LOCUS       NM_001397359            3204 bp    mRNA    linear   VRT 14-FEB-2025
DEFINITION  Gallus gallus LIM homeobox 1 (LHX1), mRNA.
ACCESSION   NM_001397359 XM_015295682
VERSION     NM_001397359.1
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 3204)
  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 3204)
  AUTHORS   Shirazi Fard,S., All-Ericsson,C. and Hallbook,F.
  TITLE     The heterogenic final cell cycle of chicken retinal Lim1 horizontal
            cells is not regulated by the DNA damage response pathway
  JOURNAL   Cell Cycle 13 (3), 408-417 (2014)
   PUBMED   24247150
  REMARK    GeneRIF: DNA damage response pathway is functional in the Lim1
            horizontal progenitor cells, but that it is not directly involved
            in the regulation of the final cell cycle that gives rise to the
            heteroploid horizontal cell population.
REFERENCE   3  (bases 1 to 3204)
  AUTHORS   Inoue,J., Ueda,Y., Bando,T., Mito,T., Noji,S. and Ohuchi,H.
  TITLE     The expression of LIM-homeobox genes, Lhx1 and Lhx5, in the
            forebrain is essential for neural retina differentiation
  JOURNAL   Dev Growth Differ 55 (7), 668-675 (2013)
   PUBMED   24024588
  REMARK    GeneRIF: Results suggest that Lhx1 and Lhx5 in the forebrain
            regulate neural retina differentiation by suppressing the
            development of the retinal pigment epithelium, before the formation
            of the optic vesicle (OV).
REFERENCE   4  (bases 1 to 3204)
  AUTHORS   Kawaue,T., Okamoto,M., Matsuyo,A., Inoue,J., Ueda,Y., Tomonari,S.,
            Noji,S. and Ohuchi,H.
  TITLE     Lhx1 in the proximal region of the optic vesicle permits neural
            retina development in the chicken
  JOURNAL   Biol Open 1 (11), 1083-1093 (2012)
   PUBMED   23213388
REFERENCE   5  (bases 1 to 3204)
  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   6  (bases 1 to 3204)
  AUTHORS   Fukui,A., Yokoo,T., Matsumoto,K., Kawamura,T., Hosoya,T. and
            Okabe,M.
  TITLE     Integration of human mesenchymal stem cells into the Wolffian duct
            in chicken embryos
  JOURNAL   Biochem Biophys Res Commun 385 (3), 330-335 (2009)
   PUBMED   19450546
REFERENCE   7  (bases 1 to 3204)
  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 LHX1 in the diencephalon during
            chick development is reported.
REFERENCE   8  (bases 1 to 3204)
  AUTHORS   James,R.G. and Schultheiss,T.M.
  TITLE     Patterning of the avian intermediate mesoderm by lateral plate and
            axial tissues
  JOURNAL   Dev Biol 253 (1), 109-124 (2003)
   PUBMED   12490201
REFERENCE   9  (bases 1 to 3204)
  AUTHORS   Sockanathan,S. and Jessell,T.M.
  TITLE     Motor neuron-derived retinoid signaling specifies the subtype
            identity of spinal motor neurons
  JOURNAL   Cell 94 (4), 503-514 (1998)
   PUBMED   9727493
REFERENCE   10 (bases 1 to 3204)
  AUTHORS   Tsuchida,T., Ensini,M., Morton,S.B., Baldassare,M., Edlund,T.,
            Jessell,T.M. and Pfaff,S.L.
  TITLE     Topographic organization of embryonic motor neurons defined by
            expression of LIM homeobox genes
  JOURNAL   Cell 79 (6), 957-970 (1994)
   PUBMED   7528105
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000323.1.
            
            On Nov 9, 2021 this sequence version replaced XM_015295682.3.
            
