GGRNA | NM_175875.4

LOCUS       NM_175875               3352 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens SIX homeobox 5 (SIX5), mRNA.
ACCESSION   NM_175875
VERSION     NM_175875.4  GI:254675329
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 3352)
  AUTHORS   Wang,S.H., Wu,C.C., Lu,Y.C., Lin,Y.H., Su,Y.N., Hwu,W.L., Yu,I.S.
            and Hsu,C.J.
  TITLE     Mutation screening of the EYA1, SIX1, and SIX5 genes in an East
            Asian cohort with branchio-oto-renal syndrome
  JOURNAL   Laryngoscope 122 (5), 1130-1136 (2012)
   PUBMED   22447252
  REMARK    GeneRIF: In East Asian populations, a SIX1 mutation has been
            reported in a Japanese family with branchio-oto (BO) syndrome,yet
            SIX5 mutations have never been reported.
REFERENCE   2  (bases 1 to 3352)
  AUTHORS   Krug,P., Moriniere,V., Marlin,S., Koubi,V., Gabriel,H.D., Colin,E.,
            Bonneau,D., Salomon,R., Antignac,C. and Heidet,L.
  TITLE     Mutation screening of the EYA1, SIX1, and SIX5 genes in a large
            cohort of patients harboring branchio-oto-renal syndrome calls into
            question the pathogenic role of SIX5 mutations
  JOURNAL   Hum. Mutat. 32 (2), 183-190 (2011)
   PUBMED   21280147
  REMARK    GeneRIF: Study reports a screening of 140 patients from 124
            families with Branchio-oto-renal and identified 36 EYA1 mutations
            in 42 unrelated patients, 2 mutations, and 1 change of unknown
            significance in SIX1 in 3 unrelated patients, but no mutation in
            SIX5.
REFERENCE   3  (bases 1 to 3352)
  AUTHORS   Yoshida,T., Kato,K., Yokoi,K., Oguri,M., Watanabe,S., Metoki,N.,
            Yoshida,H., Satoh,K., Aoyagi,Y., Nozawa,Y. and Yamada,Y.
  TITLE     Association of genetic variants with hemorrhagic stroke in Japanese
            individuals
  JOURNAL   Int. J. Mol. Med. 25 (4), 649-656 (2010)
   PUBMED   20198315
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   4  (bases 1 to 3352)
  AUTHORS   Oguri,M., Kato,K., Yokoi,K., Yoshida,T., Watanabe,S., Metoki,N.,
            Yoshida,H., Satoh,K., Aoyagi,Y., Nozawa,Y. and Yamada,Y.
  TITLE     Assessment of a polymorphism of SDK1 with hypertension in Japanese
            Individuals
  JOURNAL   Am. J. Hypertens. 23 (1), 70-77 (2010)
   PUBMED   19851296
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   5  (bases 1 to 3352)
  AUTHORS   Hoskins,B.E., Cramer,C.H., Silvius,D., Zou,D., Raymond,R.M.,
            Orten,D.J., Kimberling,W.J., Smith,R.J., Weil,D., Petit,C.,
            Otto,E.A., Xu,P.X. and Hildebrandt,F.
  TITLE     Transcription factor SIX5 is mutated in patients with
            branchio-oto-renal syndrome
  JOURNAL   Am. J. Hum. Genet. 80 (4), 800-804 (2007)
   PUBMED   17357085
  REMARK    GeneRIF: Transcription factor SIX5 is mutated in patients with
            branchio-oto-renal syndrome.
REFERENCE   6  (bases 1 to 3352)
  AUTHORS   Ohto,H., Kamada,S., Tago,K., Tominaga,S.I., Ozaki,H., Sato,S. and
            Kawakami,K.
  TITLE     Cooperation of six and eya in activation of their target genes
            through nuclear translocation of Eya
  JOURNAL   Mol. Cell. Biol. 19 (10), 6815-6824 (1999)
   PUBMED   10490620
REFERENCE   7  (bases 1 to 3352)
  AUTHORS   Winchester,C.L., Ferrier,R.K., Sermoni,A., Clark,B.J. and
            Johnson,K.J.
  TITLE     Characterization of the expression of DMPK and SIX5 in the human
            eye and implications for pathogenesis in myotonic dystrophy
  JOURNAL   Hum. Mol. Genet. 8 (3), 481-492 (1999)
   PUBMED   9949207
REFERENCE   8  (bases 1 to 3352)
  AUTHORS   Murakami,Y., Ohto,H., Ikeda,U., Shimada,K., Momoi,T. and
            Kawakami,K.
  TITLE     Promoter of mDMAHP/Six5: differential utilization of multiple
            transcription initiation sites and positive/negative regulatory
            elements
  JOURNAL   Hum. Mol. Genet. 7 (13), 2103-2112 (1998)
   PUBMED   9817928
REFERENCE   9  (bases 1 to 3352)
  AUTHORS   Klesert,T.R., Otten,A.D., Bird,T.D. and Tapscott,S.J.
  TITLE     Trinucleotide repeat expansion at the myotonic dystrophy locus
            reduces expression of DMAHP
  JOURNAL   Nat. Genet. 16 (4), 402-406 (1997)
   PUBMED   9241282
REFERENCE   10 (bases 1 to 3352)
  AUTHORS   Boucher,C.A., King,S.K., Carey,N., Krahe,R., Winchester,C.L.,
            Rahman,S., Creavin,T., Meghji,P., Bailey,M.E., Chartier,F.L. et al.
  TITLE     A novel homeodomain-encoding gene is associated with a large CpG
            island interrupted by the myotonic dystrophy unstable (CTG)n repeat
  JOURNAL   Hum. Mol. Genet. 4 (10), 1919-1925 (1995)
   PUBMED   8595416
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC074212.5, AK074826.1 and
            BC033204.1.
            This sequence is a reference standard in the RefSeqGene project.
            On Jul 24, 2009 this sequence version replaced gi:40354215.
            
