LOCUS       NM_001302357            3102 bp    mRNA    linear   ROD 11-MAR-2025
DEFINITION  Mus musculus SHOX homeobox 2 (Shox2), transcript variant 2, mRNA.
ACCESSION   NM_001302357 XM_006501214
VERSION     NM_001302357.1
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 3102)
  AUTHORS   Abassah-Oppong,S., Zoia,M., Mannion,B.J., Rouco,R., Tissieres,V.,
            Spurrell,C.H., Roland,V., Darbellay,F., Itum,A., Gamart,J.,
            Festa-Daroux,T.A., Sullivan,C.S., Kosicki,M.,
            Rodriguez-Carballo,E., Fukuda-Yuzawa,Y., Hunter,R.D., Novak,C.S.,
            Plajzer-Frick,I., Tran,S., Akiyama,J.A., Dickel,D.E.,
            Lopez-Rios,J., Barozzi,I., Andrey,G., Visel,A., Pennacchio,L.A.,
            Cobb,J. and Osterwalder,M.
  TITLE     A gene desert required for regulatory control of pleiotropic Shox2
            expression and embryonic survival
  JOURNAL   Nat Commun 15 (1), 8793 (2024)
   PUBMED   39389973
  REMARK    GeneRIF: A gene desert required for regulatory control of
            pleiotropic Shox2 expression and embryonic survival.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3102)
  AUTHORS   Lo Giudice,Q., Wagener,R.J., Abe,P., Frangeul,L. and Jabaudon,D.
  TITLE     Developmental emergence of first- and higher-order thalamic neuron
            molecular identities
  JOURNAL   Development 151 (18) (2024)
   PUBMED   39348458
REFERENCE   3  (bases 1 to 3102)
  AUTHORS   Schott,M., Leon-Perinan,D., Splendiani,E., Strenger,L., Licha,J.R.,
            Pentimalli,T.M., Schallenberg,S., Alles,J., Samut Tagliaferro,S.,
            Boltengagen,A., Ehrig,S., Abbiati,S., Dommerich,S., Pagani,M.,
            Ferretti,E., Macino,G., Karaiskos,N. and Rajewsky,N.
  TITLE     Open-ST: High-resolution spatial transcriptomics in 3D
  JOURNAL   Cell 187 (15), 3953-3972 (2024)
   PUBMED   38917789
REFERENCE   4  (bases 1 to 3102)
  AUTHORS   Yoshida,S., Tsuneoka,Y., Tsukada,T., Nakakura,T., Kawamura,A.,
            Kai,W. and Yoshida,K.
  TITLE     Primary Cilia are Required for Cell-Type Determination and
            Angiogenesis in Pituitary Development
  JOURNAL   Endocrinology 165 (8) (2024)
   PUBMED   39001875
REFERENCE   5  (bases 1 to 3102)
  AUTHORS   Li,H., Tang,Q., Yang,T., Wang,Z., Li,D., Wang,L., Li,L., Chen,Y.,
            Huang,H., Zhang,Y. and Chen,Y.
  TITLE     Segregation of morphogenetic regulatory function of Shox2 from its
            cell fate guardian role in sinoatrial node development
  JOURNAL   Commun Biol 7 (1), 385 (2024)
   PUBMED   38553636
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3102)
  AUTHORS   Blaschke,R.J., Monaghan,A.P., Schiller,S., Schechinger,B., Rao,E.,
            Padilla-Nash,H., Ried,T. and Rappold,G.A.
  TITLE     SHOT, a SHOX-related homeobox gene, is implicated in craniofacial,
            brain, heart, and limb development
  JOURNAL   Proc Natl Acad Sci U S A 95 (5), 2406-2411 (1998)
   PUBMED   9482898
REFERENCE   7  (bases 1 to 3102)
  AUTHORS   Semina,E.V., Reiter,R.S. and Murray,J.C.
  TITLE     A new human homeobox gene OGI2X is a member of the most conserved
            homeobox gene family and is expressed during heart development in
            mouse
  JOURNAL   Hum Mol Genet 7 (3), 415-422 (1998)
   PUBMED   9466998
REFERENCE   8  (bases 1 to 3102)
  AUTHORS   van Schaick,H.S., Smidt,M.P., Rovescalli,A.C., Luijten,M., van der
            Kleij,A.A., Asoh,S., Kozak,C.A., Nirenberg,M. and Burbach,J.P.
  TITLE     Homeobox gene Prx3 expression in rodent brain and extraneural
            tissues
  JOURNAL   Proc Natl Acad Sci U S A 94 (24), 12993-12998 (1997)
   PUBMED   9371788
REFERENCE   9  (bases 1 to 3102)
  AUTHORS   Ellison,J.W., Wardak,Z., Young,M.F., Gehron Robey,P.,
            Laig-Webster,M. and Chiong,W.
