LOCUS       NM_001109546            2814 bp    mRNA    linear   ROD 21-MAR-2023
DEFINITION  Rattus norvegicus visual system homeobox 1 (Vsx1), mRNA.
ACCESSION   NM_001109546 XM_001071714
VERSION     NM_001109546.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2814)
  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
REFERENCE   2  (bases 1 to 2814)
  AUTHORS   Kerschensteiner D, Liu H, Cheng CW, Demas J, Cheng SH, Hui CC, Chow
            RL and Wong RO.
  TITLE     Genetic control of circuit function: Vsx1 and Irx5 transcription
            factors regulate contrast adaptation in the mouse retina
  JOURNAL   J Neurosci 28 (10), 2342-2352 (2008)
   PUBMED   18322081
REFERENCE   3  (bases 1 to 2814)
  AUTHORS   Tang YG, Picornell Y, Su X, Li X, Yang H and Rabinowitz YS.
  TITLE     Three VSX1 gene mutations, L159M, R166W, and H244R, are not
            associated with keratoconus
  JOURNAL   Cornea 27 (2), 189-192 (2008)
   PUBMED   18216574
REFERENCE   4  (bases 1 to 2814)
  AUTHORS   Mok JW, Baek SJ and Joo CK.
  TITLE     VSX1 gene variants are associated with keratoconus in unrelated
            Korean patients
  JOURNAL   J Hum Genet 53 (9), 842-849 (2008)
   PUBMED   18626569
REFERENCE   5  (bases 1 to 2814)
  AUTHORS   Liskova P, Ebenezer ND, Hysi PG, Gwilliam R, El-Ashry MF, Moodaley
            LC, Hau S, Twa M, Tuft SJ and Bhatacharya SS.
  TITLE     Molecular analysis of the VSX1 gene in familial keratoconus
  JOURNAL   Mol Vis 13, 1887-1891 (2007)
   PUBMED   17960127
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2814)
  AUTHORS   Mintz-Hittner HA, Semina EV, Frishman LJ, Prager TC and Murray JC.
  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
REFERENCE   7  (bases 1 to 2814)
  AUTHORS   Ohtoshi A, Wang SW, Maeda H, Saszik SM, Frishman LJ, Klein WH and
            Behringer RR.
  TITLE     Regulation of retinal cone bipolar cell differentiation and
            photopic vision by the CVC homeobox gene Vsx1
  JOURNAL   Curr Biol 14 (6), 530-536 (2004)
   PUBMED   15043821
REFERENCE   8  (bases 1 to 2814)
  AUTHORS   Chow RL, Volgyi B, Szilard RK, Ng D, McKerlie C, Bloomfield SA,
            Birch DG and McInnes RR.
  TITLE     Control of late off-center cone bipolar cell differentiation and
            visual signaling by the homeobox gene Vsx1
  JOURNAL   Proc Natl Acad Sci U S A 101 (6), 1754-1759 (2004)
   PUBMED   14745032
REFERENCE   9  (bases 1 to 2814)
  AUTHORS   Heon E, Greenberg A, Kopp KK, Rootman D, Vincent AL, Billingsley G,
            Priston M, Dorval KM, Chow RL, McInnes RR, Heathcote G, Westall C,
            Sutphin JE, Semina E, Bremner R and Stone EM.
  TITLE     VSX1: a gene for posterior polymorphous dystrophy and keratoconus
  JOURNAL   Hum Mol Genet 11 (9), 1029-1036 (2002)
   PUBMED   11978762
REFERENCE   10 (bases 1 to 2814)
  AUTHORS   Chow RL, Snow B, Novak J, Looser J, Freund C, Vidgen D, Ploder L
            and McInnes RR.
  TITLE     Vsx1, a rapidly evolving paired-like homeobox gene expressed in
            cone bipolar cells
  JOURNAL   Mech Dev 109 (2), 315-322 (2001)
   PUBMED   11731243
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from CH474050.2.
            
            On Oct 4, 2007 this sequence version replaced XM_001071714.1.
            
            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##
            RNAseq introns :: single sample supports all introns SAMN13663594,
                              SAMN13663599 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
FEATURES             Location/Qualifiers
     source          1..2814
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q41"
     gene            1..2814
                     /gene="Vsx1"
                     /note="visual system homeobox 1"
                     /db_xref="GeneID:689704"
                     /db_xref="RGD:1305667"
     exon            1..612
                     /gene="Vsx1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    90..92
                     /gene="Vsx1"
                     /note="upstream in-frame stop codon"
     CDS             177..1286
                     /gene="Vsx1"
                     /note="visual system homeobox 1 homolog"
                     /codon_start=1
                     /product="visual system homeobox 1"
                     /protein_id="NP_001103016.1"
                     /db_xref="GeneID:689704"
                     /db_xref="RGD:1305667"
                     /translation="

