LOCUS       NM_001310144            3684 bp    mRNA    linear   ROD 18-MAR-2025
DEFINITION  Mus musculus paired box 6 (Pax6), transcript variant 6, mRNA.
ACCESSION   NM_001310144 XM_006498915
VERSION     NM_001310144.1
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 3684)
  AUTHORS   Serdar,L.D., Egol,J.R., Lackford,B., Bennett,B.D., Hu,G. and
            Silver,D.L.
  TITLE     mRNA stability fine-tunes gene expression in the developing cortex
            to control neurogenesis
  JOURNAL   PLoS Biol 23 (2), e3003031 (2025)
   PUBMED   39913536
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3684)
  AUTHORS   Clemot-Dupont,S., Lourenco Fernandes,J.A., Larrigan,S., Sun,X.,
            Medisetti,S., Stanley,R., El Hankouri,Z., Joshi,S.V.,
            Picketts,D.J., Shekhar,K. and Mattar,P.
  TITLE     The chromatin remodeler ADNP regulates neurodevelopmental disorder
            risk genes and neocortical neurogenesis
  JOURNAL   Proc Natl Acad Sci U S A 122 (3), e2405981122 (2025)
   PUBMED   39808658
REFERENCE   3  (bases 1 to 3684)
  AUTHORS   Georgala,P.A., Carr,C.B. and Price,D.J.
  TITLE     The role of Pax6 in forebrain development
  JOURNAL   Dev Neurobiol 71 (8), 690-709 (2011)
   PUBMED   21538923
  REMARK    Review article
REFERENCE   4  (bases 1 to 3684)
  AUTHORS   Kim,J. and Lauderdale,J.D.
  TITLE     Analysis of Pax6 expression using a BAC transgene reveals the
            presence of a paired-less isoform of Pax6 in the eye and olfactory
            bulb
  JOURNAL   Dev Biol 292 (2), 486-505 (2006)
   PUBMED   16464444
  REMARK    GeneRIF: Pax6 expression, analyzed using a BAC transgene, revealed
            the presence of a paired-less isoform in the eye and olfactory
            bulb.
REFERENCE   5  (bases 1 to 3684)
  AUTHORS   Xu,P.X., Zhang,X., Heaney,S., Yoon,A., Michelson,A.M. and Maas,R.L.
  TITLE     Regulation of Pax6 expression is conserved between mice and flies
  JOURNAL   Development 126 (2), 383-395 (1999)
   PUBMED   9847251
REFERENCE   6  (bases 1 to 3684)
  AUTHORS   Ton,C.C., Miwa,H. and Saunders,G.F.
  TITLE     Small eye (Sey): cloning and characterization of the murine homolog
            of the human aniridia gene
  JOURNAL   Genomics 13 (2), 251-256 (1992)
   PUBMED   1612585
REFERENCE   7  (bases 1 to 3684)
  AUTHORS   Hill,R.E., Favor,J., Hogan,B.L., Ton,C.C., Saunders,G.F.,
            Hanson,I.M., Prosser,J., Jordan,T., Hastie,N.D. and van
            Heyningen,V.
  TITLE     Mouse small eye results from mutations in a paired-like
            homeobox-containing gene
  JOURNAL   Nature 354 (6354), 522-525 (1991)
   PUBMED   1684639
  REMARK    Erratum:[Nature. 1992 Feb 20;355(6362):750. doi: 10.1038/355750a0.
            PMID: 1346927]
REFERENCE   8  (bases 1 to 3684)
  AUTHORS   Walther,C. and Gruss,P.
  TITLE     Pax-6, a murine paired box gene, is expressed in the developing CNS
  JOURNAL   Development 113 (4), 1435-1449 (1991)
   PUBMED   1687460
REFERENCE   9  (bases 1 to 3684)
  AUTHORS   Walther,C., Guenet,J.L., Simon,D., Deutsch,U., Jostes,B.,
            Goulding,M.D., Plachov,D., Balling,R. and Gruss,P.
  TITLE     Pax: a murine multigene family of paired box-containing genes
  JOURNAL   Genomics 11 (2), 424-434 (1991)
   PUBMED   1685142
REFERENCE   10 (bases 1 to 3684)
  AUTHORS   Theiler,K., Varnum,D.S. and Stevens,L.C.
  TITLE     Development of Dickie's small eye, a mutation in the house mouse
  JOURNAL   Anat Embryol (Berl) 155 (1), 81-86 (1978)
   PUBMED   103464
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AY064175.1, CD805985.1,
            CN539431.1, CX565124.1, CN539723.1, AK139054.1 and AL512589.4.
            
            On Jul 2, 2015 this sequence version replaced XM_006498915.2.
            
            Summary: This gene encodes a homeobox-containing protein that
            functions as a regulator of transcription. It plays a key role in
            the development of neural tissues, particularly the eye. Activity
            of this protein is also required for expression of glucagon in the
            pancreas. This gene is regulated by multiple enhancers located up
            to tens or hundreds of kilobases upstream and downstream of the
            transcription start sites. Mutations in this gene or deletion of
            these regulatory elements results in severe defects in eye
            development. Alternative splicing and the use of alternative
            promoters results in multiple transcript variants, some of which
            encode proteins that lack the N-terminal paired domain. [provided
            by RefSeq, Jul 2015].
