LOCUS       NM_001355125            3346 bp    mRNA    linear   ROD 31-DEC-2024
DEFINITION  Mus musculus LIM homeobox protein 6 (Lhx6), transcript variant 5,
            mRNA.
ACCESSION   NM_001355125 XM_017315869
VERSION     NM_001355125.1
KEYWORDS    RefSeq.
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 3346)
  AUTHORS   Luo,H., Ieong,H.C., Li,R., Huang,D., Chen,D., Chen,X., Guo,Y.,
            Qing,Y., Guo,B., Li,R., Teng,Y., Li,W., Cao,Y., Zhou,C. and Wang,W.
  TITLE     Lhx6 deficiency causes human embryonic palatal mesenchymal cell
            mitophagy dysfunction in cleft palate
  JOURNAL   Mol Med 30 (1), 183 (2024)
   PUBMED   39438838
  REMARK    GeneRIF: Lhx6 deficiency causes human embryonic palatal mesenchymal
            cell mitophagy dysfunction in cleft palate.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3346)
  AUTHORS   Eid,L., Lokmane,L., Raju,P.K., Tene Tadoum,S.B., Jiang,X.,
            Toulouse,K., Lupien-Meilleur,A., Charron-Ligez,F., Toumi,A.,
            Backer,S., Lachance,M., Lavertu-Jolin,M., Montseny,M.,
            Lacaille,J.C., Bloch-Gallego,E. and Rossignol,E.
  TITLE     Both GEF domains of the autism and developmental epileptic
            encephalopathy-associated Trio protein are required for proper
            tangential migration of GABAergic interneurons
  JOURNAL   Mol Psychiatry (2024) In press
   PUBMED   39300136
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   3  (bases 1 to 3346)
  AUTHORS   Lozovaya,N., Moumen,A. and Hammond,C.
  TITLE     Basal Forebrain Cholinergic Neurons Have Specific Characteristics
            during the Perinatal Period
  JOURNAL   eNeuro 11 (5) (2024)
   PUBMED   38755010
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3346)
  AUTHORS   Miyoshi,G., Ueta,Y., Yagasaki,Y., Kishi,Y., Fishell,G.,
            Machold,R.P. and Miyata,M.
  TITLE     Developmental trajectories of GABAergic cortical interneurons are
            sequentially modulated by dynamic FoxG1 expression levels
  JOURNAL   Proc Natl Acad Sci U S A 121 (16), e2317783121 (2024)
   PUBMED   38588430
REFERENCE   5  (bases 1 to 3346)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   6  (bases 1 to 3346)
  AUTHORS   Lavdas,A.A., Grigoriou,M., Pachnis,V. and Parnavelas,J.G.
  TITLE     The medial ganglionic eminence gives rise to a population of early
            neurons in the developing cerebral cortex
  JOURNAL   J Neurosci 19 (18), 7881-7888 (1999)
   PUBMED   10479690
REFERENCE   7  (bases 1 to 3346)
  AUTHORS   Sussel,L., Marin,O., Kimura,S. and Rubenstein,J.L.
  TITLE     Loss of Nkx2.1 homeobox gene function results in a ventral to
            dorsal molecular respecification within the basal telencephalon:
            evidence for a transformation of the pallidum into the striatum
  JOURNAL   Development 126 (15), 3359-3370 (1999)
   PUBMED   10393115
REFERENCE   8  (bases 1 to 3346)
  AUTHORS   Kimura,N., Ueno,M., Nakashima,K. and Taga,T.
  TITLE     A brain region-specific gene product Lhx6.1 interacts with Ldb1
            through tandem LIM-domains
  JOURNAL   J Biochem 126 (1), 180-187 (1999)
   PUBMED   10393337
REFERENCE   9  (bases 1 to 3346)
  AUTHORS   Tucker,A.S., Yamada,G., Grigoriou,M., Pachnis,V. and Sharpe,P.T.
  TITLE     Fgf-8 determines rostral-caudal polarity in the first branchial
            arch
  JOURNAL   Development 126 (1), 51-61 (1999)
   PUBMED   9834185
REFERENCE   10 (bases 1 to 3346)
  AUTHORS   Grigoriou,M., Tucker,A.S., Sharpe,P.T. and Pachnis,V.
  TITLE     Expression and regulation of Lhx6 and Lhx7, a novel subfamily of
            LIM homeodomain encoding genes, suggests a role in mammalian head
            development
  JOURNAL   Development 125 (11), 2063-2074 (1998)
   PUBMED   9570771
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL773525.5.
            
            On Sep 8, 2017 this sequence version replaced XM_017315869.1.