            Summary: The protein encoded by this gene is a
            homeodomain-containing transcription factor that appears to
            function in the regulation of organogenesis. This gene is located
            downstream of the dystrophia myotonica-protein kinase gene.
            Mutations in this gene are a cause of branchiootorenal syndrome
            type 2. [provided by RefSeq, Jul 2009].
            
            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 :: AK074826.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025081, ERS025083 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-947               AC074212.5         29298-30244         c
            948-2471            AK074826.1         1-1524
            2472-3227           AC074212.5         25894-26649         c
            3228-3352           BC033204.1         1299-1423
FEATURES             Location/Qualifiers
     source          1..3352
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19q13.32"
     gene            1..3352
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="SIX homeobox 5"
                     /db_xref="GeneID:147912"
                     /db_xref="HGNC:10891"
                     /db_xref="HPRD:09024"
                     /db_xref="MIM:600963"
     exon            1..1198
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    1
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="5'-most transcription start site"
     misc_feature    11
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="alternative transcription start site"
     misc_feature    27
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="alternative transcription start site"
     misc_feature    32
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="alternative transcription start site"
     misc_feature    51..53
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="upstream in-frame stop codon"
     misc_feature    55
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="alternative transcription start site"
     CDS             396..2615
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="DM locus-associated homeodomain protein; dystrophia
                     myotonica-associated homeodomain protein; sine oculis
                     homeobox homolog 5"
                     /codon_start=1
                     /product="homeobox protein SIX5"
                     /protein_id="NP_787071.2"
                     /db_xref="GI:40354216"
                     /db_xref="CCDS:CCDS12673.1"
                     /db_xref="GeneID:147912"
                     /db_xref="HGNC:10891"
                     /db_xref="HPRD:09024"
                     /db_xref="MIM:600963"
                     /translation="

