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2021-10-29 01:51:45, GGRNA.v2 : RefSeq release 207 (Jul, 2021)

LOCUS       NM_001100566            2339 bp    mRNA    linear   ROD 16-MAR-2021
DEFINITION  Rattus norvegicus orthodenticle homeobox 2 (Otx2), mRNA.
ACCESSION   NM_001100566 XM_001057814 XM_001073859 XM_224009
VERSION     NM_001100566.1
KEYWORDS    RefSeq.
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 2339)
  AUTHORS   Rohde K, Hertz H and Rath MF.
  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 2339)
  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 2339)
  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 DJ, Sahel
            JA, 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 2339)
  AUTHORS   Costello I, Nowotschin S, Sun X, Mould AW, Hadjantonakis AK, Bikoff
            EK and Robertson EJ.
  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 2339)
  AUTHORS   Hoch RV, Lindtner S, Price JD and Rubenstein JL.
  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 2339)
  AUTHORS   Kinder SJ, Tsang TE, Ang SL, Behringer RR and Tam PP.
  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 2339)
  AUTHORS   Baas D, Bumsted KM, Martinez JA, Vaccarino FM, Wikler KC and
            Barnstable CJ.
  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 2339)
  AUTHORS   Morsli H, Tuorto F, Choo D, Postiglione MP, Simeone A and Wu DK.
  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 2339)
  AUTHORS   Biben C, Stanley E, Fabri L, Kotecha S, Rhinn M, Drinkwater C, Lah
            M, Wang CC, Nash A, Hilton D, Ang SL, Mohun T and Harvey RP.
  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 2339)
  AUTHORS   Robel L, Ding M, James AJ, Lin X, Simeone A, Leckman JF and
            Vaccarino FM.
  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     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from CB580080.1 and
            JACYVU010000262.1.
            On or before Dec 18, 2009 this sequence version replaced
            XM_001057814.1, XM_001073859.1, XM_224009.3.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments and orthologous data.
            
