LOCUS       NM_007701               3234 bp    mRNA    linear   ROD 11-MAR-2025
DEFINITION  Mus musculus visual system homeobox 2 (Vsx2), transcript variant 2,
            mRNA.
ACCESSION   NM_007701
VERSION     NM_007701.3
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 3234)
  AUTHORS   Chapman,P.D., Kulkarni,A.S., Trevisan,A.J., Han,K., Hinton,J.M.,
            Deltuvaite,P., Fenno,L.E., Ramakrishnan,C., Patton,M.H.,
            Schwarz,L.A., Zakharenko,S.S., Deisseroth,K. and Bikoff,J.B.
  TITLE     A brain-wide map of descending inputs onto spinal V1 interneurons
  JOURNAL   Neuron 113 (4), 524-538 (2025)
   PUBMED   39719703
REFERENCE   2  (bases 1 to 3234)
  AUTHORS   Wutikeli,H., Yu,Y., Zhang,T., Cao,J., Nawy,S. and Shen,Y.
  TITLE     Role of Elavl-like RNA-binding protein in retinal development and
            signal transduction
  JOURNAL   Biochim Biophys Acta Mol Basis Dis 1871 (1), 167518 (2025)
   PUBMED   39307290
REFERENCE   3  (bases 1 to 3234)
  AUTHORS   Dudukcu,O., Raj,D.D.A., van de Haar,L.L., Grossouw,L.M.,
            Linders,L.E., Garritsen,O., Adolfs,Y., van Kronenburg,N.C.H.,
            Broekhoven,M.H., Kapteijns,T.H.W., Meye,F.J. and Pasterkamp,R.J.
  TITLE     Molecular diversity and migration of GABAergic neurons in the
            developing ventral midbrain
  JOURNAL   iScience 27 (11), 111239 (2024)
   PUBMED   39569362
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3234)
  AUTHORS   Renaux,E., Baudouin,C., Schakman,O., Gay,O., Martin,M.,
            Marchese,D., Achouri,Y., Rezsohazy,R., Gofflot,F. and Clotman,F.
  TITLE     Arid3c identifies an uncharacterized subpopulation of V2
            interneurons during embryonic spinal cord development
  JOURNAL   Front Cell Neurosci 18, 1466056 (2024)
   PUBMED   39479525
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3234)
  AUTHORS   Honnell,V., Sweeney,S., Norrie,J., Parks,M., Ramirez,C.,
            Jannu,A.J., Xu,B., Teubner,B., Lee,A.Y., Bell,C. and Dyer,M.A.
  TITLE     Evolutionary conservation of VSX2 super-enhancer modules in retinal
            development
  JOURNAL   Development 151 (13) (2024)
   PUBMED   38994775
  REMARK    GeneRIF: Evolutionary conservation of VSX2 super-enhancer modules
            in retinal development.
REFERENCE   6  (bases 1 to 3234)
  AUTHORS   Liu,I.S., Chen,J.D., Ploder,L., Vidgen,D., van der Kooy,D.,
            Kalnins,V.I. and McInnes,R.R.
  TITLE     Developmental expression of a novel murine homeobox gene (Chx10):
            evidence for roles in determination of the neuroretina and inner
            nuclear layer
  JOURNAL   Neuron 13 (2), 377-393 (1994)
   PUBMED   7914735
REFERENCE   7  (bases 1 to 3234)
  AUTHORS   Silver,J. and Robb,R.M.
  TITLE     Studies on the development of the eye cup and optic nerve in normal
            mice and in mutants with congenital optic nerve aplasia
  JOURNAL   Dev Biol 68 (1), 175-190 (1979)
   PUBMED   437315
REFERENCE   8  (bases 1 to 3234)
  AUTHORS   Robb,R.M., Silver,J. and Sullivan,R.T.
  TITLE     Ocular retardation (or) in the mouse
  JOURNAL   Invest Ophthalmol Vis Sci 17 (5), 468-473 (1978)
   PUBMED   640793
REFERENCE   9  (bases 1 to 3234)
  AUTHORS   Theiler,K., Varnum,D.S., Nadeau,J.H., Stevens,L.C. and Cagianut,B.
  TITLE     A new allele of ocular retardation: early development and
            morphogenetic cell death
  JOURNAL   Anat Embryol (Berl) 150 (1), 85-97 (1976)
   PUBMED   827941
REFERENCE   10 (bases 1 to 3234)
  AUTHORS   Konyukhov,B.V. and Sazhina,M.V.
  TITLE     Inhibition of DNA synthesis in embryonic mouse retina as a result
            of gene interaction
  JOURNAL   Dev Biol 45 (1), 1-6 (1975)
   PUBMED   1181211
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK143461.1, BC031869.1 and
            BC051245.1.
