LOCUS       NM_001431421            2192 bp    mRNA    linear   ROD 18-JUL-2024
DEFINITION  Rattus norvegicus orthodenticle homeobox 2 (Otx2), transcript
            variant 1, mRNA.
ACCESSION   NM_001431421 XM_006251838
VERSION     NM_001431421.1
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 2192)
  AUTHORS   Rohde,K., Hertz,H. and Rath,M.F.
  TITLE     Homeobox genes in melatonin-producing pinealocytes: Otx2 and Crx
            act to promote hormone synthesis in the mature rat pineal gland
  JOURNAL   J Pineal Res 66 (4), e12567 (2019)
   PUBMED   30803008
  REMARK    GeneRIF: The results suggest that Otx2 and Crx, both alone and in
            combination, act to control pineal melatonin synthesis.
REFERENCE   2  (bases 1 to 2192)
  AUTHORS   Xiong,Y., Ji,H., You,Z., Yao,F., Zhou,R., Song,W. and Xia,X.
  TITLE     Otx2 enhances transdifferentiation of Muller cells-derived retinal
            stem cells into photoreceptor-like cells
  JOURNAL   J Cell Mol Med 23 (2), 943-953 (2019)
   PUBMED   30451368
  REMARK    GeneRIF: Otx2 is a potential target for gene therapy of retinal
            degenerative diseases.
REFERENCE   3  (bases 1 to 2192)
  AUTHORS   Kole,C., Berdugo,N., Da Silva,C., Ait-Ali,N., Millet-Puel,G.,
            Pagan,D., Blond,F., Poidevin,L., Ripp,R., Fontaine,V., Wincker,P.,
            Zack,D.J., Sahel,J.A., Poch,O. and Leveillard,T.
  TITLE     Identification of an Alternative Splicing Product of the Otx2 Gene
            Expressed in the Neural Retina and Retinal Pigmented Epithelial
            Cells
  JOURNAL   PLoS One 11 (3), e0150758 (2016)
   PUBMED   26985665
  REMARK    GeneRIF: Otx2S is a novel variant of the Otx2 gene with a deletion
            within the homeodomain sequence. OTX2S exerts transdominant
            activity on the tyrosinase promoter when tested in the
            physiological environment of primary retinal pigmented epithelial
            cells.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2192)
  AUTHORS   Costello,I., Nowotschin,S., Sun,X., Mould,A.W., Hadjantonakis,A.K.,
            Bikoff,E.K. and Robertson,E.J.
  TITLE     Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern
            anterior mesendoderm, node, and midline development
  JOURNAL   Genes Dev 29 (20), 2108-2122 (2015)
   PUBMED   26494787
REFERENCE   5  (bases 1 to 2192)
  AUTHORS   Hoch,R.V., Lindtner,S., Price,J.D. and Rubenstein,J.L.
  TITLE     OTX2 Transcription Factor Controls Regional Patterning within the
            Medial Ganglionic Eminence and Regional Identity of the Septum
  JOURNAL   Cell Rep 12 (3), 482-494 (2015)
   PUBMED   26166575
REFERENCE   6  (bases 1 to 2192)
  AUTHORS   Kinder,S.J., Tsang,T.E., Ang,S.L., Behringer,R.R. and Tam,P.P.
  TITLE     Defects of the body plan of mutant embryos lacking Lim1, Otx2 or
            Hnf3beta activity
  JOURNAL   Int J Dev Biol 45 (1), 347-355 (2001)
   PUBMED   11291865
REFERENCE   7  (bases 1 to 2192)
  AUTHORS   Baas,D., Bumsted,K.M., Martinez,J.A., Vaccarino,F.M., Wikler,K.C.
            and Barnstable,C.J.
  TITLE     The subcellular localization of Otx2 is cell-type specific and
            developmentally regulated in the mouse retina
  JOURNAL   Brain Res Mol Brain Res 78 (1-2), 26-37 (2000)
   PUBMED   10891582
REFERENCE   8  (bases 1 to 2192)
  AUTHORS   Morsli,H., Tuorto,F., Choo,D., Postiglione,M.P., Simeone,A. and
            Wu,D.K.
  TITLE     Otx1 and Otx2 activities are required for the normal development of
            the mouse inner ear
  JOURNAL   Development 126 (11), 2335-2343 (1999)
   PUBMED   10225993
REFERENCE   9  (bases 1 to 2192)
  AUTHORS   Biben,C., Stanley,E., Fabri,L., Kotecha,S., Rhinn,M.,
            Drinkwater,C., Lah,M., Wang,C.C., Nash,A., Hilton,D., Ang,S.L.,
            Mohun,T. and Harvey,R.P.
  TITLE     Murine cerberus homologue mCer-1: a candidate anterior patterning
            molecule
  JOURNAL   Dev Biol 194 (2), 135-151 (1998)
   PUBMED   9501024
REFERENCE   10 (bases 1 to 2192)
  AUTHORS   Robel,L., Ding,M., James,A.J., Lin,X., Simeone,A., Leckman,J.F. and
            Vaccarino,F.M.
  TITLE     Fibroblast growth factor 2 increases Otx2 expression in precursor
            cells from mammalian telencephalon
  JOURNAL   J Neurosci 15 (12), 7879-7891 (1995)
   PUBMED   8613727
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000015.1.
            
