LOCUS       NM_001163678            3478 bp    mRNA    linear   PRI 29-OCT-2024
DEFINITION  Homo sapiens SHOX homeobox 2 (SHOX2), transcript variant 3, mRNA.
ACCESSION   NM_001163678
VERSION     NM_001163678.2
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3478)
  AUTHORS   Chen,X., Li,S. and Sun,B.
  TITLE     Downregulation of short-stature homeobox protein 2 suppresses
            gastric cancer cell growth and stemness in vitro and in vivo via
            inactivating wnt/beta-catenin signaling
  JOURNAL   Drug Dev Res 85 (7), e70006 (2024)
   PUBMED   39415634
  REMARK    GeneRIF: Downregulation of short-stature homeobox protein 2
            suppresses gastric cancer cell growth and stemness in vitro and in
            vivo via inactivating wnt/beta-catenin signaling.
REFERENCE   2  (bases 1 to 3478)
  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   3  (bases 1 to 3478)
  AUTHORS   Zhao,J., Lu,Y., Ren,X., Bian,T., Feng,J., Sun,H., Liu,L., She,B.,
            Liu,Y. and Ke,H.
  TITLE     Association of the SHOX2 and RASSF1A methylation levels with the
            pathological evolution of early-stage lung adenocarcinoma
  JOURNAL   BMC Cancer 24 (1), 687 (2024)
   PUBMED   38840077
  REMARK    GeneRIF: Association of the SHOX2 and RASSF1A methylation levels
            with the pathological evolution of early-stage lung adenocarcinoma.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3478)
  AUTHORS   Vo,T.T.L., Nguyen,T.N., Nguyen,T.T., Pham,A.T.D., Vuong,D.L.,
            Ta,V.T. and Ho,V.S.
  TITLE     SHOX2 methylation in Vietnamese patients with lung cancer
  JOURNAL   Mol Biol Rep 49 (5), 3413-3421 (2022)
   PUBMED   35088378
  REMARK    GeneRIF: SHOX2 methylation in Vietnamese patients with lung cancer.
REFERENCE   5  (bases 1 to 3478)
  AUTHORS   Teng,Y., Loveless,R., Benson,E.M., Sun,L., Shull,A.Y. and Shay,C.
  TITLE     SHOX2 cooperates with STAT3 to promote breast cancer metastasis
            through the transcriptional activation of WASF3
  JOURNAL   J Exp Clin Cancer Res 40 (1), 274 (2021)
   PUBMED   34465361
  REMARK    GeneRIF: SHOX2 cooperates with STAT3 to promote breast cancer
            metastasis through the transcriptional activation of WASF3.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3478)
  AUTHORS   Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M.
  TITLE     A census of human transcription factors: function, expression and
            evolution
  JOURNAL   Nat Rev Genet 10 (4), 252-263 (2009)
   PUBMED   19274049
  REMARK    Review article
REFERENCE   7  (bases 1 to 3478)
  AUTHORS   Hillman,R.T., Green,R.E. and Brenner,S.E.
  TITLE     An unappreciated role for RNA surveillance
  JOURNAL   Genome Biol 5 (2), R8 (2004)
   PUBMED   14759258
REFERENCE   8  (bases 1 to 3478)
  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   9  (bases 1 to 3478)
  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   10 (bases 1 to 3478)
  AUTHORS   De Baere,E., Speleman,F., Van Roy,N., De Paepe,A. and Messiaen,L.
  TITLE     Assignment of SHOX2 (alias OG12X and SHOT) to human chromosome
            bands 3q25-->q26.1 by in situ hybridization
  JOURNAL   Cytogenet Cell Genet 82 (3-4), 228-229 (1998)
   PUBMED   9858825
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC112502.7 and DA447204.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Oct 16, 2019 this sequence version replaced NM_001163678.1.
            
            Summary: This gene is a member of the homeobox family of genes that
            encode proteins containing a 60-amino acid residue motif that
            represents a DNA binding domain. Homeobox genes have been
            characterized extensively as transcriptional regulators involved in
            pattern formation in both invertebrate and vertebrate species.
            Several human genetic disorders are caused by aberrations in human
            homeobox genes. This locus represents a pseudoautosomal homeobox
            gene that is thought to be responsible for idiopathic short
            stature, and it is implicated in the short stature phenotype of
            Turner syndrome patients. This gene is considered to be a candidate
            gene for Cornelia de Lange syndrome. Alternative splicing results
            in multiple transcript variants. [provided by RefSeq, Jul 2009].