MTGRDGLLDGRSRSRALAPGCPPTGSRLRSFAINDLLGLEADLPTPAEPGLRSNCEAPAEATGPGPGPGLCGTCPARGALPLGLGLLCGFGAQPPSATAARARCLLLADLRLLPPAGPEPAVAQSPVHPPPALGSQQRSENISTSDGDSPSEEKNDPKMSLTLGKRKKRRHRTVFTAHQLEELEKAFGEAHYPDVYAREMLAVKTELPEDRIQVWFQNRRAKWRKREKRWGGSSVMAEYGLYGAMVRHCIPLPDSVLNSADSLQGSCAPWLLGMHKKSTEMRKPESEEKLAGLWELDHLRKGAKKDEDGPERGPGKASLNPEGSLEDVAIDLSSSSRQETKKMPSGSSTQGCTHAPGPQVLQPPQVGAS"

     misc_feature    681..851
                     /gene="Vsx1"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            613..691
                     /gene="Vsx1"
                     /inference="alignment:Splign:2.1.0"
     exon            692..815
                     /gene="Vsx1"
                     /inference="alignment:Splign:2.1.0"
     exon            816..993
                     /gene="Vsx1"
                     /inference="alignment:Splign:2.1.0"
     exon            994..2814
                     /gene="Vsx1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

aacctcgctggtgggcgcttgaatgcgtctgctccctgctgattggcgccttcaaggccgtctaggtctcacggacagcttctccagcataaaaggggtcgcctgaactggcatcctccgcacaggtggccagaaaggactcaattccccgctgctggcctagagggctgagaagcatgacgggccgggatgggcttttggatgggcgttccaggagtagagccctggcgccaggctgtccccccaccggctctcgccttcgaagcttcgccatcaacgacctgctgggattggaggcagacctgccgactccagcggagcctgggctaagatccaactgtgaagctccagcggaggcaacagggccaggaccggggccgggactctgcggcacctgccctgctcgcggagctctcccgctgggcctgggcctcctctgcggcttcggggcacagcccccttccgcgaccgccgctcgcgcacgctgcctactgctcgccgatctgcggcttctgccgcctgcaggacccgagcctgctgtcgcccagagcccggtccacccgccgcctgcgctcggcagccagcagcgcagtgagaacatctccacgtcggatggggacagtccatctgaagaaaagaatgacccgaagatgtcccttaccctgggcaagaggaagaagcggagacacaggacggttttcactgcccatcaactagaagaactggagaaggcgtttggcgaggcccactaccctgatgtgtatgctcgggagatgctggctgtgaaaacagagctcccggaagaccggatacaggtctggttccagaaccggagggccaagtggcggaagcgagagaagcgctggggtggcagcagtgtgatggctgagtacgggctctacggagccatggtgcgtcactgcattccgttgccggactccgtgctcaactctgcagacagcctgcagggctcctgtgcaccctggcttctggggatgcataaaaagtctacagagatgaggaaacctgaaagtgaagagaagttggcaggactctgggagttggaccatctcagaaagggtgctaagaaggatgaggatggacctgagaggggaccaggcaaagcgagcctgaaccctgagggcagcttggaagatgtggccattgacctgtccagctcttccaggcaggagactaagaaaatgccctcagggtccagtactcagggatgtacccacgccccagggccgcaggtgctccagcccccacaggtgggagcctcatgagactcacagattgcgcccccaaaagttggaaaaaacgtgtatttctcaggagtacttttcaggaggcaggtccaagacaaacaccttcagtttgattttcttcctgaaacgatctggataaaaaggcaacactacaacgctgaatatataacgacttagggaaagtcccacttaattctagagtggagaacatccatgcaacctctcaagctagtcaacttggttttctttcatttttcttttgtagaatttggacatggaagatttgaagttcaacgataattttagggatagagtatgatgaggctcagttaatagcacacgtgaaggcctggatttaatacccagcaccgtggaaaacagatgtagtagctcacacctgtaatcccagcactcagggggtggagacaagaggtccgacattcaagagcatcccagtttgggggggggagattattactacatggcattaattaaaatgtagttgaatcattaaatggctggtctgacctcctcacactaagttagaatagttgctttgttgaaacagggtcttgctgtgcagcccaggctagcctcattttcatgatctcctgcttcagcctccccagtgctgggttacaggtgtgaaaataattgttttacattcctaggagaagcctctaaacagaggaatgaatgaatgaatgaatgaatgaatgaacgctatactacagttccttgagctgggtctagaacatccccatctttgtgataggtggtaattttgtgttctcagtcacttgataggccttgaatattcaatgtataaacagcaaagaaagccatatgcctctcctcctctgaagtcacccggagttgtgtttaagcaattgttaaatgtctgcagactgtctgaaggtcggacccaacttattgttttttgttttttgtttttttgttttgttttttttttttgagtttatgtttgaaagcactttagtgaattggattcatgaatgttttctttccagtatttcctttcccatttatttattatttaaaaaataaatgtgtgttgtgtctggcgcaaagctacttactggccgctcaatagactctcccttcatgtcccttttaagtctggaaacgtgcagagcacgatgtctttcaggctgcaggactcagcgcagggtctatgtagtgtctggagcaggagccctggctgagccagcttttggagctcagagtctgaagaagcgttgtcagttttatgcagcttcctctgcaggttatctcaggaacacatcaggttgggctgcccccacctccacccccagtctctctagataagaaaatgggcagtctcttcctttagtctgtttttatcccatgctagttctgtagtgttacactctatattagtgaagtattaaccctgtgagatgatggcgaaatgttactaagggagagaaacccttgcggggaaagatacaaggagaaataaagatgtttaaagtacactgaaaatgaaataaataacattcga

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