GGRNA | NM_003030.4

LOCUS       NM_003030               3233 bp    mRNA    linear   PRI 07-JUL-2013
DEFINITION  Homo sapiens short stature homeobox 2 (SHOX2), transcript variant
            1, mRNA.
ACCESSION   NM_003030
VERSION     NM_003030.4  GI:254750646
KEYWORDS    RefSeq.
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 3233)
  AUTHORS   Dietrich,D., Hasinger,O., Liebenberg,V., Field,J.K., Kristiansen,G.
            and Soltermann,A.
  TITLE     DNA methylation of the homeobox genes PITX2 and SHOX2 predicts
            outcome in non-small-cell lung cancer patients
  JOURNAL   Diagn. Mol. Pathol. 21 (2), 93-104 (2012)
   PUBMED   22555092
  REMARK    GeneRIF: DNA methylation of PITX2 and SHOX2 is an independent
            prognostic biomarker for disease progression in non-small-cell lung
            cancer patients.
REFERENCE   2  (bases 1 to 3233)
  AUTHORS   Dietrich,D., Kneip,C., Raji,O., Liloglou,T., Seegebarth,A.,
            Schlegel,T., Flemming,N., Rausch,S., Distler,J., Fleischhacker,M.,
            Schmidt,B., Giles,T., Walshaw,M., Warburton,C., Liebenberg,V. and
            Field,J.K.
  TITLE     Performance evaluation of the DNA methylation biomarker SHOX2 for
            the aid in diagnosis of lung cancer based on the analysis of
            bronchial aspirates
  JOURNAL   Int. J. Oncol. 40 (3), 825-832 (2012)
   PUBMED   22108652
  REMARK    GeneRIF: A CE marked in vitro diagnostic test kit to quantify SHOX2
            DNA methylation in bronchial aspirates was developed and
            characterized.
REFERENCE   3  (bases 1 to 3233)
  AUTHORS   Kneip,C., Schmidt,B., Seegebarth,A., Weickmann,S.,
            Fleischhacker,M., Liebenberg,V., Field,J.K. and Dietrich,D.
  TITLE     SHOX2 DNA methylation is a biomarker for the diagnosis of lung
            cancer in plasma
  JOURNAL   J Thorac Oncol 6 (10), 1632-1638 (2011)
   PUBMED   21694641
  REMARK    GeneRIF: SHOX2 DNA methylation is associated with lung cancer.
REFERENCE   4  (bases 1 to 3233)
  AUTHORS   Schneider,K.U., Dietrich,D., Fleischhacker,M., Leschber,G.,
            Merk,J., Schaper,F., Stapert,H.R., Vossenaar,E.R., Weickmann,S.,
            Liebenberg,V., Kneip,C., Seegebarth,A., Erdogan,F., Rappold,G. and
            Schmidt,B.
  TITLE     Correlation of SHOX2 gene amplification and DNA methylation in lung
            cancer tumors
  JOURNAL   BMC Cancer 11, 102 (2011)
   PUBMED   21426551
  REMARK    GeneRIF: Frequent gene amplification correlated with
            hypermethylation of the SHOX2 gene locus.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3233)
  AUTHORS   Schmidt,B., Liebenberg,V., Dietrich,D., Schlegel,T., Kneip,C.,
            Seegebarth,A., Flemming,N., Seemann,S., Distler,J., Lewin,J.,
            Tetzner,R., Weickmann,S., Wille,U., Liloglou,T., Raji,O.,
            Walshaw,M., Fleischhacker,M., Witt,C. and Field,J.K.
  TITLE     SHOX2 DNA methylation is a biomarker for the diagnosis of lung
            cancer based on bronchial aspirates
  JOURNAL   BMC Cancer 10, 600 (2010)
   PUBMED   21047392
  REMARK    GeneRIF: SHOX2 DNA methylation is found in bronchial aspirates of
            lung cancer patients
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3233)
  AUTHORS   Yerges LM, Klei L, Cauley JA, Roeder K, Kammerer CM, Moffett SP,
            Ensrud KE, Nestlerode CS, Marshall LM, Hoffman AR, Lewis C, Lang
            TF, Barrett-Connor E, Ferrell RE, Orwoll ES and Zmuda JM.
  CONSRTM   MrOS Research Group
  TITLE     High-density association study of 383 candidate genes for
            volumetric BMD at the femoral neck and lumbar spine among older men
  JOURNAL   J. Bone Miner. Res. 24 (12), 2039-2049 (2009)
   PUBMED   19453261
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 3233)
  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 3233)
  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 3233)
  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 3233)
  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 BX331739.2, BC008829.2,
            AC112502.7 and AA450208.1.
            On Jul 28, 2009 this sequence version replaced gi:87044887.
            
