LOCUS       NM_001159586            1351 bp    mRNA    linear   VRT 09-APR-2020
DEFINITION  Danio rerio LIM homeobox 2a (lhx2a), mRNA.
ACCESSION   NM_001159586 XM_001335385
VERSION     NM_001159586.2
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
REFERENCE   1  (bases 1 to 1351)
  AUTHORS   Pasquier J, Cabau C, Nguyen T, Jouanno E, Severac D, Braasch I,
            Journot L, Pontarotti P, Klopp C, Postlethwait JH, Guiguen Y and
            Bobe J.
  TITLE     Gene evolution and gene expression after whole genome duplication
            in fish: the PhyloFish database
  JOURNAL   BMC Genomics 17, 368 (2016)
   PUBMED   27189481
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1351)
  AUTHORS   O'Quin KE, Yoshizawa M, Doshi P and Jeffery WR.
  TITLE     Quantitative genetic analysis of retinal degeneration in the blind
            cavefish Astyanax mexicanus
  JOURNAL   PLoS ONE 8 (2), e57281 (2013)
   PUBMED   23437360
REFERENCE   3  (bases 1 to 1351)
  AUTHORS   Miyasaka N, Morimoto K, Tsubokawa T, Higashijima S, Okamoto H and
            Yoshihara Y.
  TITLE     From the olfactory bulb to higher brain centers: genetic
            visualization of secondary olfactory pathways in zebrafish
  JOURNAL   J. Neurosci. 29 (15), 4756-4767 (2009)
   PUBMED   19369545
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BX470252.10.
            
            On Jun 25, 2015 this sequence version replaced NM_001159586.1.
            
            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 transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: FJ749249.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2168446, SAMEA2168447
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-275               BX470252.10        50563-50837
            276-460             BX470252.10        51955-52139
            461-801             BX470252.10        56771-57111
            802-989             BX470252.10        59005-59192
            990-1351            BX470252.10        65008-65369
FEATURES             Location/Qualifiers
     source          1..1351
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="21"
                     /map="21"
     gene            1..1351
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="LIM homeobox 2a"
                     /db_xref="GeneID:795283"
                     /db_xref="ZFIN:ZDB-GENE-091118-109"
     exon            1..275
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    165..167
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="upstream in-frame stop codon"
     CDS             258..1241
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="LIM homeodomain protein 2a"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx2a"
                     /protein_id="NP_001153058.2"
                     /db_xref="GeneID:795283"
                     /db_xref="ZFIN:ZDB-GENE-091118-109"
                     /translation="

MENNESGSDAPVCAGCGALISDRFYLLAAERRWHERCLKCSACQTDLESELTCFSKHGDIYCKEDYYRRFSSQRCARCHLGISATEIVMRARDLVYHLSCFSCATCHKVLLTGDHYGMKETSVYCRAHIQRECHADLYYSDMSSRETNSESHTYDEESPVHRARVRRRKNNSTADHIAYSSDVSDLGVDLSERVSCQKSKRMRTSFKHHQLRSMQSFFTHNHNPDAKDLKELAQKTGLTKRVLQVWFQNARAKFRRNCLYQESIGVDNVSDNSTLTSPSVPSPELCHGSMSPSSPSGTSPSQHTPSAARNTHSPVFSGFLLKTAFDY"

     misc_feature    294..455
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="LIM is a small protein-protein interaction domain,
                     containing two zinc fingers; Region: LIM; cl02475"
                     /db_xref="CDD:413332"
     misc_feature    order(294..296,303..305,357..359,366..368,375..377,
                     384..386,441..443,450..452)
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:259829"
     misc_feature    468..644
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="The second LIM domain of Lhx2 and Lhx9 family;
                     Region: LIM2_Lhx2_Lhx9; cd09377"
                     /db_xref="CDD:188763"
     misc_feature    order(480..482,489..491,546..548,555..557,564..566,
                     573..575,630..632,639..641)
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188763"
     misc_feature    order(855..869,873..875,924..926,942..944,981..983,
                     987..992,999..1004,1008..1016,1020..1025)
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(861..863,870..872,990..992,999..1004,1011..1013)
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    864..1022
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            276..460
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /inference="alignment:Splign:2.1.0"
     exon            461..801
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /inference="alignment:Splign:2.1.0"
     exon            802..989
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /inference="alignment:Splign:2.1.0"
     exon            990..1351
                     /gene="lhx2a"
                     /gene_synonym="si:dkey-261o10.1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ctgcacacagcaacaacccgcgggaacctgctgctgcaaacaaactctcggactgcactttatctagactggaaatttggtcaattaaaagttagatagctcttttaacggtattagttgcagatagataaataggctagatacatagacctcgagcacatggataatctcctctttggagacttttcatttttctgaggaaaattacagacattcatccttgtgcggcaagaaaggagttattttctctatatcacatggaaaacaatgaatcaggcagtgatgcgccggtgtgcgcgggctgcggcgcactgatctcagatcggttctacctgctcgcggctgaaaggcgctggcacgagcgctgtttaaagtgcagcgcatgtcaaactgacctggagtcagagctcacctgcttcagcaaacacggagacatttactgtaaggaggactattacaggaggttttcttcgcagagatgtgcgcggtgccacctgggaatctctgccacagagatagtgatgcgcgccagggatctggtctaccacctgagctgcttctcttgtgccacctgccataaagtgctgctcaccggagatcactacgggatgaaggagacgtctgtgtactgtcgagcacacatccagagagaatgtcatgcagatttgtattattcagacatgtcttctagagagacaaattctgagagtcacacatatgatgaagaaagccccgtgcacagagcacgagtccggaggaggaaaaataacagtacagctgatcatattgcatatagttcagatgtgagtgatttgggtgtggatctgtcggaaagagtgagctgtcaaaagtccaaacgcatgagaacgtcgttcaagcatcaccagctgagaagcatgcagtccttcttcacacacaaccacaatccagatgccaaagacctcaaagagctcgcccagaaaactggcctcaccaaacgtgtgctccaggtttggttccagaatgcccgtgcaaaattcagaagaaactgtctatatcaggagagcattggggtggacaatgtttcagacaattccaccctcacgtctccatctgtgccttcacctgagctgtgccacggatccatgagcccgtccagccccagcgggacctcgccatcccaacacacaccatcagccgctcgcaacacacactctcctgtcttctctggcttcctcctaaaaacagcttttgattattagtatatcagcatattggccaagtcaattgagctttattgtcattcctacatgtgaaaatgtgtctcacaggaatttgaagctgcataattaaacataatcataattataaa

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