LOCUS       NM_175875               3344 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens SIX homeobox 5 (SIX5), mRNA.
ACCESSION   NM_175875
VERSION     NM_175875.5
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 3344)
  AUTHORS   Masuda,M., Kanno,A., Nara,K., Mutai,H., Morisada,N., Iijima,K.,
            Morimoto,N., Nakano,A., Sugiuchi,T., Okamoto,Y., Masuda,S.,
            Katsunuma,S., Ogawa,K. and Matsunaga,T.
  TITLE     Phenotype-genotype correlation in patients with typical and
            atypical branchio-oto-renal syndrome
  JOURNAL   Sci Rep 12 (1), 969 (2022)
   PUBMED   35046468
  REMARK    GeneRIF: Phenotype-genotype correlation in patients with typical
            and atypical branchio-oto-renal syndrome.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3344)
  AUTHORS   Liu,Q., Li,A., Tian,Y., Liu,Y., Li,T., Zhang,C., Wu,J.D., Han,X.
            and Wu,K.
  TITLE     The expression profile and clinic significance of the SIX family in
            non-small cell lung cancer
  JOURNAL   J Hematol Oncol 9 (1), 119 (2016)
   PUBMED   27821176
  REMARK    GeneRIF: the higher expressions of SIX1-5 were associated with the
            greater possibility of the tumorigenesis in lung neoplasms
            Review article
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3344)
  AUTHORS   Morisada,N., Nozu,K. and Iijima,K.
  TITLE     Branchio-oto-renal syndrome: comprehensive review based on
            nationwide surveillance in Japan
  JOURNAL   Pediatr Int 56 (3), 309-314 (2014)
   PUBMED   24730701
  REMARK    GeneRIF: Three causative genes for BOR syndrome have been reported
            thus far: EYA1, SIX1, and SIX5, but the causative genes for
            approximately half of all BOR patients remain unknown.[review]
            Review article
REFERENCE   4  (bases 1 to 3344)
  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   5  (bases 1 to 3344)
  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   6  (bases 1 to 3344)
  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   7  (bases 1 to 3344)
  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   8  (bases 1 to 3344)
  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   9  (bases 1 to 3344)
  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
REFERENCE   10 (bases 1 to 3344)
  AUTHORS   Smith,R.J.H.
  TITLE     Branchiootorenal Spectrum Disorder
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301554
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC074212.5.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_175875.4.
            
            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 :: SRR1163655.484181.1, AK074826.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2155770, SAMEA2155984
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000317578.7/ ENSP00000316842.4
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1211              AC074212.5         29047-30257         c
            1212-2017           AC074212.5         27355-28160         c
            2018-3344           AC074212.5         25790-27116         c
FEATURES             Location/Qualifiers
     source          1..3344
