LOCUS       NM_001347609            2355 bp    mRNA    linear   ROD 18-JUN-2024
DEFINITION  Mus musculus msh homeobox 3 (Msx3), transcript variant 2, mRNA.
ACCESSION   NM_001347609 XM_006536161
VERSION     NM_001347609.1
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 2355)
  AUTHORS   Gupta,I., Yeung,J., Rahimi-Balaei,M., Wu,S.R. and Goldowitz,D.
  TITLE     Msx genes delineate a novel molecular map of the developing
            cerebellar neuroepithelium
  JOURNAL   Front Mol Neurosci 17, 1356544 (2024)
   PUBMED   38742226
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2355)
  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   3  (bases 1 to 2355)
  AUTHORS   La Manno,G., Siletti,K., Furlan,A., Gyllborg,D., Vinsland,E., Mossi
            Albiach,A., Mattsson Langseth,C., Khven,I., Lederer,A.R.,
            Dratva,L.M., Johnsson,A., Nilsson,M., Lonnerberg,P. and
            Linnarsson,S.
  TITLE     Molecular architecture of the developing mouse brain
  JOURNAL   Nature 596 (7870), 92-96 (2021)
   PUBMED   34321664
REFERENCE   4  (bases 1 to 2355)
  AUTHORS   Nie,X., Zheng,J., Ricupero,C.L., He,L., Jiao,K. and Mao,J.J.
  TITLE     mTOR acts as a pivotal signaling hub for neural crest cells during
            craniofacial development
  JOURNAL   PLoS Genet 14 (7), e1007491 (2018)
   PUBMED   29975682
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2355)
  AUTHORS   Langer,D., Martianov,I., Alpern,D., Rhinn,M., Keime,C., Dolle,P.,
            Mengus,G. and Davidson,I.
  TITLE     Essential role of the TFIID subunit TAF4 in murine embryogenesis
            and embryonic stem cell differentiation
  JOURNAL   Nat Commun 7, 11063 (2016)
   PUBMED   27026076
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2355)
  AUTHORS   Fowler,K.J., Kalitsis,P. and Choo,K.H.
  TITLE     Mouse mitotic spindle checkpoint Bub3 gene maps to the distal
            region of chromosome 7 by interspecific backcross analysis
  JOURNAL   Cytogenet Cell Genet 87 (1-2), 91-92 (1999)
   PUBMED   10640819
REFERENCE   7  (bases 1 to 2355)
  AUTHORS   Wang,W., Chen,X., Xu,H. and Lufkin,T.
  TITLE     Msx3: a novel murine homologue of the Drosophila msh homeobox gene
            restricted to the dorsal embryonic central nervous system
  JOURNAL   Mech Dev 58 (1-2), 203-215 (1996)
   PUBMED   8887328
REFERENCE   8  (bases 1 to 2355)
  AUTHORS   Shimeld,S.M., McKay,I.J. and Sharpe,P.T.
  TITLE     The murine homeobox gene Msx-3 shows highly restricted expression
            in the developing neural tube
  JOURNAL   Mech Dev 55 (2), 201-210 (1996)
   PUBMED   8861099
REFERENCE   9  (bases 1 to 2355)
  AUTHORS   Cosgrove,D., Gray,D., Dierich,A., Kaufman,J., Lemeur,M., Benoist,C.
            and Mathis,D.
  TITLE     Mice lacking MHC class II molecules
  JOURNAL   Cell 66 (5), 1051-1066 (1991)
   PUBMED   1909605
REFERENCE   10 (bases 1 to 2355)
  AUTHORS   Holland,P.W.
  TITLE     Cloning and evolutionary analysis of msh-like homeobox genes from
            mouse, zebrafish and ascidian
  JOURNAL   Gene 98 (2), 253-257 (1991)
   PUBMED   1673109
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC109205.12.
            
            On Dec 2, 2016 this sequence version replaced XM_006536161.3.
            
            Transcript Variant: This variant (2) uses an alternate splice
            junction compared to variant 1, that causes a frameshift. The
            resulting isoform (2) has a shorter and distinct C-terminus
            compared to isoform 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 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 :: AK012556.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164136, SAMN01164138
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-371               AC109205.12        58908-59278         c
            372-2355            AC109205.12        56347-58330         c
FEATURES             Location/Qualifiers
     source          1..2355
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 85.04 cM"
     gene            1..2355
                     /gene="Msx3"
                     /note="msh homeobox 3"
                     /db_xref="GeneID:17703"
                     /db_xref="MGI:MGI:106587"
     exon            1..371
                     /gene="Msx3"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    18..20
                     /gene="Msx3"
                     /note="upstream in-frame stop codon"
     CDS             90..530
                     /gene="Msx3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     homeobox, msh-like 3; homeo box, msh-like 3"
                     /codon_start=1
                     /product="homeobox protein MSX-3 isoform 2"
                     /protein_id="NP_001334538.1"
                     /db_xref="CCDS:CCDS85451.1"
                     /db_xref="GeneID:17703"
                     /db_xref="MGI:MGI:106587"
                     /translation="

