LOCUS       NM_013109               2839 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Rattus norvegicus orthodenticle homeobox 1 (Otx1), mRNA.
ACCESSION   NM_013109 XM_039091639
VERSION     NM_013109.3
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 2839)
  AUTHORS   Zhu,J., Pan,E., Pang,L., Zhou,X., Che,Y. and Liu,Z.
  TITLE     MiR-497-5p ameliorates the oxyhemoglobin-induced subarachnoid
            hemorrhage injury in vitro by targeting orthodenticle homeobox
            protein 1 (Otx1) to activate the Nrf2/HO-1 pathway
  JOURNAL   Mol Genet Genomics 299 (1), 45 (2024)
   PUBMED   38635011
  REMARK    GeneRIF: MiR-497-5p ameliorates the oxyhemoglobin-induced
            subarachnoid hemorrhage injury in vitro by targeting orthodenticle
            homeobox protein 1 (Otx1) to activate the Nrf2/HO-1 pathway.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2839)
  AUTHORS   Sakurai,Y., Kurokawa,D., Kiyonari,H., Kajikawa,E., Suda,Y. and
            Aizawa,S.
  TITLE     Otx2 and Otx1 protect diencephalon and mesencephalon from
            caudalization into metencephalon during early brain regionalization
  JOURNAL   Dev Biol 347 (2), 392-403 (2010)
   PUBMED   20816794
REFERENCE   3  (bases 1 to 2839)
  AUTHORS   Esumi,N., Kachi,S., Hackler,L. Jr., Masuda,T., Yang,Z.,
            Campochiaro,P.A. and Zack,D.J.
  TITLE     BEST1 expression in the retinal pigment epithelium is modulated by
            OTX family members
  JOURNAL   Hum Mol Genet 18 (1), 128-141 (2009)
   PUBMED   18849347
REFERENCE   4  (bases 1 to 2839)
  AUTHORS   Kimura,J., Suda,Y., Kurokawa,D., Hossain,Z.M., Nakamura,M.,
            Takahashi,M., Hara,A. and Aizawa,S.
  TITLE     Emx2 and Pax6 function in cooperation with Otx2 and Otx1 to develop
            caudal forebrain primordium that includes future archipallium
  JOURNAL   J Neurosci 25 (21), 5097-5108 (2005)
   PUBMED   15917450
REFERENCE   5  (bases 1 to 2839)
  AUTHORS   Kurokawa,D., Kiyonari,H., Nakayama,R., Kimura-Yoshida,C., Matsuo,I.
            and Aizawa,S.
  TITLE     Regulation of Otx2 expression and its functions in mouse forebrain
            and midbrain
  JOURNAL   Development 131 (14), 3319-3331 (2004)
   PUBMED   15201224
REFERENCE   6  (bases 1 to 2839)
  AUTHORS   Puelles,E., Annino,A., Tuorto,F., Usiello,A., Acampora,D.,
            Czerny,T., Brodski,C., Ang,S.L., Wurst,W. and Simeone,A.
  TITLE     Otx2 regulates the extent, identity and fate of neuronal progenitor
            domains in the ventral midbrain
  JOURNAL   Development 131 (9), 2037-2048 (2004)
   PUBMED   15105370
REFERENCE   7  (bases 1 to 2839)
  AUTHORS   Zhang,Y.A., Okada,A., Lew,C.H. and McConnell,S.K.
  TITLE     Regulated nuclear trafficking of the homeodomain protein otx1 in
            cortical neurons
  JOURNAL   Mol Cell Neurosci 19 (3), 430-446 (2002)
   PUBMED   11906214
  REMARK    GeneRIF: ventricular cells actively sequester Otx1 in the
            cytoplasm, either by preventing nuclear import or by promoting a
            balance of export over import signals.
REFERENCE   8  (bases 1 to 2839)
  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 2839)
  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
REFERENCE   10 (bases 1 to 2839)
  AUTHORS   Frantz,G.D., Weimann,J.M., Levin,M.E. and McConnell,S.K.
  TITLE     Otx1 and Otx2 define layers and regions in developing cerebral
            cortex and cerebellum
  JOURNAL   J Neurosci 14 (10), 5725-5740 (1994)
   PUBMED   7931541
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000014.1.
            
            On or before Mar 23, 2023 this sequence version replaced
            XM_039091639.1, NM_013109.2.
            
            ##Evidence-Data-START##
            Transcript exon combination :: FQ212299.1, SRR26360194.165517.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760393 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on manual assertion, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-143               JAXUCZ010000014.1  100290279-100290421 c
            144-211             JAXUCZ010000014.1  100289849-100289916 c
            212-417             JAXUCZ010000014.1  100288064-100288269 c
            418-569             JAXUCZ010000014.1  100287026-100287177 c
            570-2839            JAXUCZ010000014.1  100283406-100285675 c
FEATURES             Location/Qualifiers
     source          1..2839
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="14"
                     /map="14q22"
     gene            1..2839
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="orthodenticle homeobox 1"
                     /db_xref="GeneID:25646"
                     /db_xref="RGD:3237"
     exon            1..143
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /inference="alignment:Splign:2.1.0"
     exon            144..211
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    186..188
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="upstream in-frame stop codon"
     exon            212..417
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /inference="alignment:Splign:2.1.0"
     CDS             321..1388
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="homeobox protein OTX1-like"
                     /codon_start=1
                     /product="homeobox protein OTX1"
                     /protein_id="NP_037241.2"
                     /db_xref="GeneID:25646"
                     /db_xref="RGD:3237"
                     /translation="

