LOCUS       NM_205426               4079 bp    mRNA    linear   VRT 08-APR-2024
DEFINITION  Gallus gallus LIM homeobox 9 (LHX9), mRNA.
ACCESSION   NM_205426
VERSION     NM_205426.2
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 4079)
  AUTHORS   Tang,H., Finn,R.D. and Thomas,P.D.
  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 4079)
  AUTHORS   Burge,S., Kelly,E., Lonsdale,D., Mutowo-Muellenet,P., McAnulla,C.,
            Mitchell,A., Sangrador-Vegas,A., Yong,S.Y., 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 4079)
  AUTHORS   Avraham,O., Hadas,Y., Vald,L., Zisman,S., Schejter,A., Visel,A. and
            Klar,A.
  TITLE     Transcriptional control of axonal guidance and sorting in dorsal
            interneurons by the Lim-HD proteins Lhx9 and Lhx1
  JOURNAL   Neural Dev 4, 21 (2009)
   PUBMED   19545367
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 4079)
  AUTHORS   Sun,X., Saitsu,H., Shiota,K. and Ishibashi,M.
  TITLE     Expression dynamics of the LIM-homeobox genes, Lhx1 and Lhx9, in
            the diencephalon during chick development
  JOURNAL   Int J Dev Biol 52 (1), 33-41 (2008)
   PUBMED   18033670
  REMARK    GeneRIF: Expression dynamics of LHX9 in the diencephalon during
            chick development is reported.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000237.1.
            
            On Oct 6, 2021 this sequence version replaced NM_205426.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: L35566.1, SRR13267649.247057.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992528
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-548               JAENSK010000237.1  2295547-2296094     c
            549-751             JAENSK010000237.1  2293850-2294052     c
            752-1107            JAENSK010000237.1  2292720-2293075     c
            1108-1310           JAENSK010000237.1  2287703-2287905     c
            1311-4079           JAENSK010000237.1  2283806-2286574     c
FEATURES             Location/Qualifiers
     source          1..4079
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="8"
                     /map="8"
     gene            1..4079
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="LIM homeobox 9"
                     /db_xref="CGNC:1590"
                     /db_xref="GeneID:396397"
     exon            1..548
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    354..356
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="upstream in-frame stop codon"
     CDS             375..1568
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="homeobox protein; LIM homeobox protein 9"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx9"
                     /protein_id="NP_990757.2"
                     /db_xref="CGNC:1590"
                     /db_xref="GeneID:396397"
                     /translation="

MEIVGCRAEENTCPFRPPAMLFHGISGGHIQGIMEEMERRSKTESRLAKGGQMNGRETNMPPMSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYRRFSVQRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHFESLLQGEYPPQLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRKSPALGVDIVNYNSGCNENEADHMDRDQQPYPPSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGVDKADGTSLPAPPSADSGALTPPGTATTLTDLTNPTITVVTSVTSNLDSHEPGSPSQTTLTNLF"

