LOCUS       NM_014588               1941 bp    mRNA    linear   PRI 01-JUN-2024
DEFINITION  Homo sapiens visual system homeobox 1 (VSX1), transcript variant 1,
            mRNA.
ACCESSION   NM_014588
VERSION     NM_014588.6
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 1941)
  AUTHORS   Deva,J.P., Ngeow,Y.F. and Zin,T.
  TITLE     The association between VSX1 exon3 gene variants and keratoconus in
            Malaysian patients
  JOURNAL   Indian J Ophthalmol 71 (6), 2443-2447 (2023)
   PUBMED   37322657
  REMARK    GeneRIF: The association between VSX1 exon3 gene variants and
            keratoconus in Malaysian patients.
REFERENCE   2  (bases 1 to 1941)
  AUTHORS   Ma,W., Li,X., Yang,L., Pan,J., Chen,Y., Lu,Y., Dong,X., Li,D. and
            Gan,W.
  TITLE     High VSX1 expression promotes the aggressiveness of clear cell
            renal cell carcinoma by transcriptionally regulating FKBP10
  JOURNAL   J Transl Med 20 (1), 554 (2022)
   PUBMED   36463181
  REMARK    GeneRIF: High VSX1 expression promotes the aggressiveness of clear
            cell renal cell carcinoma by transcriptionally regulating FKBP10.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1941)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   4  (bases 1 to 1941)
  AUTHORS   Kalasidou,G., Frydas,I., Kozei,A., Syrmakesi,P., Loukovitis,E.,
            Sfakianakis,K., Balidis,M., Zachariadis,Z., Tranos,P., Kozeis,N.
            and Anogeianakis,G.
  TITLE     Contributions of VSX1 gene to keratoconus
  JOURNAL   J Biol Regul Homeost Agents 32 (6), 1515-1518 (2018)
   PUBMED   30574758
  REMARK    GeneRIF: VSX1 is involved in keratoconus and other corneal
            pathologies
REFERENCE   5  (bases 1 to 1941)
  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 1941)
  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 1941)
  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 1941)
  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 1941)
  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 1941)
  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 and DQ854807.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Dec 24, 2019 this sequence version replaced NM_014588.5.
            
            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].
            
            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 :: DQ854807.1, AF251033.1 [ECO:0000332]
            RNAseq introns              :: partial sample support SAMEA1968968,
                                           SAMEA2145544 [ECO:0000350]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000376709.9/ ENSP00000365899.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-10                AF176797.2         229-238
            11-1941             DQ854807.1         1-1931
FEATURES             Location/Qualifiers
     source          1..1941
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20p11.21"
     gene            1..1941
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="visual system homeobox 1"
                     /db_xref="GeneID:30813"
                     /db_xref="HGNC:HGNC:12723"
                     /db_xref="MIM:605020"
     exon            1..469
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     CDS             46..1143
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="isoform a is encoded by transcript variant 1;
                     transcription factor VSX1; retinal inner nuclear layer
                     homeobox protein; homeodomain protein RINX; visual system
                     homeobox 1 homolog, CHX10-like"
                     /codon_start=1
                     /product="visual system homeobox 1 isoform a"
                     /protein_id="NP_055403.2"