            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.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13267662.26010.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992393, SAMEA103992482
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-748               JAENSK010000323.1  8375474-8376221
            749-975             JAENSK010000323.1  8377032-8377258
            976-1253            JAENSK010000323.1  8377362-8377639
            1254-1419           JAENSK010000323.1  8377994-8378159
            1420-1820           JAENSK010000323.1  8378542-8378942
            1821-3204           JAENSK010000323.1  8379020-8380403
FEATURES             Location/Qualifiers
     source          1..3204
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="19"
                     /map="19"
     gene            1..3204
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="LIM homeobox 1"
                     /db_xref="CGNC:4028"
                     /db_xref="GeneID:396381"
     exon            1..748
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    567..569
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="upstream in-frame stop codon"
     CDS             579..1799
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="domesticus (clone 2.3 kB) lim-1; LIM homeobox
                     protein 1; homeobox protein Lim-1"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx1"
                     /protein_id="NP_001384288.1"
                     /db_xref="CGNC:4028"
                     /db_xref="GeneID:396381"
                     /translation="

MVHCAGCKRPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRCFGTKCAGCAQGISPSDLVRRARSKVFHLNCFTCMMCNKQLSTGEELYIIDENKFVCKEDYLNNSNTAKENSLHSATTGSDPSLSPDSQDPSQDDAKDSESANVSDKETGSNENDDQNLGAKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRMKQLSALGARRHAFFRSPRRMRPLVDRLEPGELLPNGPFSFYGDYQSEYYGPGGNYEFFPQGPPSSQAQTPVELPFGAAGGPPGTPLGALEHPLPGHHPPGEAQRFPDMLAHPAGDSPSPEPTLPGSLHSMSAEVFGPSPPFSSISVNGGANYGNHLSHPPEMNEAAVW"