            
            Transcript Variant: This variant (5) has multiple differences
            compared to variant 1. These differences result in distinct 5' and
            3' UTRs, the use of a downstream start codon and a translational
            frameshift in the 3' coding region compared to variant 1. The
            encoded isoform (4, also known as Lhx6.1b) has a shorter N-terminus
            and a distinct C-terminus compared to isoform 1. Variants 4 and 5
            both encode the same isoform (4).
            
            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 :: SRR1660817.182780.1,
                                           SRR1660811.150704.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164142 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-253               AL773525.5         155405-155657       c
            254-325             AL773525.5         155018-155089       c
            326-508             AL773525.5         154470-154652       c
            509-630             AL773525.5         153982-154103       c
            631-851             AL773525.5         145337-145557       c
            852-952             AL773525.5         142730-142830       c
            953-1048            AL773525.5         142444-142539       c
            1049-1223           AL773525.5         142086-142260       c
            1224-3346           AL773525.5         133077-135199       c
FEATURES             Location/Qualifiers
     source          1..3346
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 24.17 cM"
     gene            1..3346
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /note="LIM homeobox protein 6"
                     /db_xref="GeneID:16874"
                     /db_xref="MGI:MGI:1306803"
     exon            1..253
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            254..325
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     CDS             257..1303
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /note="isoform 4 is encoded by transcript variant 5;
                     LIM/homeobox protein Lhx6; LIM-homeodomain protein 6.1;
                     LIM/homeobox protein Lhx6.1"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx6 isoform 4"
                     /protein_id="NP_001342054.1"
                     /db_xref="CCDS:CCDS38111.1"
                     /db_xref="GeneID:16874"
                     /db_xref="MGI:MGI:1306803"
                     /translation="MAQPGSGCKATTRCLEGTAPPAMAQSDAEALAGALDKDEGRASP
                     CTPSTPSVCSPPSAASSVPSAGKNICSSCGLEILDRYLLKVNNLIWHVRCLECSVCRT
                     SLRQQNSCYIKNKEIYCKMDYFSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACF
                     SCKRQLSTGEEFGLVEEKVLCRIHYDTMIENLKRAAENGNGLTLEGAVPSEQDSQPKP
                     AKRARTSFTAEQLQVMQAQFAQDNNPDAQTLQKLADMTGLSRRVIQVWFQNCRARHKK
                     HTPQHPVPPSGAPPTRLPSALSDDIHYSPFSSPERARMVTLHGYIESHPFSVLTLPAL
                     AHLSMGTTQLPLSR"
     exon            326..508
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            509..630
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            631..851
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            852..952
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            953..1048
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            1049..1223
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     exon            1224..3346
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3306..3311
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /note="hexamer: AATAAA"
     polyA_site      3342
                     /gene="Lhx6"
                     /gene_synonym="Lhx6.1"
                     /note="major polyA site"
ORIGIN      
        1 ccactaccac caccaccacc cccatctcct ttttattttc tttctttctc tcttttctcc
       61 tttttgcatt ttgtaccgag agtaggagaa gggagggggc ggagggagaa aaaaattcga
      121 tttttaatta ctaccattaa aaaatcaaat ttgcaattct ttgggcggcc tgatggatct