                     /db_xref="CCDS:CCDS13168.1"
                     /db_xref="GeneID:30813"
                     /db_xref="HGNC:HGNC:12723"
                     /db_xref="MIM:605020"
                     /translation="MTGRDSLSDGRTSSRALVPGGSPRGSRPRGFAITDLLGLEAELP
                     APAGPGQGSGCEGPAVAPCPGPGLDGSSLARGALPLGLGLLCGFGTQPPAAARAPCLL
                     LADVPFLPPRGPEPAAPLAPSRPPPALGRQKRSDSVSTSDEDSQSEDRNDLKASPTLG
                     KRKKRRHRTVFTAHQLEELEKAFSEAHYPDVYAREMLAVKTELPEDRIQVWFQNRRAK
                     WRKREKRWGGSSVMAEYGLYGAMVRHCIPLPDSVLNSAEGGLLGSCAPWLLGMHKKSM
                     GMIRKPGSEDKLAGLWGSDHFKEGSSQSESGSQRGSDKVSPENGLEDVAIDLSSSARQ
                     ETKKVHPGAGAQGGSNSTALEGPQPGKVGAT"
     exon            470..548
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     exon            549..672
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     exon            673..853
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     exon            854..1941
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1918..1923
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="hexamer: AATAAA"
     polyA_site      1941
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="major polyA site"
ORIGIN      
        1 gcaaacggga tccagagagg ctcgcgcctt gcttgctaag gaaccatgac cggccgggac
       61 tcgctttccg acgggcgcac tagcagcagg gcgctggtgc ctggcggttc ccctaggggc
      121 tcgcgccccc ggggcttcgc catcacggac ctgctgggct tggaggccga gctgccggcg
      181 cccgctggcc caggacaggg atctggctgc gagggtccgg cagtcgcgcc gtgcccgggc
      241 ccggggcttg acggctccag cctggcgcgt ggggccctac cgctgggact cggcctcctc
      301 tgtggcttcg gcacgcagcc gccggcggcc gctcgagcac cctgcctgct cctagcggac
      361 gtgccgttcc tgccgcccag gggccccgag cccgctgccc cgctggctcc cagccgtccg
      421 ccgcctgcgc tcggccgcca gaagcgcagc gacagcgtct ccacgtccga tgaggacagc
      481 cagtctgaag acaggaatga cctaaaggca tcccccacct tgggcaagag gaagaagcgg
      541 cggcacagga cagttttcac tgctcaccag ctggaagagt tggagaaggc attcagcgag
      601 gcccactacc ctgatgtgta tgcccgagaa atgctggctg tgaaaactga gctccccgaa
      661 gaccggatac aggtctggtt tcaaaaccgc agggccaaat ggcgcaagcg ggagaagcgc
      721 tggggcggca gcagcgtgat ggccgagtac gggctgtacg gggccatggt gcgccactgc
      781 atcccgctgc cagactccgt gctcaactcc gccgagggcg gcctgctggg ctcctgcgcg
      841 ccctggctcc tggggatgca taaaaaatcc atggggatga taaggaagcc aggaagtgaa
      901 gataagttgg caggactctg gggctctgac cacttcaaag aaggttctag ccagagtgag
      961 tcaggatcac agagaggctc agataaagtg agccctgaga atggcttgga agatgtggct
     1021 attgacctct ccagctctgc ccggcaggag accaagaaag tgcaccctgg ggctggtgct
     1081 caaggaggct ccaactccac ggcactggag gggccccagc cagggaaggt gggagccaca
     1141 tgagacccac aggtcccact gtcaaaggct gaaaatgtgc atattcctca ctggcatttt
     1201 ccaaaagaca aaaattgtcc aagacatata ctctcagttt gattttcttc tgacaatgtc
     1261 aagataaaat gcaatgccac ttgctttaag aggacagatg agtgacctag ggaaaattct
     1321 atttcattct agaatggaaa cggttcctta atggcacttt aaccagttaa cttggtgcaa
     1381 aacttttgat tctcttttgt agcttgagca gggaggatcc gaagttcaaa aatgatttca
     1441 ctgctgggca tcatttgaga tgtgtggttc aatgtactgt atagatgaat aggttaggtc
     1501 tgatgtcctc attctcaatt aggaaatata aaattgttta atatccagaa gaatctgata
     1561 tcatcatagt gaagactcca tacagacaca tgaatgaatt atattgtctt taccttgaac
     1621 ttggccttgg atatttcaat tttcttgtta gggagtaatt ttgtgttttc ttgagtgtca
     1681 cttgataggc tatgcatatt ggaattcaaa gaaacccata ctctagtcgt ttctgcattt
     1741 cctttaaaaa tagcatggga tcatatttaa acaattgttg gatagctgga aacagtgttt
     1801 ttaggtcaga ccaggctttt ggtctttcaa aatttgtgat tgaaagcact ttagtgactt
     1861 ggattttgta aatctttcct ttcctgcgtt tcctttgcca tttatttatt ctttaaaaat
     1921 aaacattttg tggtgtgttt a
//