     misc_feature    588..743
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="The first LIM domain of Lhx1 (also known as Lim1)
                     and Lhx5; Region: LIM1_Lhx1_Lhx5; cd09367"
                     /db_xref="CDD:188753"
     misc_feature    order(588..590,597..599,651..653,660..662,669..671,
                     678..680,729..731,738..740)
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188753"
     misc_feature    765..932
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="The second LIM domain of Lhx1 (also known as Lim1)
                     and Lhx5; Region: LIM2_Lhx1_Lhx5; cd09375"
                     /db_xref="CDD:188761"
     misc_feature    order(765..767,774..776,831..833,840..842,849..851,
                     858..860,918..920,927..929)
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188761"
     misc_feature    951..1139
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="propagated from UniProtKB/Swiss-Prot (P53411.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1119..1289
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    1464..1694
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /note="propagated from UniProtKB/Swiss-Prot (P53411.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            749..975
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /inference="alignment:Splign:2.1.0"
     exon            976..1253
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1254..1419
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1420..1820
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1821..3204
                     /gene="LHX1"
                     /gene_synonym="LIM-1; LIM-homeobox; LIM1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcacggacggcggccccgctccgcgccgctcgggccatggcaccgcggctgcagcctgcgcccgtctgaccgcgggcggcccgatgccctgcgcccgcgctgtcctcgtcttgtcgtctttttttttgctttttgctttttttgcttttttttcttttccctcctttaatttctgtttgggaaaagcagatgcactttgactcctgactgctctacctcagacctgagaacaaactcgtcacgcttctcggcggttttttgattatcgccggtttcgttttatctgagcgccgatttctgcgccgccgcgcgtcggcctcagccgggccgggcccgggacccgcggccctgggacagcgaccgaccgaaggcttctctccctcccgtcctttttcttctcttccgcttttccaaggcttttttttttttttaatattaatattaacaataacaacatacacacataaaaaaaaaaaaaagcaaacccacgccgctgttgtcgtctttttgtttttatttcgatttttcgcttgccatctgggacgccgataccccactctcagaaataaccaaagacaatggttcactgtgcgggctgcaaaaggccaatcttggaccggttcttgttgaatgtactggacagggcttggcatgtgaagtgtgttcagtgctgtgaatgtaaatgcaatttgacagagaaatgcttttcgcgagaaggcaagctttactgcaaaaacgacttctttcggtgtttcgggaccaagtgtgcgggctgtgcccagggcatctcccccagcgacctggtccgcagggcgcggagcaaagtgttccacttgaactgttttacgtgtatgatgtgcaacaagcagctctccaccggcgaggagctctatatcatagacgaaaacaagttcgtctgcaaagaagattacctaaataacagcaatactgccaaagaaaacagcctgcattcagctaccaccggcagtgaccccagcctgtcccccgactcccaagacccctcccaggacgacgccaaggactcggaaagcgccaacgtgtccgacaaggagacgggcagcaacgagaacgacgaccagaacctgggggccaagcggcgggggccccgcaccaccatcaaagccaaacagctagagactctgaaggccgccttcgcggccacccccaaacccacgcggcacatcagggagcagctggcgcaggagaccggcctcaacatgcgcgtcatccaggtgtggttccagaaccgccgctccaaggagcgccgcatgaagcagctgagcgcgctgggcgcccgccggcacgccttcttccgcagcccgcgcaggatgcggccgctggtggaccgcctggagcccggcgagctgctccccaacgggcccttctccttctacggagattaccagagcgagtactacggccccgggggcaactacgagttcttcccgcaaggcccgccctcctcgcaggcgcagacgccggtggagctgccgttcggggcggcgggcggaccgccgggcacgccgctgggcgcgttggagcacccgctgcccgggcaccacccgcccggagaggcgcagcgcttccccgacatgctggcgcaccccgccggggactcgcccagccccgagcccaccctgcccggctccctgcactccatgtccgcggaagtgttcggccccagtcctccgttctcctcgatatccgtcaacggcggtgctaactacggcaatcacttgtcacacccaccagaaatgaacgaagcggctgtgtggtagctttaagcgaactgggtctaaacaatgtcacctcgggaacgaactgcgcccggcggctccgagcggagcgctgctgcagagcgggacgatcccggtgtgcgtttgtcaccgacacggggacctgcgtgtgccatgacaaaggaactggtgaagctgtacagtaacgcgccgccgcgccgtgggatggcgtgagtgtggttaccccgtcggatgtcaccccgagagccacaatccttaggaactcctcgtttagaaaaaaaaacaaacagtgattgaatggcggaaaggtgaaaggaaagggggaaaagctgcaagaactctgagcgctcccgataaggatggttctggcgttccgcatttgtttgttcatttttctctctcaaagttcaaccacgagaaactctttagcttcagccattgcagcctgctgagcaccaggtgggacaacttttctttctccttttttttttttctcctttgttgttttttttccggttgttgttttcttcttttgtttccctccccaaataacgaatactaaatgttgagccctcggcaccaactcttctaccttcacaatgctacacatacaaaacctcctcatcatagcaaaggtcgccgtcggacctctaaggcgaatgacttgaaaagaaaaaaaaaatacaaaaaaaaaaaaaaccacaaaaaaacaaacgaacaaaaagcattctaccttcacaaagagagcgaagcaaaacgaaaagactctattgaactaaaacagtcaactgtttacgtctaacgttaaattcaggagctcgatgttttactaacaaatcctgttttagaacctcttgttcgaaagcaaaatattttgagcagccaaccaaaatagttccttttcttttctgtagatgtacaaagcgatcgcagggcttgtggttcactgtgctagtttgtcaaaggtgttgtttacagaaggcaaagagaaacccgcgaatcccagaccgttgccaaataaagggaatctatagcacaaatactgtcaggtgctccgcaccagcaacccggagaggcgtttccaaatgtcacaaggttaaaaccagaacagaacgaacatctttgctgatttttagtcctgttgaacattcatggaattgttaatatgacttatatagacccacacaggttttatttttgtgtctttaaaatgaaagtccaaaatatttaaattttatggtcaaatatgcagtcgacagctgctacttttttctttatatattaaatttctcatatgtcttttattgttcgaataaacctaagcttgtgtgacctccagtgcatattagaccattcactgtatgaaagaaaacatgttggataaaaatttgtgcgtttttaataaaattagaaaatgggacgttta

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