            On Jul 16, 2024 this sequence version replaced XM_006251838.5.
            
            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 :: SRR26643298.56737.1,
                                           SRR22582416.452160.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760433, SAMN12840106
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-103               JAXUCZ010000015.1  24432374-24432476   c
            104-179             JAXUCZ010000015.1  24432147-24432222   c
            180-395             JAXUCZ010000015.1  24427476-24427691   c
            396-547             JAXUCZ010000015.1  24426352-24426503   c
            548-2192            JAXUCZ010000015.1  24422876-24424520   c
FEATURES             Location/Qualifiers
     source          1..2192
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="15"
                     /map="15p14"
     gene            1..2192
                     /gene="Otx2"
                     /note="orthodenticle homeobox 2"
                     /db_xref="GeneID:305858"
                     /db_xref="RGD:1305705"
     exon            1..103
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     exon            104..179
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    176..178
                     /gene="Otx2"
                     /note="upstream in-frame stop codon"
     exon            180..395
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     CDS             299..1168
                     /gene="Otx2"
                     /note="homeobox Otx2; orthodenticle homolog 2; homeobox
                     protein OTX2-like"
                     /codon_start=1
                     /product="homeobox protein OTX2"
                     /protein_id="NP_001418350.1"
                     /db_xref="GeneID:305858"
                     /db_xref="RGD:1305705"
                     /translation="

MMSYLKQPPYAVNGLSLTTSGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQNKVRPAKKKTSPAREVSSESGTSGQFTPPSSTSVPTIASSSAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPMHHQLPGPGATLSPMGTNAVTSHLNQSPASLSTQGYGASSLGFNSTTDCLDYKDQTASWKLNFNADCLDYKDQTSSWKFQVL"

     misc_feature    413..580
                     /gene="Otx2"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    755..1000
                     /gene="Otx2"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:427350"
     exon            396..547
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     exon            548..2192
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agcaaatctccctgagagcggaaccttcctcagctccaactcagcctccactcttattaaaaaataaaaatcgctaaaggagcgcagtcgccacatccactttgatagctggctacttggaattttgaaggataatttgatttttttttttcttttcaagcgtccaatgcggctttaagttccgtcactccaaatccacccaccaaggaccctgaccctgtccactccaggcgaatcgagaccgtccggctgggtccccccaatttgggccgactttgcgcctccaaacaaccttagcatgatgtcttatctaaagcaaccgccttacgcagtcaatgggctgagtctgaccacttcgggtatggacttgctgcatccctccgtgggctacccggccactccccggaaacagcggagggagaggactactttcacgagggcacaacttgacgttctggaagctctgtttgccaagacccggtacccagacatcttcatgcgggaggaggtagcactgaaaatcaacttgccagagtccagggtgcaggtatggtttaagaatcgaagagctaagtgccgtcagcaacagcagcagcaacagaacggaggtcagaacaaagtgagacctgccaaaaagaagacctccccagctcgggaagtgagttcagagagtggaacaagtggccagttcactcccccctctagtacctcagtcccaaccattgccagcagcagtgctccagtgtctatctggagcccggcctccatctccccactgtctgaccccttgtccacctcctcctcctgcatgcagaggtcctaccccatgacctatactcaggcttcaggttatagtcaaggctatgctggctcgacttcctactttgggggcatggactgtggatcttacttgacccctatgcatcaccagcttcctggaccaggggccacactcagtcccatgggtaccaatgctgttaccagccacctcaatcagtccccagcttctctttccacccagggatatggagcttcaagcttgggttttaactcaaccactgattgcttggattataaggaccaaactgcctcttggaagcttaacttcaatgctgactgcttggattataaggatcagacatcctcatggaaattccaggttttgtgaagacccgtaggagctattttttctttttttgtgggtgatttttaaatatgctgggctggacattccagttttagccaggcattggttaaaagagttagatgggatgatgctctcagactcctggtcaaagttaccgagaggcatagaaggaaaaaggaagggccttagaagggtccatcaaccagcaacctgagatggataaactaatctacttaagattctgttatagttctagatcattggtttttctgatttgcaaatgattgatccaaatatattctagcaacacgcaaccaaacaccactccaagcgaaaatcaaacacaactgagtaggggagggaaggtcatggccttcaaagcaggcgtgatctgatgttttagccaatctttggttgactcttaggaatggacaatgtcccaagctcattcacgtttcatgaccaactggtagttggcactgaaaaccttttcagggctgtgtgaattgtgcgactgattgtcctagatgcactactttatttaaaagaaaaaaaaaaaaagctgacgctcatacggagtcaatatgtagtttaagagacaatcagtgtgtgtcttatataaatggtacatctgtggtttttaatctgtgctagacttcaaaactgtgatctcctgttattgtatgcaaccttgaactccacctccacaggggttcttctgtgattaaataggttataattataagcaaaaattcagagcaactgaatactgatctagaacgatttacctttggctggaggtgagctgccctgctgtctctggacaaggatcgagaagaagcaaaaggagcctaattcgcccgtaatttaacgttggtaagcctggcagtcaaaaagacattggtcaattgctctgaccctgatgaattttaaactgagatcattgtcatttatgcttgcagatgttaactggaagttatatatgcataaacccttcctggatttggctgatatgtataattatattaaaatggttctagcacaa

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