GGRNA | NR_045951.1

LOCUS       NR_045951               2163 bp    RNA     linear   PRI 17-JUL-2013
DEFINITION  Homo sapiens visual system homeobox 1 (VSX1), transcript variant 6,
            non-coding RNA.
ACCESSION   NR_045951
VERSION     NR_045951.1  GI:372266167
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 2163)
  AUTHORS   Verma,A., Das,M., Srinivasan,M., Prajna,N.V. and Sundaresan,P.
  TITLE     Investigation of VSX1 sequence variants in South Indian patients
            with sporadic cases of keratoconus
  JOURNAL   BMC Res Notes 6, 103 (2013)
   PUBMED   23506487
  REMARK    GeneRIF: lack of VSX1 pathogenic variations in a large number of
            unrelated sporadic keratoconus patients tend to omit its role, and
            corroborate the involvement of other genetic, environmental or
            behavioural factors in the development of this complex disorder
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2163)
  AUTHORS   Jeoung,J.W., Kim,M.K., Park,S.S., Kim,S.Y., Ko,H.S., Wee,W.R. and
            Lee,J.H.
  TITLE     VSX1 gene and keratoconus: genetic analysis in Korean patients
  JOURNAL   Cornea 31 (7), 746-750 (2012)
   PUBMED   22531431
  REMARK    GeneRIF: Our results suggest that the VSX1 gene and its mutations
            with amino acid changes do not play a major role in the
            pathogenesis of keratoconus.
REFERENCE   3  (bases 1 to 2163)
  AUTHORS   Saee-Rad,S., Hashemi,H., Miraftab,M., Noori-Daloii,M.R.,
            Chaleshtori,M.H., Raoofian,R., Jafari,F., Greene,W., Fakhraie,G.,
            Rezvan,F. and Heidari,M.
  TITLE     Mutation analysis of VSX1 and SOD1 in Iranian patients with
            keratoconus
  JOURNAL   Mol. Vis. 17, 3128-3136 (2011)
   PUBMED   22171159
  REMARK    GeneRIF: A significant association between keratoconus patients and
            VSX1 genetic alterations, is reported.
REFERENCE   4  (bases 1 to 2163)
  AUTHORS   De Bonis,P., Laborante,A., Pizzicoli,C., Stallone,R., Barbano,R.,
            Longo,C., Mazzilli,E., Zelante,L. and Bisceglia,L.
  TITLE     Mutational screening of VSX1, SPARC, SOD1, LOX, and TIMP3 in
            keratoconus
  JOURNAL   Mol. Vis. 17, 2482-2494 (2011)
   PUBMED   21976959
  REMARK    GeneRIF: A novel mutation p.G239R and previously reported mutations
            were found in VSX1 in Italian patients with keratoconus.
REFERENCE   5  (bases 1 to 2163)
  AUTHORS   Dorval,K.M., Bobechko,B.P., Ahmad,K.F. and Bremner,R.
  TITLE     Transcriptional activity of the paired-like homeodomain proteins
            CHX10 and VSX1
  JOURNAL   J. Biol. Chem. 280 (11), 10100-10108 (2005)
   PUBMED   15647262
  REMARK    GeneRIF: CHX10 and VSX1 may control retinal bipolar cell
            specification or differentiation by repressing genes required for
            the development of other cell types
REFERENCE   6  (bases 1 to 2163)
  AUTHORS   Bisceglia,L., Ciaschetti,M., De Bonis,P., Campo,P.A., Pizzicoli,C.,
            Scala,C., Grifa,M., Ciavarella,P., Delle Noci,N., Vaira,F.,
            Macaluso,C. and Zelante,L.
  TITLE     VSX1 mutational analysis in a series of Italian patients affected
            by keratoconus: detection of a novel mutation
  JOURNAL   Invest. Ophthalmol. Vis. Sci. 46 (1), 39-45 (2005)
   PUBMED   15623752
  REMARK    GeneRIF: Mutational analysis of the VSX1 gene in a series of
            Italian patients revealed one novel mutation and confirmed an
            important role played by this gene in a significant proportion of
            patients affected by keratoconus
            GeneRIF: Observational study of genotype prevalence. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 2163)
  AUTHORS   Mintz-Hittner,H.A., Semina,E.V., Frishman,L.J., Prager,T.C. and
            Murray,J.C.
  TITLE     VSX1 (RINX) mutation with craniofacial anomalies, empty sella,
            corneal endothelial changes, and abnormal retinal and auditory
            bipolar cells
  JOURNAL   Ophthalmology 111 (4), 828-836 (2004)
   PUBMED   15051220
  REMARK    GeneRIF: The new mutation in the VSX1 (RINX) gene described in this
            report results in abnormal craniofacial features, absence of the
            roof of the sella turcica, and anomalous development of the corneal
            endothelium.
REFERENCE   8  (bases 1 to 2163)
  AUTHORS   Heon,E., Greenberg,A., Kopp,K.K., Rootman,D., Vincent,A.L.,
            Billingsley,G., Priston,M., Dorval,K.M., Chow,R.L., McInnes,R.R.,
            Heathcote,G., Westall,C., Sutphin,J.E., Semina,E., Bremner,R. and
            Stone,E.M.
  TITLE     VSX1: a gene for posterior polymorphous dystrophy and keratoconus
  JOURNAL   Hum. Mol. Genet. 11 (9), 1029-1036 (2002)
   PUBMED   11978762
  REMARK    GeneRIF: Mutations in VSX1 homeobox gene results in impaired DNA
            binding and is associated with posterior polymorphous dystrophy and
            keratoconus
REFERENCE   9  (bases 1 to 2163)
  AUTHORS   Hayashi,T., Huang,J. and Deeb,S.S.
  TITLE     RINX(VSX1), a novel homeobox gene expressed in the inner nuclear
            layer of the adult retina
  JOURNAL   Genomics 67 (2), 128-139 (2000)
   PUBMED   10903837
REFERENCE   10 (bases 1 to 2163)
  AUTHORS   Semina,E.V., Mintz-Hittner,H.A. and Murray,J.C.
  TITLE     Isolation and characterization of a novel human paired-like
            homeodomain-containing transcription factor gene, VSX1, expressed
            in ocular tissues
  JOURNAL   Genomics 63 (2), 289-293 (2000)
   PUBMED   10673340
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF176797.2, AL080312.14,
            DQ854810.1 and BM680858.1.
            