            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 (1) represents the longest
            transcript and encodes the longest 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 :: BC008829.2 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025081, ERS025082 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-3                 BX331739.2         345-347
            4-1542              BC008829.2         4-1542
            1543-2830           AC112502.7         20366-21653         c
            2831-3233           AA450208.1         1-403               c
FEATURES             Location/Qualifiers
     source          1..3233
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q25.32"
     gene            1..3233
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="short stature homeobox 2"
                     /db_xref="GeneID:6474"
                     /db_xref="HGNC:10854"
                     /db_xref="MIM:602504"
     exon            1..485
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    125..127
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="upstream in-frame stop codon"
     CDS             140..1207
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="isoform b is encoded by transcript variant 1; SHOX
                     homologous gene on chromosome 3; short stature homeobox
                     protein 2; paired-related homeobox protein SHOT; homeobox
                     protein Og12X"
                     /codon_start=1
                     /product="short stature homeobox protein 2 isoform b"
                     /protein_id="NP_003021.3"
                     /db_xref="GI:254750647"
                     /db_xref="CCDS:CCDS33884.2"
                     /db_xref="GeneID:6474"
                     /db_xref="HGNC:10854"
                     /db_xref="MIM:602504"
                     /translation="

MEELTAFVSKSFDQKVKEKKEAITYREVLESGPLRGAKEPTGCTEAGRDDRSSPAVRAAGGGGGGGGGGGGGGGGGGVGGGGAGGGAGGGRSPVRELDMGAAERSREPGSPRLTEGRRKPTKAEVQATLLLPGEAFRFLVSPELKDRKEDAKGMEDEGQTKIKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQENQLHKGVLIGAASQFEACRVAPYVNVGALRMPFQQDSHCNVTPLSFQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPPFGLPLATLAADSASAASVVAAAAAAKTTSKNSSIADLRLKAKKHAAALGL

"
     misc_feature    632..808
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:28970"
     misc_feature    order(632..646,650..652,701..703,719..721,758..760,
                     764..769,776..781,785..793,797..802)
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(638..640,647..649,767..769,776..781,788..790)
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     exon            486..557
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:1.39.8"
     exon            558..766
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:1.39.8"
     variation       586
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace="a"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:1140219"
     exon            767..824
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:1.39.8"
     exon            825..913
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:1.39.8"
     exon            914..3223
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /inference="alignment:Splign:1.39.8"
     variation       1145
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:1063254"
     variation       1505
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1063256"
     variation       1562
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:1048243"
     variation       2302..2303
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace=""
                     /replace="acatat"
                     /replace="ca"
                     /replace="cata"
                     /db_xref="dbSNP:67436323"
     variation       2302
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace="cac"
                     /replace="tat"
                     /db_xref="dbSNP:71302261"
     variation       2812
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1140222"
     STS             2993..3142
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
                     /standard_name="RH92222"
                     /db_xref="UniSTS:88362"
     polyA_site      3223
                     /gene="SHOX2"
                     /gene_synonym="OG12; OG12X; SHOT"
ORIGIN