MATLPAEPSAGPAAGGEAVAAAAATEEEEEEARQLLQTLQAAEGEAAAAAGAGAGAAAAGAEGPGSPGVPGSPPEAASEPPTGLRFSPEQVACVCEALLQAGHAGRLSRFLGALPPAERLRGSDPVLRARALVAFQRGEYAELYRLLESRPFPAAHHAFLQDLYLRARYHEAERARGRALGAVDKYRLRKKFPLPKTIWDGEETVYCFKERSRAALKACYRGNRYPTPDEKRRLATLTGLSLTQVSNWFKNRRQRDRTGAGGGAPCKSESDGNPTTEDESSRSPEDLERGAAPVSAEAAAQGSIFLAGTGPPAPCPASSSILVNGSFLAASGSPAVLLNGGPVIINGLALGEASSLGPLLLTGGGGAPPPQPSPQGASETKTSLVLDPQTGEVRLEEAQSEAPETKGAQVAAPGPALGEEVLGPLAQVVPGPPTAATFPLPPGPVPAVAAPQVVPLSPPPGYPTGLSPTSPLLNLPQVVPTSQVVTLPQAVGPLQLLAAGPGSPVKVAAAAGPANVHLINSGVGVTALQLPSATAPGNFLLANPVSGSPIVTGVAVQQGKIILTATFPTSMLVSQVLPPAPGLALPLKPETAISVPEGGLPVAPSPALPEAHALGTLSAQQPPPAAATTSSTSLPFSPDSPGLLPNFPAPPPEGLMLSPAAVPVWSAGLELSAGTEGLLEAEKGLGTQAPHTVLRLPDPDPEGLLLGATAGGEVDEGLEAEAKVLTQLQSVPVEEPLEL

"
     misc_feature    <975..1292
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:35135"
     misc_feature    1017..1166
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /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(1017..1019,1068..1070,1086..1088,1125..1127,
                     1131..1136,1143..1148,1152..1160,1164..1166)
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(1134..1136,1143..1148,1155..1157)
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     exon            1199..2004
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /inference="alignment:Splign:1.39.8"
     exon            2005..3331
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /inference="alignment:Splign:1.39.8"
     variation       2061
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:2014377"
     variation       2298
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2014576"
     STS             3033..3186
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /standard_name="STS-N23083"
                     /db_xref="UniSTS:51570"
     polyA_signal    3306..3311
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
     polyA_site      3331
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
ORIGIN