            Summary: The protein encoded by this gene contains a paired-like
            homeodomain and binds to the core of the locus control region of
            the red/green visual pigment gene cluster. The encoded protein may
            regulate expression of the cone opsin genes early in development.
            Mutations in this gene can cause posterior polymorphous corneal
            dystrophy and keratoconus. Alternatively spliced transcript
            variants encoding different isoforms have been described. [provided
            by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (6) differs in the 3' UTR and
            coding region, compared to variant 1. This variant is represented
            as non-coding because the use of the 5'-most supported
            translational start codon, as used in variant 1, renders the
            transcript a candidate for nonsense-mediated mRNA decay (NMD).
            
            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 :: DQ854810.1 [ECO:0000332]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-22                AF176797.2         1-22
            23-32               AL080312.14        54677-54686         c
            33-248              AF176797.2         23-238
            249-1553            DQ854810.1         1-1305
            1554-1792           AL080312.14        43574-43812         c
            1793-2163           BM680858.1         1-371               c
FEATURES             Location/Qualifiers
     source          1..2163
                     /organism="Homo sapiens"
                     /mol_type="transcribed RNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20p11.21"
     gene            1..2163
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /note="visual system homeobox 1"
                     /db_xref="GeneID:30813"
                     /db_xref="HGNC:12723"
                     /db_xref="MIM:605020"
     misc_RNA        1..2163
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /product="visual system homeobox 1, transcript variant 6"
                     /db_xref="GeneID:30813"
                     /db_xref="HGNC:12723"
                     /db_xref="MIM:605020"
     exon            1..707
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    284..940
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /inference="COORDINATES:
                     alignment:Blast2seq::RefSeq|NM_001256271.1"
                     /note="primary ORF has stop codon >50 nucleotides from the
                     terminal splice site; nonsense-mediated mRNA decay (NMD)
                     candidate"
     exon            708..786
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /inference="alignment:Splign:1.39.8"
     exon            787..910
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /inference="alignment:Splign:1.39.8"
     variation       1541
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199690191"
     polyA_signal    2131..2136
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
     polyA_site      2152
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPD; RINX"
ORIGIN