MMSYLKQPPYGMNGLGLAGPAMDLLHPSVGYPATPRKQRRERTTFTRSQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQSGNGTKSRPVKKKSSPVRESSGSESSGQFTPPAVSSSASSSSSASSASANPAAAAAAGLGGNPVAAASSLSTPTASSIWSPASISPGSAPASVSVPEPLGAPSNASCMQRSVAAGAATAAASYPMSYGQGGSYGQGYPAPSSSYFGGVDCSSYLAPMHSHHHPHQLSPMAPSSMAGHHHHHPHAHHPLSQSSGHHHHHHHHHHHQGYGGSGLAFNSADCLDYKEPAAAAASSAWKLNFNSPDCLDYKDQASWRFQVL"

     misc_feature    435..605
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    594..752
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="propagated from UniProtKB/Swiss-Prot (Q63410.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    852..1142
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:427350"
     misc_feature    1089..1238
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /note="propagated from UniProtKB/Swiss-Prot (Q63410.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            418..569
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /inference="alignment:Splign:2.1.0"
     exon            570..2839
                     /gene="Otx1"
                     /gene_synonym="OTX1X"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggccccctattggcggccgggccccgttacgcactcgcctcgcgttcacatactcggggagggcagtagaaaggtgatcaatcttcatcaggctacatttccaatcacctaaacaaccgagcaagacaagccactccgacaaggttggctgcccgcgggtctcggtgagggcgcgaggtagatggtgaagagccgcggcagccgagggcaggccaggccccaagaagcaacagcttgaaggacgtcgcagtgggagccctgaactgctcctggcctcaggccccctggatccgtcggggcgcctccacccggctgttagcatgatgtcttacctcaaacaacccccatacggcatgaacgggctgggcctagctggccctgccatggacctcctgcacccttccgtgggctaccctgccaccccgcggaagcagcgacgggagcgcaccaccttcacgcgctcacagctggacgtgctcgaggcgctgttcgcaaagactcgctacccagacatcttcatgcgcgaggaggtggctctcaagatcaacctgcccgagtccagagtccaggtttggttcaagaaccgccgagccaagtgccgccagcagcagcagagcgggaatggaacgaaaagccggccggtcaagaagaagtcgtctccggtgcgcgagagctcgggttccgagagcagcggccagttcacgccgcccgccgtatctagctctgcgtcttcgtctagctcagcgtccagtgcctccgctaacccggcggctgctgcggccgcgggcctgggtgggaacccggtggcagccgcgtcctctctgagcacgcctactgcttcgtccatctggagcccggcctccatctctcccggctcagcgccggcatccgtatcagtgccagagccattaggcgctccgagcaacgcctcatgcatgcagcgctcggtagccgcaggtgcggccactgccgcggcctcctaccctatgtcctatggccagggcggaagctatggccagggctaccccgcgccttcctcttcttactttggcggtgtagactgcagctcctaccttgcgcccatgcactctcatcaccacccgcaccagcttagccccatggcaccctcctccatggctggccaccaccaccaccacccgcacgcgcaccacccactgagccaatcttcaggccaccaccaccaccaccatcaccaccaccaccaccaaggttatggaggctctgggctcgccttcaactctgccgactgcttggattacaaggagcccgccgccgccgctgcttcctctgcctggaaactcaacttcaactctcccgactgtctggactataaggaccaagcctcatggcggttccaggtcttgtgagcccaggagggaaaggaagtggagaagaaacgcaactaccttcgccctccgtggtccctatcatgttgctgctgctgctgctgctgctgctgctgctgctgctgctgctgctgctgctgcaccgcccgcctttgccttggcttttccaaaacttaattttcactccccaaaagatgttcattgcctgcactgccgctcccgtctgtgctccacttgctcgggggtggagggtgcagccccttctcccccttggacgtggggcccggtgctcctacttggccctcagtttcttcatgggatagcagtgtgctccccctctccactcgtgtgtcaccccctcaagtctctctggacagcttgtatgcacttggagccttctgaggctctcctctctgaccctctctgttttgagctcaacagttttatttattctttctggacactgaagtcactaactggcgaatatctaccgttcggagtgcgcttgtacacatacctccaactcaacccctccaccgtttctagcagactgtcgccgcttcagctgatccagctccccaccggcaggcccaagcttccagcatttccgtctccccaatggtgagcgctgggccaggcttgcgggaggagtgtgccccagcctccttccctgccctgcgctggactgagtcaagcttccgccgcagcgggaatgctgtacatagtcaggtccgttccaaggaccacttaaagtttttagttgctgttggttgaactgagcttctctcttgttttagcgtccaagaaacagaactttaaaatatatacatcacatatatatacacatattatatataacagaagcaaaaaatattccccctttgttcccgttcctctctttctcaaacgatagcggttcttatttttcagttgtttccaagctgtcctgccctcttcacacctccctttgtgtatttattaaagaaacccgcttggttttaggaagctgggctctggaggatcggaagtgaagaaaacagctaagtcagggtacaggggtcgggctaggctgggcagggcgcaagactgacccttcgccagtctaagcacaatatcaaagcgtcagcttagaaacaaacaaacaaaaattggtgaaattacaacattgtgggaagcaaaccgagcccgagttccaggtccaatttcctgtatgtctctctttaaaacacccctgtctgttccgtgagtttttagtgaaccttcattctccgaaatctgcggagaatacctgtgtatctatcagttttggttttggccgcttggtccagtaggtgggaaagtaatttgtaaatttgatttgtccgatgtgaagatcacaaattacttgttgagatgtaaggcagtccgtctcctcttcctctttatctacattatttcccgaaaataaaagcaaattaatgaatggctcgtca

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