LOCUS       NM_001042577            2080 bp    mRNA    linear   ROD 04-MAR-2025
DEFINITION  Mus musculus LIM homeobox protein 9 (Lhx9), transcript variant 3,
            mRNA.
ACCESSION   NM_001042577
VERSION     NM_001042577.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2080)
  AUTHORS   Oikonomakos,I., Tedesco,M., Motamedi,F.J., Peitzsch,M., Nef,S.,
            Bornstein,S.R., Schedl,A., Steenblock,C. and Neirijnck,Y.
  TITLE     In vitro differentiation of mouse pluripotent stem cells into
            corticosteroid-producing adrenocortical cells
  JOURNAL   Stem Cell Reports 19 (9), 1289-1303 (2024)
   PUBMED   39178848
REFERENCE   2  (bases 1 to 2080)
  AUTHORS   Bertho,M., Caldeira,V., Hsu,L.J., Low,P., Borgius,L. and Kiehn,O.
  TITLE     Excitatory Spinal Lhx9-Derived Interneurons Modulate Locomotor
            Frequency in Mice
  JOURNAL   J Neurosci 44 (18), e1607232024 (2024)
   PUBMED   38438260
  REMARK    GeneRIF: Excitatory Spinal Lhx9-Derived Interneurons Modulate
            Locomotor Frequency in Mice.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2080)
  AUTHORS   McCallum-Loudeac,J., Moody,E., Williams,J., Johnstone,G.,
            Sircombe,K.J., Clarkson,A.N. and Wilson,M.J.
  TITLE     Deletion of a conserved genomic region associated with adolescent
            idiopathic scoliosis leads to vertebral rotation in mice
  JOURNAL   Hum Mol Genet 33 (9), 787-801 (2024)
   PUBMED   38280229
REFERENCE   4  (bases 1 to 2080)
  AUTHORS   Cheffer,A., Garcia-Miralles,M., Maier,E., Akol,I., Franz,H.,
            Srinivasan,V.S.V. and Vogel,T.
  TITLE     DOT1L deletion impairs the development of cortical
            parvalbumin-expressing interneurons
  JOURNAL   Cereb Cortex 33 (19), 10272-10285 (2023)
   PUBMED   37566909
REFERENCE   5  (bases 1 to 2080)
  AUTHORS   Sinclair-Wilson,A., Lawrence,A., Ferezou,I., Cartonnet,H.,
            Mailhes,C., Garel,S. and Lokmane,L.
  TITLE     Plasticity of thalamocortical axons is regulated by serotonin
            levels modulated by preterm birth
  JOURNAL   Proc Natl Acad Sci U S A 120 (33), e2301644120 (2023)
   PUBMED   37549297
REFERENCE   6  (bases 1 to 2080)
  AUTHORS   Lee,K.J., Dietrich,P. and Jessell,T.M.
  TITLE     Genetic ablation reveals that the roof plate is essential for
            dorsal interneuron specification
  JOURNAL   Nature 403 (6771), 734-740 (2000)
   PUBMED   10693795
REFERENCE   7  (bases 1 to 2080)
  AUTHORS   Bertuzzi,S., Porter,F.D., Pitts,A., Kumar,M., Agulnick,A.,
            Wassif,C. and Westphal,H.
  TITLE     Characterization of Lhx9, a novel LIM/homeobox gene expressed by
            the pioneer neurons in the mouse cerebral cortex
  JOURNAL   Mech Dev 81 (1-2), 193-198 (1999)
   PUBMED   10330499
REFERENCE   8  (bases 1 to 2080)
  AUTHORS   Retaux,S., Rogard,M., Bach,I., Failli,V. and Besson,M.J.
  TITLE     Lhx9: a novel LIM-homeodomain gene expressed in the developing
            forebrain
  JOURNAL   J Neurosci 19 (2), 783-793 (1999)
   PUBMED   9880598
REFERENCE   9  (bases 1 to 2080)
  AUTHORS   Lee,K.J., Mendelsohn,M. and Jessell,T.M.
  TITLE     Neuronal patterning by BMPs: a requirement for GDF7 in the
            generation of a discrete class of commissural interneurons in the
            mouse spinal cord
  JOURNAL   Genes Dev 12 (21), 3394-3407 (1998)
   PUBMED   9808626
REFERENCE   10 (bases 1 to 2080)
  AUTHORS   Helms,A.W. and Johnson,J.E.
  TITLE     Progenitors of dorsal commissural interneurons are defined by MATH1
            expression
  JOURNAL   Development 125 (5), 919-928 (1998)
   PUBMED   9449674
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC154398.6 and BC072623.1.
            
            Transcript Variant: This variant (3) uses an alternate splice site
            in the 3' coding region, compared to variant 1. The resulting
            isoform (c) has a longer, distinct C-terminus that encodes an
            intact LIM homeodomain, compared to isoform a.