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19q13.32"
     gene            1..3344
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="SIX homeobox 5"
                     /db_xref="GeneID:147912"
                     /db_xref="HGNC:HGNC:10891"
                     /db_xref="MIM:600963"
     exon            1..1211
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /inference="alignment:Splign:2.1.0"
     CDS             409..2628
                     /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_787071.3"
                     /db_xref="CCDS:CCDS12673.1"
                     /db_xref="GeneID:147912"
                     /db_xref="HGNC:HGNC:10891"
                     /db_xref="MIM:600963"
                     /translation="MATLPAEPSAGPAAGGEAVAAAAATEEEEEEARQLLQTLQAAEG
                     EAAAAAGAGAGAAAAGAEGPGSPGVPGSPPEAASEPPTGLRFSPEQVACVCEALLQAG
                     HAGRLSRFLGALPPAERLRGSDPVLRARALVAFQRGEYAELYRLLESRPFPAAHHAFL
                     QDLYLRARYHEAERARGRALGAVDKYRLRKKFPLPKTIWDGEETVYCFKERSRAALKA
                     CYRGNRYPTPDEKRRLATLTGLSLTQVSNWFKNRRQRDRTGAGGGAPCKSESDGNPTT
                     EDESSRSPEDLERGAAPVSAEAAAQGSIFLAGTGPPAPCPASSSILVNGSFLAASGSP
                     AVLLNGGPVIINGLALGEASSLGPLLLTGGGGAPPPQPSPQGASETKTSLVLDPQTGE
                     VRLEEAQSEAPETKGAQVAAPGPALGEEVLGPLAQVVPGPPTAATFPLPPGPVPAVAA
                     PQVVPLSPPPGYPTGLSPTSPLLNLPQVVPTSQVVTLPQAVGPLQLLAAGPGSPVKVA
                     AAAGPANVHLINSGVGVTALQLPSATAPGNFLLANPVSGSPIVTGVALQQGKIILTAT
                     FPTSMLVSQVLPPAPGLALPLKPETAISVPEGGLPVAPSPALPEAHALGTLSAQQPPP
                     AAATTSSTSLPFSPDSPGLLPNFPAPPPEGLMLSPAAVPVWSAGLELSAGTEGLLEAE
                     KGLGTQAPHTVLRLPDPDPEGLLLGATAGGEVDEGLEAEAKVLTQLQSVPVEEPLEL"
     exon            1212..2017
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /inference="alignment:Splign:2.1.0"
     exon            2018..3344
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3319..3324
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="hexamer: AATAAA"
     polyA_site      3344
                     /gene="SIX5"
                     /gene_synonym="BOR2; DMAHP"
                     /note="major polyA site"
ORIGIN      
        1 gcagaggacc ctggagacgg aggcgtgcag aagctcagtc tcggggcgga ggcttcgcgc
       61 ccttagtcct cctggacggc ccgttacctt ctgcgttgtc ccgatgggga aactgaggcc
      121 ctgagccaga agcacacgct ggggggaggc agaaagcgcg gccagaggcg gagggaaaac
      181 aaagggagaa tcacagacag acgggagggg gacggacaca cacaagggga cagagacccg
      241 agtggagagc tggatctcgc cttcccggcg tggggcgcag ggtcggccag aaagaagatc
      301 gagaagagcg gggagtgggg gcgaaaaggg gggacaggtg ggggaggagg ctggggaaag
      361 cccgagggag gaagagaggg agggaggaac ttcccaaagt tgcaaaacat ggctaccttg
      421 cctgcggagc cgagcgcggg gccggcggct gggggggagg cggtggcggc ggcggcggcg
      481 accgaagagg aggaggagga agcgcgccag ctcttgcaga ctttgcaggc ggccgagggt
      541 gaggcggcgg cggcggccgg ggccggggcg ggcgcagcgg ctgcgggagc tgagggcccg
      601 ggatccccgg gcgtccccgg gtcgcccccc gaggccgctt ccgaaccgcc cacgggcctc
      661 cgcttctcgc ccgagcaggt ggcgtgcgtc tgcgaggcgc tgctccaggc gggccacgcc
      721 ggccgcttga gccgcttcct gggcgcactg cccccggccg agcgcctacg tggcagcgac
      781 ccggtgttgc gcgcgcgggc cctggtggcc ttccagcggg gcgagtacgc cgagctctac