      181 cactgattga cagttggaat tgacactctg gctacctctt atcttgggca ttcacgacaa
      241 tttctaattg caggtgatgg cccagccagg gtccggctgc aaagcgacca cccgctgtct
      301 cgaagggacc gctccgcctg ccatggctca gtcagacgca gaggccttgg caggcgctct
      361 ggacaaggac gaaggtagag cctccccatg tacgcccagc acaccgtctg tctgctcgcc
      421 gccctctgct gcctcttccg tgccgtctgc cggcaagaat atctgctcca gttgcggtct
      481 ggagatcctg gaccggtatc tgctcaaggt caacaacctc atctggcacg tgcggtgcct
      541 cgagtgctcc gtgtgtcgca catcgctgag gcagcagaat agctgctaca tcaagaacaa
      601 ggagatctac tgcaagatgg actacttcag ccgatttgga accaagtgcg cccggtgcgg
      661 cagacaaatc tatgccagtg actgggtgcg gcgcgcacgc ggcaatgcct accacctggc
      721 atgtttcgcc tgcttttcct gcaagcgcca gctatccacc ggtgaggaat tcggcctcgt
      781 tgaggagaag gtgctttgcc gcatccatta cgacaccatg atcgagaacc tcaagagggc
      841 cgccgagaac gggaacggtc tcacgctgga gggggcagtg ccctcggaac aggacagtca
      901 gcccaagcca gccaagcgcg cgcggacgtc cttcaccgca gagcaattgc aggttatgca
      961 ggcgcagttc gcgcaggaca acaacccgga cgcgcagacg ctgcagaagc tagcggacat
     1021 gacgggcctc agtcgcaggg tcatccaggt gtggtttcaa aactgccgag cgcgtcataa
     1081 aaagcataca ccgcagcacc cagtgccgcc ctctggggca cccccgaccc gcctcccttc
     1141 tgccctgtcc gacgacatcc actactctcc gttcagcagc ccagagaggg cgcgcatggt
     1201 caccttgcac ggctacattg agagtcatcc tttttcagta ctaacgctgc cggcgcttgc
     1261 acatctgtcc atgggcacca cacagctgcc cctcagccgc tgagatccag catccagctg
     1321 tggccaggga tccaccacct ctgtgtacac cctcacccgc tgctgtcctg ccctctgcca
     1381 gtggccccat caacccaggc ctggtctttc cctctcctgc tgagaaccag aacccaccag
     1441 gagcagcaga gtccctctct gggaaggcag gctccctgaa atgtggcatc agcatgaaaa
     1501 caagcagcct gtctttcctc attaactggg agtcccactt acctactgtc agctgatcac
     1561 agcagcaatg gctaattcag tccgagtcaa caacagcctc ctacttcaca ggttctcttc
     1621 tcccccacat tggcctttat ttactacttc cttggaacca tctccaaatt ccaaatagcc
     1681 aacaaccccc aacattatat actctgctgc ttttgtctgg aaaactctac agtgtttgtg
     1741 ggatatcccc aaaggaaagc tgtgttctaa ttttatcatt tccatctgtc tggttatgtc
     1801 aagttaactc agaaaaagaa gagacactga ccaaccctga gaggcccaac agggcagaga
     1861 tggaggcctg cccagatgaa gaggcagagg atgggcaggg atgggtgcca aagacccccc
     1921 ccccaattgg cttggaggag aaggactggg tacgctggac ttggagaggt gacgagagtt
     1981 tcatggagag aaaagaggaa acttgggggg ggcggagttt cccccaccca attacctagc
     2041 aggagtcgtg gaaaggatgg cgtctgatct gcacgatgac accactgaat gtttaggtgg
     2101 gctagcatta gcgacccttg ttggccactt ttcagtcctg agatgagggc ctgagccagt
     2161 cttctctagg ggtgggatga gactactcac gaggaccaag gaacagagcc cagagaaaca
     2221 gcagccagaa tattagttct gattcatccc cgagggaaga gaggtaccca tggcttcagt
     2281 gagcacatgc caagcccagg atgccagctg gcacctctgc aatctcccca ccaaatacac
     2341 agagccagct ctacccactc ctaagagcag aggccaactc taaagaaagg tctcaggtta
     2401 cacaggcccc cccacttatg ttttcagggg atgccattta tcccaagctt atcctgtaat
     2461 tctagaatga cttggtgtcc tgatgcactt ctcaccagag gctgcctagc agcatgtgtt
     2521 agccaaagtc ttcctccttg ttttgagaag actccaggac aggacaggca aattcatggt
     2581 atgtatgcag ttgctgctcc tgcttcacct gtggcagaca tcgctaatcg atcacagcac
     2641 tctatctctc agagtctgga taagaattcc catgcttgtt gggacgagac caactgtgct
     2701 gttgctatgg gacctggagg agggttaggc atgggtgaca ccccagaagg gaactttcat
     2761 cttttccctt ccaaaaattg tcaactgact gaggacaaag agaaagcacc tcccagaaag
     2821 ctgtgagcgt ggtttggttc agaactccag caccctgtgc caggcactga ctcaagcaag
     2881 aggaacctgg cctgatccct gactttgggg aacccagatc tttcctttga tttttgctcc
     2941 taatgatcaa aaccccaatt gcaaccatgt ggcaagtggc cagctgagcc caggttactt
     3001 ggtacccact ctgccttgag ccttccttcc cccagggcct atttcttgtg tggatcacgt
     3061 ggcagtagca tgttgcagtc agacgtctcc actaccctgt tgagaacagc ctgggaatgt
     3121 acaggtcatc gaggctattt atttaaacac acacacacac acacacacac acacacacac
     3181 acacacacac acgggggaac acacacaaat ggaaaaaaat tgtaagcact ttttttgtaa
     3241 aaccaatgtc tgttttgtta catacctttc atgttgtgct ttgtaaatgt cttatttgtg
     3301 taataaataa agttaatgcg agtagaagtg ccggcactta aaccca
//