            
            Transcript Variant: This variant (3) lacks an alternate in-frame
            exon and uses an alternate in-frame splice site in the coding
            region, compared to variant 1, resulting in an isoform (c) that is
            shorter than isoform b.
            
            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 :: SRR14038191.1763650.1,
                                           SRR14038195.2603355.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2142680
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000483851.7/ ENSP00000419362.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-686               AC112502.7         29697-30382         c
            687-1155            DA447204.1         1-469
            1156-3478           AC112502.7         19867-22189         c
FEATURES             Location/Qualifiers
     source          1..3478
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q25.32"
     gene            1..3478
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="SHOX homeobox 2"
                     /db_xref="GeneID:6474"
                     /db_xref="HGNC:HGNC:10854"
                     /db_xref="MIM:602504"
     exon            1..742
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:2.1.0"
     CDS             397..1356
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="isoform c is encoded by transcript variant 3; SHOX
                     homologous gene on chromosome 3; short stature homeobox 2;
                     paired-related homeobox protein SHOT; homeobox protein
                     Og12X"
                     /codon_start=1
                     /product="short stature homeobox protein 2 isoform c"
                     /protein_id="NP_001157150.1"
                     /db_xref="CCDS:CCDS54664.1"
                     /db_xref="GeneID:6474"
                     /db_xref="HGNC:HGNC:10854"
                     /db_xref="MIM:602504"
                     /translation="MEELTAFVSKSFDQKVKEKKEAITYREVLESGPLRGAKEPTGCT
                     EAGRDDRSSPAVRAAGGGGGGGGGGGGGGGGGGVGGGGAGGGAGGGRSPVRELDMGAA
                     ERSREPGSPRLTEVSPELKDRKEDAKGMEDEGQTKIKQRRSRTNFTLEQLNELERLFD
                     ETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQENQLHKGVLIGAASQFEACR
                     VAPYVNVGALRMPFQQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPPFGLPLAT
                     LAADSASAASVVAAAAAAKTTSKNSSIADLRLKAKKHAAALGL"
     exon            743..951
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:2.1.0"
     exon            952..1009
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:2.1.0"
     exon            1010..1098
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:2.1.0"
     exon            1099..3478
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3350..3355
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="hexamer: AATGAA"
     polyA_site      3372
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
     regulatory      3404..3409
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="hexamer: ATTAAA"
     polyA_site      3424
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="major polyA site"
     regulatory      3458..3463
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="hexamer: AATATA"
     polyA_site      3478
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
ORIGIN      
        1 gctatcagat ctgaactctc cgcaggaaga attgtcaaag atcttaacat tgaacaagcg
       61 cgctccggca gggaagcatc agttcccatt tccctccggc agcccccgcc ccttctcttc
      121 tcctcctcct cctccctctc ctcttcaccc ttctccccct cttcctcttc ttcctcctcc
      181 tcctcttctt acttcttttt ctccttctac ttctcctcct ctttcttctt tcttctcctc
      241 tttttcttct tctttctcct cctccctctc ctcccccacc tcctgtccca ttgatgtgtt
      301 attattgggg gggctggagc agtaaaaaaa gaagaaggaa aaaaagagcg gggctctgct
      361 ggcagaggtt gagcgccggg ctgacgtgcg gcggcgatgg aagaacttac ggcgttcgtc