MARATFDMNAAGLEARGGGHTEHGPLPFSVESLLEAERVPGSESGELGVERPLGASKPGAWPPPVAHSCPPRKCSVSRSQALKSDRAVKARKSKVPRALHPAPSANTKPIANHGRHSPPRSCWRLSASFTRSNTYPLRSAPSSPAA"

     exon            372..2355
                     /gene="Msx3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1182..1187
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Msx3"
                     /note="hexamer: AATAAA"
     polyA_site      1209
                     /gene="Msx3"
                     /note="major polyA site"
ORIGIN      

cacagagcccaaggtcctagcaaaataaaccgccgctgggtcccacgcgtcccagccgggcggctagccccgcacccgccatcccatgcatggcccgggcgacattcgacatgaacgcggcggggctcgaagctcgcggcgggggccacacagagcacggaccactccccttcagcgtcgagtctctgctggaggctgagcgcgtaccgggctccgagtctggggagctgggggtggagaggccgctcggcgcctcgaagcctggagcctggccccctccagtcgcgcactcttgtcccccacgtaagtgctcagtctcccggtctcaggccctgaaaagcgaccgcgctgtcaaggctcgaaagtccaaggtgccccgagccctccaccctgcaccctccgcaaacacaaaaccaatcgcaaaccacggacgccattcaccaccgcgcagctgctggcgcttgagcgcaagtttcaccagaagcaatacttatccattgcggagcgcgccgagttctccagcagcttgagcctcactgagactcaggtcaagatctggtttcagaaccgccgagccaaagccaagcggctgcaggaagctgagctggagaagctgaagctggcagcgaagccactactgccggcggcgtttgccctgcccttcccgctgggcacccagctgcacagctccgcggccactttcggcggcaacgcggttcctgggatcctcgccgggcctgtcgcggcctatggcatgtactacttgtcttagatcatggaatcaagccctaacctcttggttaggctcagggttgcgcacagttctgcctgccgctgatgctcctggtaacttttgacttttcattttagtcttccccccccccctcctcctgtttatacggtgttatacttgatgactggagcctatttatagacatcttacaaatactttaaaccttcctaaaaccttgcccacatcaatctgtttttctgaaagaaaacacaccgtcatatagtccttgaaacagacaaaagcagttcttcctatttcttacaaagcagtcgacaaagtatttctggagtgggtgtgctccctgtattcactctgcccggacaccgaggacttcagagaggctcgattgagctggcataagaaaacaaattccataagaagaaatcaaaataaaaaatgagataatcggacggttagaaattactgtctctccaactgttgtgaccaaatggaaacttttacactttttaggttttataccattattatttttttttttagagtatatgtcgttcaaggagctagaggcaaacgctggatggacttggaagtaggggaggggactgttggcgccatgccctaatgtaagggtggctgctgcccccagcatcttctgagcttcttcgaaaagagcctgctggggggagacagagggctgaaggcagcagggaccaacctctagcctcttgccagcaggtgtccagtcaataaagagaagaaagtgagagttgagcatctcagatctcccattgtgggtgcggtaggaggtgaggcctgtgaaggtcccagaagagttactctgagtgccggctgcctctgtaattctggtgctccgtagaaaagcggaggacttgtttaggaatccggacttgtacctttattctacctttatccgaggaaagaaaacaggccatctgagctgttctgtcctatcctgttcggtctcaatcctatcatgcaagattgaggcccttagggtacctgacaacgggcactaatacaccccatggctgtttccacaggacacttttgctgcaatctagagactttagctggagtgtgttgagggctcacaacagtcccctggagtcacagcccaggacctttgacaggccctcctgccagccttcgggcaggggaggaagaacctgcctgcagagggctgctggttgtgtgttcatgagaacatggaatttcacagtgatagatggcccagggttaggatgctctggttgggaggaagggaaggactgggctatgctcggcagtccaagccagctccaggaaaactgctgtcccgtgaccttcactggtccatcagctccaaataaaaccgaaaagataatattgcatggaattgcctattgatacgtattgacagtcttctgccctgtgtctcttggaaaaattggaaaccagataggtttggttttgttttgagaccaaatcgtcactatgtagccctaactgatctaggacttgctattctccaaggacagccttagacttaccttgcctccacttgcctcccaagttctgggattaaagacataccacaatgc

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