     misc_feature    492..554
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90881.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    555..746
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="The first LIM domain of Lhx2; Region: LIM1_Lhx2;
                     cd09469"
                     /db_xref="CDD:188853"
     misc_feature    order(585..587,594..596,648..650,657..659,666..668,
                     675..677,732..734,741..743)
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188853"
     misc_feature    759..935
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="The second LIM domain of Lhx2 and Lhx9 family;
                     Region: LIM2_Lhx2_Lhx9; cd09377"
                     /db_xref="CDD:188763"
     misc_feature    order(771..773,780..782,837..839,846..848,855..857,
                     864..866,921..923,930..932)
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188763"
     misc_feature    1176..1346
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    1362..1463
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90881.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1506..1565
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90881.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            549..751
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /inference="alignment:Splign:2.1.0"
     exon            752..1107
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1108..1310
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1311..4079
                     /gene="LHX9"
                     /gene_synonym="LH-2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agcagtcccaaatccaacctacaggcactgggaactttaaagcaaccagggactgcttgaaaatagcacttctttttgctttctttgtattcaaaactgtatcctctcccgaccggttctgccgccccaggtccgagtctctccggtcaggagccccggctttccagaacagtaacagctcctttagctcgcttttcttctttgatttttcaaactaattattattacgttttcttccccttgtttgttttccgcacaccttcaggaagccctcggtgcttgagcaaagagaagctcctattgcaacctccttccctgtgccgtgcgcctcggtgtaaacattttggatgatctaaagactctggggtctgtatatggaaatagtggggtgcagagcagaagaaaatacttgtcctttccgtcccccagccatgcttttccacgggatctccggaggccacatccaaggaatcatggaggagatggagaggcgatccaagaccgagtcccgcctggccaaagggggacagatgaacggccgagaaacgaacatgccccccatgagccccgagaagcccgctttgtgcgctgggtgtggagggaagatctcagacagatattacctgctggctgttgacaaacaatggcacctcaggtgtcttaagtgctgtgaatgtaaactggctttggagtcagaactcacctgctttgccaaggacggcagtatttactgcaaggaggattactacagaaggttctccgtgcagagatgtgcccgctgccaccttgggatctcagcctctgaaatggtcatgagagccagggagtcggtttatcacttgagctgcttcacctgcaccacctgcaacaagactctgaccacgggcgatcactttggcatgaaggacaacctggtttactgcagggcccacttcgagtcccttttacaaggagaatacccccctcagctgagctacaccgagttggcagccaagagcggagggctggccctgccctacttcaacggcacgggcaccgtgcagaaggggaggcccaggaaacgaaaaagccctgccctgggagtggacatcgtcaactacaactcaggttgtaatgagaacgaggcagatcacatggacagagaccagcagccttatcccccatcccagaagacaaagcgcatgcgcacctccttcaaacaccaccagcttcgtaccatgaagtcctactttgctatcaaccacaacccagatgccaaggacctcaagcagcttgcccagaaaacaggcctgaccaagagagttctgcaggtttggtttcaaaacgcaagagccaaattcagaaggaaccttttgcggcaggagaatgggggtgtcgataaagcggacggcacctcacttccggcaccgccctccgcagacagcggcgctctcactccacccggcactgcgaccactttaacagacctgaccaatcccactatcactgtagtgacatcagtgacctctaacttggacagccacgaacccgggagcccctcacaaactaccttaacgaaccttttctaacattgccgttttttttttttaatttttatttttattcttactcttcttctttattattattattattattattattattattttgattattttcaagccttttttttttttaaacaaaataacaaacccacaaaatatttgggaaaataaacagcttgatgtgtagcatctgcagccacttggcaaatgagtttgaagtaatatgttgctataataaacaagcatttgttgttgataaattgtactcaaatttttttaattcatcagacaaccgaagagaagttctgaatcattctaataagtgcctcttaaaattgtatgttacttatttccacaatcttgaaagaaacatgattaccacttctactacaaagcccagaagtttcttttccctccctgataaccagataaaagtcagtataattatagacaaaagaatgctgctttcacgattgtatgttcacttccagaacccaagatttccttttatttttataatgcatctaaaagttttgtacgatttattttttaaatgtagacaaataaatacgacatggattaaatcgttgacctagtcagactgcaagtcccagtgcttctttgtaacgcgttagtgccaaggccgccccccccgggcacgctgggagccccgcggggccgagcgctgcactgcagccttgcacccagcccacaccgagggctgcagccggtgggggcctggagtggggcccatcgagcacagctgaggctgggggtccccgagctcacctctgcgagttacggagggcaagggtgggaaacgccctccggaatgagctcgctgctgtaagggtattgttagagcagagcaacagctcgaggtgggagtccctctgatctgacatatcgcacagggaggggttttcattctgctctgcagtcgaacggcacagattcagaattaaattaaaaaaaaagggcagtttgctactcggcctccatgccgtactactaaagcaaacagggggtcatccagctactctagtgagcacaaaaatgatttcaatgatgcacaagcacgtgcactgttaaaagaagcttttgataaatcacagtttttcagggaaatggaaataagcaaaatataatttattaagatgtttaaggaacatggttttagtacgacttattcattactattttgaatttaccgtagctgtttcctgagattgtatcagattctttgtttaacacaccaccttaaaatctttagttccttgctatccttaacacacgctttaccttttttttaactttgtataaaaggacaaaatgttagcaaaaattcttacaaaattgggaattggcagcggataattttaaagcagataaactcagaagccttgtggatgctgatctcaatacatttcttagtttacaatagcggactttctttttttaattttatttaagctaaaagtctgaatggtctgggcagtggtgaatgttcatttgtatccttttattgtagttgaacaccaattagattgtggagagtctcagaaacaaaaccgaacaaaaaccagtcaagatctatgtcttgcttttagtggattgttaagaataactttgcacatataccccactttttagacaccatcaaatctctttttttggtggtcaaagtggctatttaatatattttaaaggtgtcctttttggctgtataaatgtgtggttacatattgacagttcactgcccacattaaagtgcattattgtaatttttgctcagggtttttagaaaattagcacagaaaagtagcttatttttaaaaaaagatgatggaagagatgttaacactgtaatagaagaaaggtgtgtttgccattatatatttagcaagtatggttatcatcttctacggatattaaatcttgacttttcctatttctattatcttatgggcatttaccactaaccagaccaaacaaccttggtaaggctgagatctttattaatacacttttacaggtaaaaatattgatacttataaattttgttctttgacagaacaatatatggtactagagatctactttattaagtagactaattaaaactcagttctactatgtgccttatgatataccttgggagtaagtttgtgaaaaatcaggatatatgtgttgtttgttaaattaactgttttaagcccttttgacacctcactagttttgtactgttttacctcttatttctgaaactctttttatggtgtatcctgttagaggggacaaacatgtcatagaaagcagttgtgcactctttcagatatagttgataaatccaataatcttatatattgagcttcgtgtttatagtacagtaagtggtctagcaaaattgtccatgtttctttgtttattgataaatgcattgtatagaaactatttcccctaaatatttatggaccaaacaattgtgatatatcctattaaatttgtgtgaataaaccattttgaatctaa

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