      421 tccaagtctt ttgaccagaa agtgaaggag aagaaggagg cgatcacgta ccgggaggtg
      481 ctggagagcg ggccgctgcg cggggccaag gagccgaccg gctgcaccga ggcgggccgc
      541 gacgaccgca gcagcccggc agtccgggcg gccggcggag gcggcggcgg aggaggcgga
      601 ggcggcggcg gaggaggcgg aggaggtgta ggaggaggag gagcaggcgg aggagctgga
      661 ggagggcgct ctcccgtccg ggagctggac atgggcgccg ccgagagaag cagggagccg
      721 ggcagcccgc gactgacgga ggtgtccccg gagctgaaag atcgcaaaga ggatgcgaaa
      781 gggatggagg acgaaggcca gaccaaaatc aagcagaggc gaagtcggac caatttcacc
      841 ctggaacaac tcaatgagct ggagaggctt tttgacgaga cccactatcc cgacgccttc
      901 atgcgagagg aactgagcca gcgactgggc ctgtcggagg cccgagtgca ggtttggttt
      961 caaaatcgaa gagctaaatg tagaaaacaa gaaaatcaac tccataaagg tgttctcata
     1021 ggggccgcca gccagtttga agcttgtaga gtcgcacctt atgtcaacgt aggtgcttta
     1081 aggatgccat ttcagcaggt tcaggcgcag ctgcagctgg acagcgctgt ggcgcacgcg
     1141 caccaccacc tgcatccgca cctggccgcg cacgcgccct acatgatgtt cccagcaccg
     1201 cccttcggac tgccgctcgc cacgctggcc gcggattcgg cttccgccgc ctcggtagtg
     1261 gcggccgcag cagccgccaa gaccaccagc aagaactcca gcatcgccga tctcagactg
     1321 aaagccaaaa agcacgccgc agccctgggt ctgtgacgcc aacgccagca ccaatgtcgc
     1381 gcctgtcccg cggcactcag cctgcacgcc ctccgcgccc cgctgcttct ccgttacccc
     1441 tttgagacct cgggagccgg ccctcttccc gcctcactga ccatccctcg tcccctatcg
     1501 catcttggac tcggaaagcc agactccacg caggaccagg gatctcacga ggcacgcagg
     1561 ctccgtggct cctgcccgtt ttcctactcg agggcctaga attgggtttt gtaggagcgg
     1621 gtttggggga gtctggagag agactggaca ggggagtgct ggaaccgcgg agtttggctc
     1681 accgcaaagc tgcaacgatg gactcttgca tagaaaaaaa aatcttgtta acaatgaaaa
     1741 aatgagcaaa caaaaaaatc gaaagacaaa cgggagagaa aaagaggaag ggaacttatt
     1801 tcttaactgc tatttggcag aagctgaaat tggagaacca aggagcaaaa acaaatttta
     1861 aaattaaagt attttataca tttaaaaata tggaaaaaca acccagacga ttctcgagag
     1921 actgggggga gttaccaact taaatgtgtg tttttaaaaa tgcgctaaga aggcaaagca
     1981 gaaagaagag gtatacttat ttaaaaaact aagatgaaaa aagtgcgcag ctgggaagtt
     2041 cacaggtttt gaaactgacc tttttctgcg aagttcacgt taacacgaga aatttgatga
     2101 gagaggcggg cctcctttta cgttgaatca gatgctttga gtttaaaccc accatgtatg
     2161 gaagagcaag aaaagagaaa atattaaaac gaggagagag aaaaataata ttaacacaaa
     2221 aaaatgccac agacaatgat ttctctgaga aattattatg gcaaaactgt ctggactgct
     2281 gacagtaaat tccggtttgc atgttacttg tattccattg atggtgtgtc tcctcccacc
     2341 cccttatctc ccatgcactc actccatttt catcttcact atgaaaaaca ataccaaaag
     2401 tatctggaaa ttgatatata tatatccata tatatatatc atatatttgc catatatata
     2461 tatatatata tatatatata tatatatata tatttgccct gtctttgatc ctggggaaca
     2521 aaagaaaaaa gtcagaaagg gaaaaaatta cactcattgt cctaagaaga cagaggtggg
     2581 cagaatatgt ggggaaagga aaaagaaaac aagaccacca aatgaaataa tgaaggtaca
     2641 gcgcctcgct gtgccagaca cagtaggcgc tcaatcagta ttagttccca ccattcccct
     2701 tttcttgtgt tccttcttgt tggtttcctg aagtcctatt tgaagacagt ggtttatttc
     2761 cccctctcta tcccgtcaaa ttcaccttaa ataacaccca gctagataca ggcactaggt
     2821 ttgtgtaaga tatgttgata cacacgaaca aagtttattt tgactataat gtgtggactg
     2881 actttcaaca tttgcatttt atctcacaaa ggtgtatcta ttcaagtaac cttttttttt
     2941 tgtttgtttg tttctttttt gttttttttt ttcttttggt tgtttgtttc aattcatgta
     3001 gctatttaaa ctgggatacc ttggactaag ccagtctgta tcccaattcg ctagcaagcc
     3061 taagtttgtg gggttttgtt tttgtttttg ttttaccttc taatttacaa gaaagaggaa
     3121 aagctcttct aactgaactt tggtatgcgg ttgagctttg taactatttg ttctccatga
     3181 aaacaaaatt atttatattt gacatatttt tttctagtgt attaagttat tttaaacaaa
     3241 agatgttatc tcatgacgtg ttgtcagtac aaaatgtgtc gcctccaatt ctgttaaacc
     3301 ttttaaataa gtgccaagtt attaattgaa gacactttgc gatcaattga atgaaaatat
     3361 cgtttcattt gatggggttc gagtcatctt tgttcctgtt actattaaaa tatccgggat
     3421 agtctttccc ttttgattaa tgcgtatcac tctctcgaat ataccaactt ggaaaagc
//