            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 :: mixed/partial sample support SAMEA5760393,
                              SAMEA5760396 [ECO:0000350]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-613               CB580080.1         1-613
            614-694             JACYVU010000262.1  4058286-4058366     c
            695-2339            JACYVU010000262.1  4054810-4056454     c
FEATURES             Location/Qualifiers
     source          1..2339
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10116"
                     /chromosome="15"
                     /map="15p14"
     gene            1..2339
                     /gene="Otx2"
                     /note="orthodenticle homeobox 2"
                     /db_xref="GeneID:305858"
                     /db_xref="RGD:1305705"
     exon            1..87
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     exon            88..163
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     exon            164..326
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    254..256
                     /gene="Otx2"
                     /note="upstream in-frame stop codon"
     exon            327..542
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     CDS             446..1315
                     /gene="Otx2"
                     /note="homeobox Otx2; orthodenticle homolog 2; homeobox
                     protein OTX2-like"
                     /codon_start=1
                     /product="homeobox protein OTX2"
                     /protein_id="NP_001094036.1"
                     /db_xref="GeneID:305858"
                     /db_xref="RGD:1305705"
                     /translation="
MMSYLKQPPYAVNGLSLTTSGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQNKVRPAKKKTSPAREVSSESGTSGQFTPPSSTSVPTIASSSAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPMHHQLPGPGATLSPMGTNAVTSHLNQSPASLSTQGYGASSLGFNSTTDCLDYKDQTASWKLNFNADCLDYKDQTSSWKFQVL"
     misc_feature    order(560..574,578..580,629..631,647..649,686..688,
                     692..697,704..709,713..721,725..727)
                     /gene="Otx2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(566..568,575..577,695..697,704..709,716..718)
                     /gene="Otx2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    569..727
                     /gene="Otx2"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:395001"
     misc_feature    908..1147
                     /gene="Otx2"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:397546"
     STS             452..692
                     /gene="Otx2"
                     /standard_name="Otx2"
                     /db_xref="UniSTS:144106"
     exon            543..694
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     STS             606..726
                     /gene="Otx2"
                     /standard_name="Otx2"
                     /db_xref="UniSTS:530694"
     exon            695..2339
                     /gene="Otx2"
                     /inference="alignment:Splign:2.1.0"
     STS             972..1182
                     /gene="Otx2"
                     /standard_name="PMC304098P1"
                     /db_xref="UniSTS:272520"
     STS             972..1180
                     /gene="Otx2"
                     /standard_name="PMC263842P1"
                     /db_xref="UniSTS:272330"
     STS             990..1907
                     /gene="Otx2"
                     /standard_name="OTX2_1019"
                     /db_xref="UniSTS:277547"
     STS             1017..1471
                     /gene="Otx2"
                     /standard_name="Otx2"
                     /db_xref="UniSTS:516143"
     STS             1370..1471
                     /gene="Otx2"
                     /standard_name="Otx2"
                     /db_xref="UniSTS:516144"
     STS             2116..2300
                     /gene="Otx2"
                     /standard_name="RH136748"
                     /db_xref="UniSTS:218837"
     STS             2198..2301
                     /gene="Otx2"
                     /standard_name="BB256399"
                     /db_xref="UniSTS:209023"
ORIGIN      
agcggaaccttcctcagctccaactcagcctccactcttattaaaaaataaaaatcgctaaaggagcgcagtcgccacatccactttgatagctggctacttggaattttgaaggataatttgatttttttttttcttttcaagcgtccaatgcggctttaaggagtgcggctccaccaacccgggaactgcacactgaggtcggggctcctggtccagatcacccggccgaggccgctagttggacaggttttaaaggcgactctgcctagtgtggttcaggggacgcgcgccccagcctccgcgcgcacctggagcggccagagttccgtcactccaaatccacccaccaaggaccctgaccctgtccactccaggcgaatcgagaccgtccggctgggtccccccaatttgggccgactttgcgcctccaaacaaccttagcatgatgtcttatctaaagcaaccgccttacgcagtcaatgggctgagtctgaccacttcgggtatggacttgctgcatccctccgtgggctacccggccactccccggaaacagcggagggagaggactactttcacgagggcacaacttgacgttctggaagctctgtttgccaagacccggtacccagacatcttcatgcgggaggaggtagcactgaaaatcaacttgccagagtccagggtgcaggtatggtttaagaatcgaagagctaagtgccgtcagcaacagcagcagcaacagaacggaggtcagaacaaagtgagacctgccaaaaagaagacctccccagctcgggaagtgagttcagagagtggaacaagtggccagttcactcccccctctagtacctcagtcccaaccattgccagcagcagtgctccagtgtctatctggagcccggcctccatctccccactgtctgaccccttgtccacctcctcctcctgcatgcagaggtcctaccccatgacctatactcaggcttcaggttatagtcaaggctatgctggctcgacttcctactttgggggcatggactgtggatcttacttgacccctatgcatcaccagcttcctggaccaggggccacactcagtcccatgggtaccaatgctgttaccagccacctcaatcagtccccagcttctctttccacccagggatatggagcttcaagcttgggttttaactcaaccactgattgcttggattataaggaccaaactgcctcttggaagcttaacttcaatgctgactgcttggattataaggatcagacatcctcatggaaattccaggttttgtgaagacccgtaggagctattttttctttttttgtgggtgatttttaaatatgctgggctggacattccagttttagccaggcattggttaaaagagttagatgggatgatgctctcagactcctggtcaaagttaccgagaggcatagaaggaaaaaggaagggccttagaagggtccatcaaccagcaacctgagatggataaactaatctacttaagattctgttatagttctagatcattggtttttctgatttgcaaatgattgatccaaatatattctagcaacacgcaaccaaacaccactccaagcgaaaatcaaacacaactgagtaggggagggaaggtcatggccttcaaagcaggcgtgatctgatgttttagccaatctttggttgactcttaggaatggacaatgtcccaagctcattcacgtttcatgaccaactggtagttggcactgaaaaccttttcagggctgtgtgaattgtgcgactgattgtcctagatgcactactttatttaaaagaaaaaaaaaaaaagctgacgctcatacggagtcaatatgtagtttaagagacaatcagtgtgtgtcttatataaatggtacatctgtggtttttaatctgtgctagacttcaaaactgtgatctcctgttattgtatgcaaccttgaactccacctccacaggggttcttctgtgattaaataggttataattataagcaaaaattcagagcaactgaatactgatctagaacgatttacctttggctggaggtgagctgccctgctgtctctggacaaggatcgagaagaagcaaaaggagcctaattcgcccgtaatttaacgttggtaagcctggcagtcaaaaagacattggtcaattgctctgaccctgatgaattttaaactgagatcattgtcatttatgcttgcagatgttaactggaagttatatatgcataaacccttcctggatttggctgatatgtataattatattaaaatggttctagcacaa
//

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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]