            
            On Aug 22, 2014 this sequence version replaced NM_007701.2.
            
            Summary: This gene encodes a member of the Vsx (visual system
            homeobox) family which belongs to the larger PRD homeobox class.
            The encoded protein is required for eye organogenesis and controls
            retinal development. Disruption of this gene is associated with
            ocular retardation J (orJ), a mouse disease which causes
            microphthalmia, retinal degeneration and optic nerve aplasia.
            Alternative splicing results in multiple transcript variants.
            [provided by RefSeq, Aug 2014].
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the 3' coding region, compared to variant 1. This
            results in a shorter protein (isoform 2), compared to isoform 1.
            
            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 :: BC051245.1, L34808.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164136, SAMN01164137
                                           [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
            1-24                AK143461.1         1-24
            25-3203             BC031869.1         1-3179
            3204-3234           BC051245.1         3169-3199
FEATURES             Location/Qualifiers
     source          1..3234
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="12"
                     /map="12 39.28 cM"
     gene            1..3234
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /note="visual system homeobox 2"
                     /db_xref="GeneID:12677"
                     /db_xref="MGI:MGI:88401"
     exon            1..485
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /inference="alignment:Splign:2.1.0"
     CDS             116..1201
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /note="isoform 2 is encoded by transcript variant 2;
                     homeobox protein CHX10; ceh-10 homeodomain-containing
                     homolog; ocular retardation; C. elegans ceh-10 homeo
                     domain containing homolog"
                     /codon_start=1
                     /product="visual system homeobox 2 isoform 2"
                     /protein_id="NP_031727.1"
                     /db_xref="CCDS:CCDS36493.1"
                     /db_xref="GeneID:12677"
                     /db_xref="MGI:MGI:88401"
                     /translation="MTGKAGEALSKPKSETVAKSTSGGAPARCTGFGIQEILGLNKEP
                     PSSHPRAALDGLAPGHLLAARSVLSPAGVGSMGLLGPGGLPGFYTQPTFLEVLSDPQS
                     VHLQPLGRASGPLDTSQTASSDSEDVSSSDRKMSKSALNQTKKRKKRRHRTIFTSYQL
                     EELEKAFNEAHYPDVYAREMLAMKTELPEDRIQVWFQNRRAKWRKREKCWGRSSVMAE
                     YGLYGAMVRHSIPLPESILKSAKDGIMDSCAPWLLGMHKKSLEAAAESGRKPEVERQA
                     LPKLDKMEQEERAPEAQAAISQEELRENSIAALRAKAQEHSTKVLGTVSGPDSLARNA
                     EKPEEEDATEEDRPAEKLSPPQLEDMA"
     exon            486..570
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /inference="alignment:Splign:2.1.0"
     exon            571..694
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /inference="alignment:Splign:2.1.0"
     exon            695..875
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /inference="alignment:Splign:2.1.0"
     exon            876..3204
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3180..3185
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /note="hexamer: AATAAA"
     polyA_site      3204
                     /gene="Vsx2"
                     /gene_synonym="Chx10; Hox-10; Hox10; or"
                     /note="major polyA site"
ORIGIN      
        1 gagcattaga caccggaggg ggcacctggg accaacttca cgaagcgggg agcccggcgg
       61 gggggcttgg gggagcaaaa gacccgcggc ctcagcccct ccaaagaacc gggagatgac
      121 ggggaaagcg ggggaagcgc tgagcaagcc caaatccgag acagtggcca agagtacctc