  TITLE     PHOG, a candidate gene for involvement in the short stature of
            Turner syndrome
  JOURNAL   Hum Mol Genet 6 (8), 1341-1347 (1997)
   PUBMED   9259282
REFERENCE   10 (bases 1 to 3102)
  AUTHORS   Rovescalli,A.C., Asoh,S. and Nirenberg,M.
  TITLE     Cloning and characterization of four murine homeobox genes
  JOURNAL   Proc Natl Acad Sci U S A 93 (20), 10691-10696 (1996)
   PUBMED   8855241
  REMARK    Erratum:[Proc Natl Acad Sci U S A 1996 Dec 24;93(26):15522]
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC122870.4, AK032007.1 and BB363478.1.
            
            On Oct 15, 2014 this sequence version replaced XM_006501214.1.
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the 3' terminal exon, compared to variant 1. The
            encoded isoform (2) is shorter compared to isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: AK032007.1, AK145063.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164137, SAMN01164138
                                           [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
            1-460               AC122870.4         85713-86172
            461-924             AK032007.1         8-471
            925-1022            AK032007.1         473-570
            1023-1040           AK032007.1         572-589
            1041-3098           AK032007.1         591-2648
            3099-3102           BB363478.1         284-287
FEATURES             Location/Qualifiers
     source          1..3102
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 30.76 cM"
     gene            1..3102
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /note="SHOX homeobox 2"
                     /db_xref="GeneID:20429"
                     /db_xref="MGI:MGI:1201673"
     exon            1..561
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /inference="alignment:Splign:2.1.0"
     CDS             216..1175
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /note="isoform 2 is encoded by transcript variant 2; short
                     stature homeobox protein 2; OG-12; homeobox protein Og12X;
                     paired family homeodomain protein Prx3; short stature
                     homeobox 2"
                     /codon_start=1
                     /product="short stature homeobox protein 2 isoform 2"
                     /protein_id="NP_001289286.1"
                     /db_xref="GeneID:20429"
                     /db_xref="MGI:MGI:1201673"
                     /translation="MEELTAFVSKSFDQKVKEKKEAITYREVLESGPLRGAKEPGCVE
                     PGRDDRSSPAVRAAGGGGGAGGGGGGGGGGGGGAGGGGAGGGAGGGRSPVRELDMGAA
                     ERSREPGSPRLTEVSPELKDRKDDAKGMEDEGQTKIKQRRSRTNFTLEQLNELERLFD
                     ETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQENQLHKGVLIGAASQFEACR
                     VAPYVNVGALRMPFQQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPPFGLPLAT
                     LAADSASAASVVAAAAAAKTTSKNSSIADLRLKAKKHAAALGL"
     exon            562..770
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /inference="alignment:Splign:2.1.0"
     exon            771..828
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /inference="alignment:Splign:2.1.0"
     exon            829..917
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /inference="alignment:Splign:2.1.0"
     exon            918..3102
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3080..3085
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /note="hexamer: ATTAAA"
     polyA_site      3102
                     /gene="Shox2"
                     /gene_synonym="6330543G17Rik; OG12; Og12x; Prx3; SHOT"
                     /note="major polyA site"
ORIGIN      
        1 cctcctctta cttctttttc tccttctact tctcctcttc tttcttctcc tctttttctt
       61 cttcctcctc ctccctctcc tcccccatcc ccctgcccca ttgatgtgtt attattgggg