            
            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 :: SRR7345562.2318575.1, AF113518.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164138, SAMN01164139
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-635               AC154398.6         3889-4523
            636-1399            BC072623.1         649-1412
            1400-2080           AC154398.6         14709-15389
FEATURES             Location/Qualifiers
     source          1..2080
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="1"
                     /map="1 60.82 cM"
     gene            1..2080
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /note="LIM homeobox protein 9"
                     /db_xref="GeneID:16876"
                     /db_xref="MGI:MGI:1316721"
     exon            1..637
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /inference="alignment:Splign:2.1.0"
     CDS             464..1657
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /note="isoform c is encoded by transcript variant 3;
                     LIM/homeobox protein Lhx9"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx9 isoform c"
                     /protein_id="NP_001036042.1"
                     /db_xref="CCDS:CCDS35726.1"
                     /db_xref="GeneID:16876"
                     /db_xref="MGI:MGI:1316721"
                     /translation="MEIVGCRAENNSCPFRPPAMLFHGISGGHIQGIMEEMERRSKTE
                     ARLTKGTQLNGRDAGMPPLSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECK
                     LALESELTCFAKDGSIYCKEDYYRRFSVQRCARCHLGISASEMVMRARDSVYHLSCFT
                     CSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPPQLSYTELAAKSGGLALPYFNG
                     TGTVQKGRPRKRKSPALGVDIVNYNSGCNENEADHLDRDQQPYPPSQKTKRMRTSFKH
                     HQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGV
                     DKADGTSLPAPPSADSGALTPPGTATTLTDLTNPTVTVVTTVTSNMDSHEPGSPSQTT
                     LTNLF"
     exon            638..840
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /inference="alignment:Splign:2.1.0"
     exon            841..1196
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /inference="alignment:Splign:2.1.0"
     exon            1197..1399
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /inference="alignment:Splign:2.1.0"
     exon            1400..2080
                     /gene="Lhx9"
                     /gene_synonym="3110009O07Rik; LH2B"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 agtccccaac gcaacctaca ggcactggga acttgcaggc agccggggac cgctgaatct
       61 agcacttcgt tctctttctt tgtgttcaaa actatttttc tttcttcctt agattttgtt
      121 ttcctccccc ccacttcaac ccccctcggc agttgttttc cattagtaac tcgatctctc
      181 gctgcagtta gaatcgcctg cttttccctc cgtccgcgtt tgtttgtttt ctgcacatct
      241 ccttctggaa aaccctggat atcccccccc cccgccccct tccccgtcgt tcttttgcct
      301 cggtcttttc cctctcaagt agagctattt ctactctgtc gttttcttct ttcctctctt
      361 gtccctgttc cccaacgcgt ctctacgctt ctgcatcgcg cagccctgtg cggtcgcttt
      421 tgcttcttca ctcgaatgaa ctgagagccc caggcgtgtg tttatggaaa tagtggggtg
      481 ccgagccgaa aacaattcgt gtcctttccg ccccccagcc atgctcttcc acggaatctc
      541 cggaggccac atccaaggta tcatggagga gatggagcgc agatccaaga ctgaggcccg
      601 tctgaccaaa ggcactcagc tcaacggccg cgacgcgggt atgccccctc tcagcccgga
      661 gaagcctgct ctgtgcgccg gctgcggggg caagatctcc gacaggtact atctgctggc
      721 cgtagacaaa cagtggcatc ttaggtgcct gaagtgctgt gaatgtaagc tggctctgga
      781 atctgagctc acctgctttg ccaaggacgg tagcatttac tgcaaggagg attattacag
      841 aaggttctct gtgcagagat gtgcccgctg ccaccttggc atttccgcct ctgagatggt
      901 catgcgcgcc cgagactctg tctaccatct gagctgcttc acttgttcca cttgcaacaa
      961 gaccttgacc acgggcgacc atttcgggat gaaggacagc ctggtgtact gccgcgcaca
     1021 cttcgagacc ctcttgcaag gggaatatcc acctcagctg agctacacgg agctggcggc
     1081 caagagcggc ggcttggctt tgccttactt caatggcact ggcaccgtgc agaaggggcg
     1141 gccccggaag cggaagagcc cagctctggg agtggacatc gtgaattaca actcaggttg
     1201 taatgagaac gaggcagacc acttggaccg ggaccagcag ccttatccac cttcacagaa
     1261 gaccaaacgg atgcgaactt ctttcaagca tcaccagctc cggaccatga aatcctactt
     1321 tgctatcaac cataacccag atgccaagga cctcaaacag cttgctcaaa aaacaggcct
     1381 gaccaaaaga gttttacagg tttggttcca aaacgcacga gccaaattca gaaggaacct
     1441 tttgcggcag gagaatgggg gtgttgataa agctgacggc acgtcgcttc cggccccgcc
     1501 ctcagcagac agcggcgctc tcactccacc cggcactgcg accactttaa cagacctgac
     1561 caatcccact gtcactgtag tgacaactgt gacctctaac atggacagcc acgaacccgg
     1621 aagcccctca caaactacct taacgaacct tttctaacat tggttttttt ggttttgttt
     1681 tttgtttttt gttttttaaa gaattctttc tctttttatt attattctaa tattattatt
     1741 ttattattta caagactttt tttccttcta acccacaaga tatttgggga ataaaatagc
     1801 agcttggtgt gtagcatcta caccacttgg ctatgagttt acagtattgt cgcttttaaa
     1861 tgaacaaatt tggtctgcaa gatgtatttg accttttttc tttaatcagt ttttttttca
     1921 gttggtaagg gaagattttg aatcattcta ataagtgcct cttaaaattg tatgttactt
     1981 atttccagaa tctcgaaggg aaaaaatggt attacgatgg gcgaattata ttccttttcc
     2041 tgtgatcagg ttattaattg atttttctta caattaaaaa
//