cctagaatgggggtggggtggggtggggtgggctggacagaagagaggaggagaaggaggtgactgaggggactgcagctgggtgggcggtaaccgaggggaggggaactggtggcgtccccatctcgcggggtccggaacggcgacgcgcccgcgcccagctgattggagcccttcaggcctcccgcgcccgaccggcagcccaatcctataaagcttcctctaagctgggccctccgcaaacgggatccagagaggctcgcgccttgcttgctaaggaaccatgaccggccgggactcgctttccgacgggcgcactagcagcagggcgctggtgcctggcggttcccctaggggctcgcgcccccggggcttcgccatcacggacctgctgggcttggaggccgagctgccggcgcccgctggcccaggacagggatctggctgcgagggtccggcagtcgcgccgtgcccgggcccggggcttgacggctccagcctggcgcgtggggccctaccgctgggactcggcctcctctgtggcttcggcacgcagccgccggcggccgctcgagcaccctgcctgctcctagcggacgtgccgttcctgccgcccaggggccccgagcccgctgccccgctggctcccagccgtccgccgcctgcgctcggccgccagaagcgcagcgacagcgtctccacgtccgatgaggacagccagtctgaagacaggaatgacctaaaggcatcccccaccttgggcaagaggaagaagcggcggcacaggacagttttcactgctcaccagctggaagagttggagaaggcattcagcgaggcccactaccctgatgtgtatgcccgagaaatgctggctgtgaaaactgagctccccgaagaccggatacagagggtgagacattgggctgcagagaaatgaagtgaacctgctaagccgattgtcaaatggatgagaaactcagagccaaggatcgggaaaacacccttaaagaacgagtgcaaacttctgctcctggaggctcccgttcactggactttgcaggagacacacaggctccccagaccccgtggtggtgcctgatgaccttcagctgaaccctgtaatgctgctaaagtctgcccctctggagaagtgctcaggtagcattgttctgcctcaggaagcatgccgattttcctgtgtcatccttgatgatcactgctaccagacttgccccctgcagggcaccccatgtgcaaggaattcaacaacctaggagttgaaagcattggtctcccaagttcagtgtgttcttttccgtatctattaccagctgatgagaataaacctgcagtcatgacagctaggtcctagtgacaggtgcagaaagctgctcttacagaaactcccctccttattaagaggctttgtctatcactcggaactgcttctactcaagattatctgttgaaagggaactgtccataccagggcattgttctgacttttctggacttcctcaacccaaaatgccttgaagaaaaaaaaaaaagaccctgagtgttagggcagggtctcactctgtctccaggctggagtgcagtggcacaatcatagctcaccgcaacctctaactcctgggctgaagtgatcctcccacctcagtctcctatgttgctaggattacagcgtgagccactgccccagctactccaacttaagagttcccccaaggctggctgcccttctcctctccttccatcatgaatgacacatgggcatccccttcggctagcatggctgacctgtgcctgcctgggtgctcagcttggcacccatgtgagtttgcagcctgaaattttaaatggaggagtttctgtgcttttctgccctgattcctcttactgaccctctaagtcaccagctgtggtcgtctcctctttgacccctgatctcaacccgggctttgaaatgtgtttgttcacataattgtccattacccatccttcctgtcattgcagaatctgttgtctcatactgacattttaagactttttttcactttcttctgttgaagatcacctactaagaagtacttcctccttttcattctttctttataagaattaattaaattttaattgacaaaaaaaaaaaaaaaa

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