      121 gggctggagc agtaaaaaaa gaaggaggaa aaaaagagcg gggctcggca gggagagctt
      181 gagcgcgagg ttgaccggcg gcggcagcgg ccgcgatgga agaacttacg gcgttcgtct
      241 ccaagtcttt tgaccagaaa gtgaaggaga agaaggaggc catcacgtac cgggaggtgc
      301 tagagagcgg gccgctgcgc ggggccaaag agcccggttg cgtcgagccg ggccgcgacg
      361 accgcagcag cccggcagtc cgggcggccg gcggaggcgg cggcgcggga ggaggcggag
      421 gcggaggcgg aggaggcgga ggaggtgctg gaggaggagg agcaggcgga ggagctggag
      481 gagggcgctc tcccgtccgg gagctggaca tgggagccgc ggagcggagc agggagcccg
      541 gcagcccgcg gctgacggag gtgtcccctg aactgaagga tcgcaaagac gatgcgaaag
      601 ggatggagga cgaaggccag accaaaatca agcagaggcg aagtcggacc aattttaccc
      661 tggaacaact caacgagctg gagaggcttt tcgatgagac ccactatcca gacgctttca
      721 tgcgcgagga attgagccag cgactggggc tctctgaggc ccgagtacag gtttggtttc
      781 aaaatcgaag agctaagtgt agaaaacagg aaaatcaact tcacaaaggt gtccttatag
      841 gagccgctag ccagtttgaa gcttgtagag ttgcacccta tgtcaacgta ggtgctttaa
      901 ggatgccatt tcagcaggtt caggcgcagc tgcagctgga cagcgccgtg gcgcacgcgc
      961 accaccacct gcatccgcac ctggccgcgc acgcgcctta catgatgttc ccggcaccgc
     1021 ccttcggact gccgctggcc acgctggccg cggactcggc ctcggccgcc tcggtggtgg
     1081 ccgctgccgc cgccgccaag accaccagca agaactccag catcgcggat ctcagactga
     1141 aagctaaaaa gcacgcggcc gccctgggtc tgtgacgccg gcgccagcgc cacggtcggt
     1201 ggagcctcct aagcggcgcg atcctgcacg ccctccgcga ccggcttctc ccgcacccgc
     1261 ttctgaccgt cgcccaggcc tgtcccttcc ccgctgactg ccgccttttc tttctgcacc
     1321 ctggatcccc agggcgggac tctgcgctgg acccgggatc ccacgagggc caccagccca
     1381 ggggctcctg cccacccgcc cttgggacta aaattcggct ttgtaggagc gggtttgggg
     1441 aagtctggat agagactgga caaaggagtg tggccacagt gagaagtgga tagcgccaca
     1501 gctgcggcga tggactcgtt cataggaata aaatcttgct aacagcaaat gagcaaaaac
     1561 aaaaaagaat agagaacaaa ctagaaagaa aacgagaaag ggagcttgtt tcatattgct
     1621 atttggctgg aattagagag agaacgacga agcaaaaaca attcttaaaa ttattttgta
     1681 cataaaaata cggaaaaata acctggatga atcttgagag aaagggggag ggagggattt
     1741 accaactaaa atgtatgttt tttttttaat ggtccaagaa aacaaaacag aaggaagagg
     1801 tatacttatt taaagaatta agatggaaaa aaagcgcagc tgggaagttc acaggttttg
     1861 aagctgacct ttttctgcga agttcacttt aataggagac atttgataag agaggcgggc
     1921 ctccttttac gttgaatctg atgctttgag ttttaaaaca ccatgtatgg aagagcaaga
     1981 agagggaaga cagtgtgaaa acgaggaggg aaaaaaggac gttcatacaa aaaagaaaga
     2041 aaagaaaaga aaaagcgata ccacagacag tgattcctct gagaaattta cattatggca
     2101 gaactgtcca gactgctgac agtcaattct ggtttgcatg ttactagtat tccattgatg
     2161 gtgtcccctc ccctcccact ctcacgtgca ctcactacac tttcattctc agtatgaaaa
     2221 gcgtctggaa attgatgtga atccatatat aatttgtccg gcctttgatc ccaaggggca
     2281 aagggaaaaa aaaagtgtca taagggagta aaatacactc tgagtcttcc aagaacacgg
     2341 aggctgttag gaaatatggg caaagaaaag agaagagcaa atgaagtcac gaaggtacac
     2401 tgcagggcat cgtgataggc gctttatctg ttctctacct tttcgtgaat tccctcttgc
     2461 tagtttaagt cctatttgag gacaatgctt tattcccacc ccacccctcc tctctatcct
     2521 gtcaaattca ccttaaacga tacccagcta ggtacagaca ctaggtttgt gtataatatg
     2581 ttgataaaca cgaacaaagt ttattttggc tataatgtgt gaactaatgg ttgactttca
     2641 acatttgcat tttatctcac aaaagtgtat ctattcaagt aatctttgtt tttgtttcaa
     2701 ttcatgtagc tatttaaaca gggatacctt gggctaagca acctgtagcc ccaattctct
     2761 agcaagcctc tttagaaccc cctttaattt acatgaaaga ggaaaagctc ttcttactga
     2821 actttggtat gcgtttgagc tttgtaacta tttgttctcc atgaaaacaa aattatttat
     2881 atttgccata ttttttctag tgtattaagt tattttaaac gaaagaagat gctgttatga
     2941 cgtgttgtca gtacaaaatg tttcagctcc acttctgtta aaccttttaa ataagtgcca
     3001 agttattaac ctaagacaat tgaatgaaaa tagtattgtt tcatttgatg gggtgcgcgt
     3061 catctttgtt cttgttacta ttaaaatatc cgggatactc tt
//