            
            Transcript Variant: This variant (6) differs in the 5' UTR and
            lacks an in-frame exon in the 5' coding region compared to variant
            1. It initiates from the P1 promoter. The encoded isoform (2) is
            shorter than isoform 1. Variants 4, 5, and 6 encode the same
            protein (isoform 2).
            
            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 :: SRR1660811.124082.1,
                                           SRR1660817.176099.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164132
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-179               AY064175.1         101-279
            180-195             CD805985.1         19-34
            196-987             CN539431.1         14-805
            988-1492            CX565124.1         323-827
            1493-2174           CN539723.1         32-713
            2175-2687           AK139054.1         1686-2198
            2688-2688           AL512589.4         88762-88762
            2689-3684           AK139054.1         2200-3195
FEATURES             Location/Qualifiers
     source          1..3684
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 55.31 cM"
     gene            1..3684
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /note="paired box 6"
                     /db_xref="GeneID:18508"
                     /db_xref="MGI:MGI:97490"
     exon            1..229
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            230..309
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            310..370
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     CDS             361..1629
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /note="isoform 2 is encoded by transcript variant 6;
                     paired box protein Pax-6; oculorhombin; Dickie's small
                     eye; paired box gene 6"
                     /codon_start=1
                     /product="paired box protein Pax-6 isoform 2"
                     /protein_id="NP_001297073.1"
                     /db_xref="CCDS:CCDS57181.1"
                     /db_xref="GeneID:18508"
                     /db_xref="MGI:MGI:97490"
                     /translation="MQNSHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR
                     ILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVSKIAQYKRECPSIFAWEI
                     RDRLLSEGVCTNDNIPSVSSINRVLRNLASEKQQMGADGMYDKLRMLNGQTGSWGTRP
                     GWYPGTSVPGQPTQDGCQQQEGGGENTNSISSNGEDSDEAQMRLQLKRKLQRNRTSFT
                     QEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRR
                     QASNTPSHIPISSSFSTSVYQPIPQPTTPVSSFTSGSMLGRTDTALTNTYSALPPMPS
                     FTMANNLPMQPPVPSQTSSYSCMLPTSPSVNGRSYDTYTPPHMQTHMNSQPMGTSGTT
                     STGLISPGVSVPVQVPGSEPDMSQYWPRLQ"
     exon            371..501
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            502..717
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            718..883
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            884..1042
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            1043..1125
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            1126..1276
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            1277..1392
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            1393..1543
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     exon            1544..3684
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2490..2495
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /note="hexamer: ATTAAA"
     polyA_site      2516
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /note="major polyA site"
     regulatory      2611..2616
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /note="hexamer: ATTACA"
     polyA_site      2636
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
     regulatory      2898..2903
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
                     /note="hexamer: ATTAAA"
     polyA_site      2919
                     /gene="Pax6"
                     /gene_synonym="1500038E17Rik; AEY11; Dey; Gsfaey11; Pax-6;
                     Sey"
ORIGIN      
        1 ggatctgaga attgctctca cacaccaacc cagcagcgtc cgtggagaaa actctcacga
       61 gcaactcctt taaaataccg tcatttcaaa ccgttgtggt ctttaagcaa caacaggggg
      121 gggggaccca aacaacaaaa accaaaaaaa aaaaaaaaaa aaaaaaaaaa gccctcaaaa