gagacggaggcgtgcagaagctcagtctcggggcggaggcttcgcgcccttagtcctcctggacggcccgttaccttctgcgttgtcccgatggggaaactgaggccctgagccagaagcacacgctggggggaggcagaaagcgcggccagaggcggagggaaaacaaagggagaatcacagacagacgggagggggacggacacacacaaggggacagagacccgagtggagagctggatctcgccttcccggcgtggggcgcagggtcggccagaaagaagatcgagaagagcggggagtgggggcgaaaaggggggacaggtgggggaggaggctggggaaagcccgagggaggaagagagggagggaggaacttcccaaagttgcaaaacatggctaccttgcctgcggagccgagcgcggggccggcggctgggggggaggcggtggcggcggcggcggcgaccgaagaggaggaggaggaagcgcgccagctcttgcagactttgcaggcggccgagggtgaggcggcggcggcggccggggccggggcgggcgcagcggctgcgggagctgagggcccgggatccccgggcgtccccgggtcgccccccgaggccgcttccgaaccgcccacgggcctccgcttctcgcccgagcaggtggcgtgcgtctgcgaggcgctgctccaggcgggccacgccggccgcttgagccgcttcctgggcgcactgcccccggccgagcgcctacgtggcagcgacccggtgttgcgcgcgcgggccctggtggccttccagcggggcgagtacgccgagctctaccggctactcgagagccgccccttccccgccgcccaccacgccttcctgcaggacctctacctgcgcgcgcgctaccatgaggccgagcgggcccgcggccgcgcgcttggcgcagtggacaagtatcgactgcgcaagaagttcccgctgcccaagaccatctgggacggcgaggagacagtctactgcttcaaggagcgctcccgcgcagcgctcaaggcctgctaccgcggcaaccgctaccccacgccggacgagaagcgccgcctggccacactcaccggcctgtcgctcacgcaggtcagcaactggttcaagaaccggcgacagcgcgaccggaccggggccggaggcggcgcgccctgcaagagcgagtctgatgggaatcccacgactgaggacgagtccagccgaagtcctgaggacctggagagaggggcggccccagtgtccgccgaggccgctgcccagggctccatattcctggcagggaccggccctcccgcgccttgcccggcttcctcctccatcctggtgaacgggagcttcctggcagccagcggctccccagcagtgctcctcaacgggggccccgtcatcatcaacggcctggccctgggcgaggcctccagcctgggcccgctgctgctcactgggggcgggggtgcccctccaccgcagcccagccctcagggggccagcgagaccaagacctctctggtcctggaccctcagacaggggaggtgcggctggaggaggctcagtcggaggcccctgagaccaaaggggcccaggtggctgctccgggaccagcccttggagaggaggtcctggggcccctggcccaagtggtgcctggccccccgacggctgccacctttcctctgcccccggggccagtgcctgctgtggctgccccacaagtggtaccgctctccccacccccggggtatcccacgggcctgagccccacctccccactattgaacctgccccaggtagtacccacctcacaggtggtgaccctgccccaggctgtggggcccctgcagctgttggcagccgggccaggcagccctgtgaaggtggcagctgcagcaggccctgccaatgtgcacctcatcaactccggggtgggcgtgactgccctgcagctgccttcggccactgccccaggaaacttcctcctggccaaccctgtgtctggcagccccatcgtgacgggtgtggccgtgcagcagggcaagatcatcctcaccgccaccttccccaccagcatgctcgtctcccaggtcctgccgccagcccccggcctggccctgccactgaagccagagacggccatctccgtgcctgagggaggcctcccggtggcccccagccctgctctcccagaggctcacgccctaggcaccctttctgcacagcagccaccccccgccgctgccaccacctccagcaccagcctgcccttctcccctgactcccctggcctcctgcccaacttcccggcgcccccaccagaggggctgatgttgtcacccgcggccgtgcctgtctggtcagcagggctggaactaagcgcaggaacagaggggctgctggaagcggaaaaggggctggggacacaggccccccacaccgtgctgaggctgccagaccccgaccctgaggggctgctcctgggggccaccgcagggggtgaggttgacgaggggttggaagctgaggccaaggttctgacccagctccagtcggtgcctgtggaggagcccttggaactgtgacccagtgtggccccgtggcctctcccgacattggtgctgaagacgcagggacaggaatgggaggggggagccccagaaatgcggttgctgaagaccccagtcaccacatccttctgcctgggtggcctctccaagccctggtggtgctgggggttgtatccccggccacctcctgtccaggtctccatccccctttggatgggaggcctctctgttacagccctccccatgctgtgccctgccatatacgtgggggactcagggtcctgactcaggggccctgccccctccacttggtactagctgtaagcggaacaccctgccccagggccggacttccagcccccagagccctctccctgtcactccctgaaacactattaatagctctgccgatagctggtgttgtcacaactgcctggaatccgaaggtggaggacaggcagccccgcgcccctgagactggagaccctccccagtgtggcatttcctgccaggggcggggggtggggcagctgtggggagacgggggtcttccttcaccagctcccctcgactcaagcccttgtcctcattatccggcccagaccaaagattccctcatccctgggggcagccctgccgctgtgtctcctttgtatcctaaatctttatttttctaggacatgttatgcctccattttcaattaaaataaagttatcggattacaccaccaaaaaaaaaaaaaaaaaaaaaa

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