      841 cggctactcg agagccgccc cttccccgcc gcccaccacg ccttcctgca ggacctctac
      901 ctgcgcgcgc gctaccatga ggccgagcgg gcccgcggcc gcgcgcttgg cgcagtggac
      961 aagtatcgac tgcgcaagaa gttcccgctg cccaagacca tctgggacgg cgaggagaca
     1021 gtctactgct tcaaggagcg ctcccgcgca gcgctcaagg cctgctaccg cggcaaccgc
     1081 taccccacgc cggacgagaa gcgccgcctg gccacactca ccggcctgtc gctcacgcag
     1141 gtcagcaact ggttcaagaa ccggcgacag cgcgaccgga ccggggccgg aggcggcgcg
     1201 ccctgcaaga gcgagtctga tgggaatccc acgactgagg acgagtccag ccgaagtcct
     1261 gaggacctgg agagaggggc ggccccagtg tccgccgagg ccgctgccca gggctccata
     1321 ttcctggcag ggaccggccc tcccgcgcct tgcccggctt cctcctccat cctggtgaac
     1381 gggagcttcc tggcagccag cggctcccca gcagtgctcc tcaacggggg ccccgtcatc
     1441 atcaacggcc tggccctggg cgaggcctcc agcctgggcc cgctgctgct cactgggggc
     1501 gggggtgccc ctccaccgca gcccagccct cagggggcca gcgagaccaa gacctctctg
     1561 gtcctggacc ctcagacagg ggaggtgcgg ctggaggagg ctcagtcgga ggcccctgag
     1621 accaaagggg cccaggtggc tgctccggga ccagcccttg gagaggaggt cctggggccc
     1681 ctggcccaag tggtgcctgg ccccccgacg gctgccacct ttcctctgcc cccggggcca
     1741 gtgcctgctg tggctgcccc acaagtggta ccgctctccc cacccccggg gtatcccacg
     1801 ggcctgagcc ccacctcccc actattgaac ctgccccagg tagtacccac ctcacaggtg
     1861 gtgaccctgc cccaggctgt ggggcccctg cagctgttgg cagccgggcc aggcagccct
     1921 gtgaaggtgg cagctgcagc aggccctgcc aatgtgcacc tcatcaactc cggggtgggc
     1981 gtgactgccc tgcagctgcc ttcggccact gccccaggaa acttcctcct ggccaaccct
     2041 gtgtctggca gccccatcgt gacgggtgtg gccctgcagc agggcaagat catcctcacc
     2101 gccaccttcc ccaccagcat gctcgtctcc caggtcctgc cgccagcccc cggcctggcc
     2161 ctgccactga agccagagac ggccatctcc gtgcctgagg gaggcctccc ggtggccccc
     2221 agccctgctc tcccagaggc tcacgcccta ggcacccttt ctgcacagca gccacccccc
     2281 gccgctgcca ccacctccag caccagcctg cccttctccc ctgactcccc tggcctcctg
     2341 cccaacttcc cggcgccccc accagagggg ctgatgttgt cacccgcggc cgtgcctgtc
     2401 tggtcagcag ggctggaact aagcgcagga acagaggggc tgctggaagc ggaaaagggg
     2461 ctggggacac aggcccccca caccgtgctg aggctgccag accccgaccc tgaggggctg
     2521 ctcctggggg ccaccgcagg gggtgaggtt gacgaggggt tggaagctga ggccaaggtt
     2581 ctgacccagc tccagtcggt gcctgtggag gagcccttgg aactgtgacc cagtgtggcc
     2641 ccgtggcctc tcccgacatt ggtgctgaag acgcagggac aggaatggga ggggggagcc
     2701 ccagaaatgc ggttgctgaa gaccccagtc accacatcct tctgcctggg tggcctctcc
     2761 aagccctggt ggtgctgggg gttgtatccc cggccacctc ctgtccaggt ctccatcccc
     2821 ctttggatgg gaggcctctc tgttacagcc ctccccatgc tgtgccctgc catatacgtg
     2881 ggggactcag ggtcctgact caggggccct gccccctcca cttggtacta gctgtaagcg
     2941 gaacaccctg ccccagggcc ggacttccag cccccagagc cctctccctg tcactccctg
     3001 aaacactatt aatagctctg ccgatagctg gtgttgtcac aactgcctgg aatccgaagg
     3061 tggaggacag gcagccccgc gcccctgaga ctggagaccc tccccagtgt ggcatttcct
     3121 gccaggggcg gggggtgggg cagctgtggg gagacggggg tcttccttca ccagctcccc
     3181 tcgactcaag cccttgtcct cattatccgg cccagaccaa agattccctc atccctgggg
     3241 gcagccctgc cgctgtgtct cctttgtatc ctaaatcttt atttttctag gacatgttat
     3301 gcctccattt tcaattaaaa taaagttatc ggattacacc acca
//