      181 ctcttgacag gagccttgac aacgacgaaa gagaggatgc ctcttaaagg cagaagactt
      241 taaccaaggg cggtgagcag atgtgtgaga tcttctattc tagaagtgga cgtatatccc
      301 agttctcaga gccccgtatt cgagccccgt gggatccgga ggctgccaac cagctccagc
      361 atgcagaaca gtcacagcgg agtgaatcag cttggtggtg tctttgtcaa cgggcggcca
      421 ctgccggact ccacccggca gaagatcgta gagctagctc acagcggggc ccggccgtgc
      481 gacatttccc gaattctgca ggtatccaac ggttgtgtga gtaaaattct gggcaggtat
      541 tacgagactg gctccatcag acccagggca atcggaggga gtaagccaag agtggcgact
      601 ccagaagttg taagcaaaat agcccagtat aaacgggagt gcccttccat ctttgcttgg
      661 gaaatccgag acagattatt atccgagggg gtctgtacca acgataacat acccagtgtg
      721 tcatcaataa acagagttct tcgcaacctg gctagcgaaa agcaacagat gggcgcagac
      781 ggcatgtatg ataaactaag gatgttgaac gggcagaccg gaagctgggg cacacgccct
      841 ggttggtatc ccgggacttc agtaccaggg caacccacgc aagatggctg ccagcaacag
      901 gaaggagggg gagagaacac caactccatc agttctaacg gagaagactc ggatgaagct
      961 cagatgcgac ttcagctgaa gcggaagctg caaagaaata gaacatcttt tacccaagag
     1021 cagattgagg ctctggagaa agagtttgag aggacccatt atccagatgt gtttgcccgg
     1081 gaaagactag cagccaaaat agatctacct gaagcaagaa tacaggtatg gttttctaat
     1141 cgaagggcca aatggagaag agaagagaaa ctgaggaacc agagaagaca ggccagcaac
     1201 actcctagtc acattcctat cagcagcagc ttcagtacca gtgtctacca gccaatccca
     1261 cagcccacca cacctgtctc ctccttcaca tcaggttcca tgttgggccg aacagacacc
     1321 gccctcacca acacgtacag tgctttgcca cccatgccca gcttcaccat ggcaaacaac
     1381 ctgcctatgc aacccccagt ccccagtcag acctcctcat actcgtgcat gctgcccacc
     1441 agcccgtcag tgaatgggcg gagttatgat acctacaccc ctccgcacat gcaaacacac
     1501 atgaacagtc agcccatggg cacctcgggg accacttcaa caggactcat ttcacctgga
     1561 gtgtcagttc ccgtccaagt tcccgggagt gaacctgaca tgtctcagta ctggcctcga
     1621 ttacagtaaa gagagaagga gagagcatgt gatcgagaga ggaaattgtg ttcactctgc
     1681 caatgactat gtggacacag cagttgggta ttcaggaaag aaagagaaat ggcggttaga
     1741 agcacttcac tttgtaactg tcctgaactg gagcccggga atggactaga accaaggacc
     1801 tttgcgtaca gaaggcacgg tatcagttgg aacaaatctt cattttggta tccaaacttt
     1861 tattcatttt ggtgtattat ttgtaaatgg gcattggtat gttataatga agaaaagaac
     1921 aacacaggct gttggatcgc ggatctgtgt tgctcatgtg gttgtttaaa ggaaaccatg
     1981 atcgacaaga tttgccatgg atttaagagt tttatcaaga tatatcaaat acttctcccc
     2041 atctgttcat agtttatgga ctgatgttcc aagtttgtat cattcctttg catataattg
     2101 aacctgggac aacacacact agatatatgt aaaaactatc tgttggtttt ccaaaggttg
     2161 ttaacagatg aagtttatgt gcaaaaaagg gtaagatatg aattcaagga gaagttgata
     2221 gctaaaaggt agagtgtgtc ttcgatataa tacaatttgt tttatgtcaa aatgtaagta
     2281 tttgtcttcc ctagaaatcc tcagaatgat ttctataata aagttaattt catttatatt
     2341 tgacaagaat actctataga tgttttatac acattttcat gcaatcattt gtttctttct
     2401 tggccagcaa aagttaattg ttcttagata tagctgtatt actgttcaca gtccaatcat
     2461 tttgtgcatc tagaattcat tcctaatcaa ttaaaagtgc ttgcaagagt tttaaaccta
     2521 agtgttttgc agttgttcac aaatacatat caaaattaac cattgttgat tgtaaaaaaa
     2581 aaaccatgcc aaagcctttg tattttcttt attacactat tttcttttta accttatagt
     2641 gtggtgttac aaattttgtt cccacattag gttaatgtcc taaatcaatg gttactttca
     2701 tatattccat tttacaacct gatggtcctc aaagaaataa tttttacaga tatcagaagt
     2761 tggtaatgta ttgtaaaaaa acctaaaaca aaacacagct agctgtatgt aggtctgcat
     2821 cccacaatgt gtacagaaaa tagtaatatt tcaaatttat ctatttattt gattttaaag
     2881 ctcaaagtgt agaagtaatt aaaaaaatgc aacaagggat tcactaggaa ttgttttgaa
     2941 ttagagctgg catttttaac ctgggcaacc aatccccaca atgattccac tacagtcata
     3001 ttcaaaggtt gagttcttaa acaagatcct ctgacagctg ttgccaatct cagataaccc
     3061 ttcttgctgt cctgtctccc cactctttgc ataagaggca tcggctccca ttgaacccct
     3121 ccagctgctc ccatgtgtgt cttgctttcg gtgctgtggt gggtggttgg agggtggagg
     3181 ggatgttgca tgtcaaggaa taatgagcac agacacacta agagacaaca acaaagcgga
     3241 ctgtgactgg ccggtgggag ttaaaggcct tcagtcattg gcagcttaag ccaaacattc
     3301 ccaaatctat gaagcagggc ccattgttgg tcagttgtca tttgcgaaga agcacagatc
     3361 tgatcatgtt taaagtggca gcatgcaggg caggagtgcc tgagcccaag caatggagag
     3421 aaaaaaaagg aagcttttgt tggttagaaa aaggcctgcc tgctattttc tgcctgttct
     3481 gtgcaacact taagtcacat agacacattt tcttcagcga gcttgagaga gagaaactct
     3541 ggggtcctgg ccacctagat taaaaataca aggagactca tcctaggggg aaggcacttc
     3601 actgactccc aactctgagg atttttggtt ttgtaaatcg caaaaggcaa atgatcagaa
     3661 ataaattgat tggaggattt caac
//
