacagagatctgtgtttattttgctgcactgactgacacaacagaaagcaaacagaccgaattagaaattaaacccaaatgggaacagggggaggaatcgggctgaaagtcatccccagcccttgctgggcccgaggaggcagcccagcgcagcctggcaccccgctagctctttgctggtgccccactcactcccccatcgctaggtaggtaggtagagctaggacttttgtactactgattttttgaaggacagttttcaatgtgtaataatatatcggtttaggtgtgcagtgtttgaaagagagactgggagaaagaaagaaaacaaacctcaatcaatagtattgtttttgttgtaagatattgtaaccttgtataaacgcaaacattttcttttcctttagcttaaaggcctggggtagaacgtattcaaacaaacgaaaaaggttttaaaagttcaggaaattaaaaaaaaaaaaaagaattaaaaaaaaaatcatttaaaacattgccacgtgaggtttgtgccatgcaatgttaatgcctatgcagccatgtattagcagttcattacagtggaacattaaaaaaaaacaaaagaacaaacagacttgcagcttggtcctttccatgtttttttcaaagtaagttattgcacttgcagcttcctttcttttgtttgttcgtttgtttgtttggggggaggggagggctgggatttctgggcactactttttctttttccagttttttaaaggggtgcaattgctgggaaggccccccgctcccgaggccccgtggccacggaggtacaagcactgttgttgttgttttggtttgcaataaactccttctcttctctcctctcaactggaa
//

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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]