cctcctccctctcctcccccacctcctgtcccattgatgtgttattattgggggggctggagcagtaaaaaaagaagaaggaaaaaaagagcggggctctgctggcagaggttgagcgccgggctgacgtgcggcggcgatggaagaacttacggcgttcgtctccaagtcttttgaccagaaagtgaaggagaagaaggaggcgatcacgtaccgggaggtgctggagagcgggccgctgcgcggggccaaggagccgaccggctgcaccgaggcgggccgcgacgaccgcagcagcccggcagtccgggcggccggcggaggcggcggcggaggaggcggaggcggcggcggaggaggcggaggaggtgtaggaggaggaggagcaggcggaggagctggaggagggcgctctcccgtccgggagctggacatgggcgccgccgagagaagcagggagccgggcagcccgcgactgacggagggtagaaggaagccaacgaaagctgaggtccaggctacgctgcttctcccgggcgaggcgtttcggtttcttgtgtccccggagctgaaagatcgcaaagaggatgcgaaagggatggaggacgaaggccagaccaaaatcaagcagaggcgaagtcggaccaatttcaccctggaacaactcaatgagctggagaggctttttgacgagacccactatcccgacgccttcatgcgagaggaactgagccagcgactgggcctgtcggaggcccgagtgcaggtttggtttcaaaatcgaagagctaaatgtagaaaacaagaaaatcaactccataaaggtgttctcataggggccgccagccagtttgaagcttgtagagtcgcaccttatgtcaacgtaggtgctttaaggatgccatttcagcaggatagtcattgcaacgtgacgcccttgtcctttcaggttcaggcgcagctgcagctggacagcgctgtggcgcacgcgcaccaccacctgcatccgcacctggccgcgcacgcgccctacatgatgttcccagcaccgcccttcggactgccgctcgccacgctggccgcggattcggcttccgccgcctcggtagtggcggccgcagcagccgccaagaccaccagcaagaactccagcatcgccgatctcagactgaaagccaaaaagcacgccgcagccctgggtctgtgacgccaacgccagcaccaatgtcgcgcctgtcccgcggcactcagcctgcacgccctccgcgccccgctgcttctccgttacccctttgagacctcgggagccggccctcttcccgcctcactgaccatccctcgtcccctatcgcatcttggactcggaaagccagactccacgcaggaccagggatctcacgaggcacgcaggctccgtggctcctgcccgttttcctactcgagggcctagaattgggttttgtaggagcgggtttgggggagtctggagagagactggacaggggagtgctggaaccgcggagtttggctcaccgcaaagctgcaacgatggactcttgcatagaaaaaaaaatcttgttaacaatgaaaaaatgagcaaacaaaaaaatcgaaagacaaacgggagagaaaaagaggaagggaacttatttcttaactgctatttggcagaagctgaaattggagaaccaaggagcaaaaacaaattttaaaattaaagtattttatacatttaaaaatatggaaaaacaacccagacgattctcgagagactggggggagttaccaacttaaatgtgtgtttttaaaaatgcgctaagaaggcaaagcagaaagaagaggtatacttatttaaaaaactaagatgaaaaaagtgcgcagctgggaagttcacaggttttgaaactgacctttttctgcgaagttcacgttaacacgagaaatttgatgagagaggcgggcctccttttacgttgaatcagatgctttgagtttaaacccaccatgtatggaagagcaagaaaagagaaaatattaaaacgaggagagagaaaaataatattaacacaaaaaaatgccacagacaatgatttctctgagaaattattatggcaaaactgtctggactgctgacagtaaattccggtttgcatgttacttgtattccattgatggtgtgtctcctcccacccccttatctcccatgcactcactccattttcatcttcactatgaaaaacaataccaaaagtatctggaaattgatatatatatatccatatatatatatcatatatttgccatatatatatatatatatatatatatatatatatatatatatttgccctgtctttgatcctggggaacaaaagaaaaaagtcagaaagggaaaaaattacactcattgtcctaagaagacagaggtgggcagaatatgtggggaaaggaaaaagaaaacaagaccaccaaatgaaataatgaaggtacagcgcctcgctgtgccagacacagtaggcgctcaatcagtattagttcccaccattccccttttcttgtgttccttcttgttggtttcctgaagtcctatttgaagacagtggtttatttccccctctctatcccgtcaaattcaccttaaataacacccagctagatacaggcactaggtttgtgtaagatatgttgatacacacgaacaaagtttattttgactataatgtgtggactgactttcaacatttgcattttatctcacaaaggtgtatctattcaagtaaccttttttttttgtttgtttgtttcttttttgtttttttttttcttttggttgtttgtttcaattcatgtagctatttaaactgggataccttggactaagccagtctgtatcccaattcgctagcaagcctaagtttgtggggttttgtttttgtttttgttttaccttctaatttacaagaaagaggaaaagctcttctaactgaactttggtatgcggttgagctttgtaactatttgttctccatgaaaacaaaattatttatatttgacatatttttttctagtgtattaagttattttaaacaaaagatgttatctcatgacgtgttgtcagtacaaaatgtgtcgcctccaattctgttaaaccttttaaataagtgccaagttattaattgaagacactttgcgatcaattgaatgaaaatatcgtttcatttgaaaaaaaaaaa

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