      181 ggggggcgcc ccggccaggt gcacagggtt cggcatccag gagatcctag gcttgaacaa
      241 ggagcctccc agctcccacc cgcgggctgc cctcgacggc ctggcccctg ggcatttgtt
      301 agctgcgcgc tccgttctca gcccggcagg agtgggcagc atggggctgc tggggcccgg
      361 gggacttccc ggcttctaca cacagcccac cttcttggaa gtgctgtccg atccgcagag
      421 cgtccacttg cagccactag gcagagcgtc ggggccgctg gacaccagcc agacggccag
      481 ctccgattcc gaagatgttt cctccagtga ccgaaaaatg tccaaatcgg ctttaaacca
      541 gaccaagaag cgtaagaagc ggcgacacag gacaatcttt acttcctacc agctagagga
      601 gctggagaaa gcattcaatg aagcccacta cccagatgtc tacgcccggg agatgctggc
      661 catgaaaacg gagctcccag aagacaggat acaggtgtgg ttccagaacc gcagagccaa
      721 gtggaggaag agggagaagt gctggggccg gagcagcgtc atggctgagt atggtctcta
      781 tggagccatg gtgaggcact cgatccccct gccagagtct atcctcaagt ctgccaagga
      841 tggcataatg gattcctgtg ccccatggct actggggatg cacaaaaagt cgctggaggc
      901 agcagctgag tcgggaagga agcccgaggt ggaacgccag gccctgccca agctcgacaa
      961 gatggagcag gaggaacggg ccccagaggc ccaggcagcc atctcccagg aagaactgag
     1021 ggagaacagc attgccgccc tccgagccaa agctcaggaa cacagcacca aggttctggg
     1081 gactgtatct gggcctgaca gcctggccag aaatgctgag aagccagaag aagaggacgc
     1141 cacggaggaa gacaggccag ctgagaagct cagcccaccg cagctggagg acatggctta
     1201 gggcaagggc tgctggcctc ggaactgctc ttctccagcc ctgcagccct gcggtgtggc
     1261 gagttctctc tgaggcaagg cccatgtctg gcttctgcca cacctcccca cacctcaggc
     1321 ccgcaattac ccccacgact ctagaaacag accaattctg tccgtagctt tggaccatgc
     1381 tgagacatcc tggacatact cccgatccag cgtcctcagc ctcagcccag cttccctgcc
     1441 tccaaagcct tcttgctacc ccgacatcga ggtcctgcta cgtcatccct gagagactct
     1501 tgtccaagcc tatcccttat tctctgctct ctaagccttc ctccccagct tagccccctc
     1561 atgggcggct gcgcccactg ctgtaaaccc agcccacagc cgggcagagc tgtgattgga
     1621 ttgaggccct gcctcggtgt cccgagcacc ccagcacttt gcaggcaggc ttttccctct
     1681 tcacctgttc cttctcgcag acctggaccc tggctggctc ctgctgtgtg aatgcacagc
     1741 cgggtcacgt gggtcctgct gtgaggatgc actgctcagc tggtccacgg tgtaacctct
     1801 gcattctctg ccctgcctgc tgatgggcag attcaagtct aaacagggca actctcagat
     1861 tgagtccttc cccaaacctg tctcacgccg tgctgtagat catcctcagg ccttctccgc
     1921 accgagcctg ccctacatgt tcctcctttg cagaggtggg ccacaccacc ttgtcagtgt
     1981 ctaggccctg cagcctgagg gcggggcgct tctcggcaat gctgtggctt gctttactgc
     2041 tggtgagccc tcacccagag cttttgcacc ccagggcctg ggtgtctgaa gcattttgac
     2101 ccttctgcct atgactttga cttgctagtt aaggcttctt tctagagctt cctgtagccc
     2161 agtggctctc aagcttccta atgctatgac ctttaataca gttccttgtg ttgtggtgac
     2221 cacccccccc caacctttaa atgtatttca ttgctacttc ataactgtaa ttttgctact
     2281 gttatgaatc aaaatgtaaa tatttgatat gtggaatatc tgattatgtg acttcctcca
     2341 aaggggccat gggggtcatg acccacaggt tgagaactgc tgttgtagcc cattggttca
     2401 catgtgcctg ctttagagaa aatgggtgca gcttaaaagc cccggacatg gcctcacttt
     2461 gacctaggca gtcctaaaag gccaagccaa aatcagaccc acgctatcta tctatacaca
     2521 cacgcacacg cacacatgca cgcatgcacg cacgctgtat aacatgaaag gtacggggaa
     2581 agctcaaaga acaaggcagg tagctagtaa aaaaaccaga ctaagctaca gacgctcata
     2641 gctccgtgcc agctgtatgc ccagaaaggt gtccatagat aaggagccat gttggactga
     2701 atgccttctg cctgcaaagg agtggcactg tccatactga tggcatgtct tcagatgtcc
     2761 ctgtctgcag atgtctctgt ctgcagatgc cccttccacc tggctttata catgtactag
     2821 gggtgcagag ccttctgggg tcctctgctc ctgtattccc aggccaacca caagaccccc
     2881 tttatcctgt gaagttaccc cacctaccac ttcacaaaaa aggcccgggc agtgagttgt
     2941 gattttaaat ctgttttgac agttgatttc ttcttcgttc tcttcataga cttctcccgc
     3001 ttctgagttc ttatcttctc ccgggttgag atgttgacta tagtcctggt gtgtaaatag
     3061 tgtacataat gtgagaagga agaagctgga cactgaggtg ttcgaaacac tgaattgtca
     3121 taacttttag gtattcaaag cataatttct gtgctgtttt ctgtaaagac acaagcaaga
     3181 ataaaattca tgcaaagact gctaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaa
//
