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2024-03-28 22:04:20, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_014562               2872 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens orthodenticle homeobox 1 (OTX1), transcript variant 1,
            mRNA.
ACCESSION   NM_014562
VERSION     NM_014562.3  GI:315113904
KEYWORDS    RefSeq.
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 2872)
  AUTHORS   Liu,X., Malenfant,P., Reesor,C., Lee,A., Hudson,M.L., Harvard,C.,
            Qiao,Y., Persico,A.M., Cohen,I.L., Chudley,A.E., Forster-Gibson,C.,
            Rajcan-Separovic,E., Lewis,M.E. and Holden,J.J.
  TITLE     2p15-p16.1 microdeletion syndrome: molecular characterization and
            association of the OTX1 and XPO1 genes with autism spectrum
            disorders
  JOURNAL   Eur. J. Hum. Genet. 19 (12), 1264-1270 (2011)
   PUBMED   21750575
  REMARK    GeneRIF: XPO1 and OXT1 may contribute to ASD in 2p15-p16.1 deletion
            cases and non-deletion cases of ASD mapping to this chromosome
            region.
REFERENCE   2  (bases 1 to 2872)
  AUTHORS   Terrinoni,A., Pagani,I.S., Zucchi,I., Chiaravalli,A.M., Serra,V.,
            Rovera,F., Sirchia,S., Dionigi,G., Miozzo,M., Frattini,A.,
            Ferrari,A., Capella,C., Pasquali,F., Curto,F.L., Albertini,A.,
            Melino,G. and Porta,G.
  TITLE     OTX1 expression in breast cancer is regulated by p53
  JOURNAL   Oncogene 30 (27), 3096-3103 (2011)
   PUBMED   21478910
  REMARK    GeneRIF: established that the p53 protein directly induces OTX1
            expression by acting on its promoter
            Erratum:[Oncogene. 2011 Jul 7;30(27):3104. Curto, F L [corrected to
            Curto, F Lo]]
REFERENCE   3  (bases 1 to 2872)
  AUTHORS   Larsen,K.B., Lutterodt,M.C., Mollgard,K. and Moller,M.
  TITLE     Expression of the homeobox genes OTX2 and OTX1 in the early
            developing human brain
  JOURNAL   J. Histochem. Cytochem. 58 (7), 669-678 (2010)
   PUBMED   20354145
  REMARK    GeneRIF: The early expression of OTX1 in proliferative cell layers
            of the human fetal brain supports the concept that this homeobox
            gene is important in neuronal cell development and differentiation.
REFERENCE   4  (bases 1 to 2872)
  AUTHORS   Omodei,D., Acampora,D., Russo,F., De Filippi,R., Severino,V., Di
            Francia,R., Frigeri,F., Mancuso,P., De Chiara,A., Pinto,A.,
            Casola,S. and Simeone,A.
  TITLE     Expression of the brain transcription factor OTX1 occurs in a
            subset of normal germinal-center B cells and in aggressive
            Non-Hodgkin Lymphoma
  JOURNAL   Am. J. Pathol. 175 (6), 2609-2617 (2009)
   PUBMED   19893048
  REMARK    GeneRIF: This study identifies OTX1 as a molecular marker for
            high-grade germinal center derived Non-Hodgkin Lymphoma
REFERENCE   5  (bases 1 to 2872)
  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   6  (bases 1 to 2872)
  AUTHORS   Francks,C., Fisher,S.E., Olson,R.K., Pennington,B.F., Smith,S.D.,
            DeFries,J.C. and Monaco,A.P.
  TITLE     Fine mapping of the chromosome 2p12-16 dyslexia susceptibility
            locus: quantitative association analysis and positional candidate
            genes SEMA4F and OTX1
  JOURNAL   Psychiatr. Genet. 12 (1), 35-41 (2002)
   PUBMED   11901358
  REMARK    GeneRIF: Fine mapping of the chromosome 2p12-16 dyslexia
            susceptibility locus candidate gene
REFERENCE   7  (bases 1 to 2872)
  AUTHORS   Weimann,J.M., Zhang,Y.A., Levin,M.E., Devine,W.P., Brulet,P. and
            McConnell,S.K.
  TITLE     Cortical neurons require Otx1 for the refinement of exuberant
            axonal projections to subcortical targets
  JOURNAL   Neuron 24 (4), 819-831 (1999)
   PUBMED   10624946
REFERENCE   8  (bases 1 to 2872)
  AUTHORS   Nagao,T., Leuzinger,S., Acampora,D., Simeone,A., Finkelstein,R.,
            Reichert,H. and Furukubo-Tokunaga,K.
  TITLE     Developmental rescue of Drosophila cephalic defects by the human
            Otx genes
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 95 (7), 3737-3742 (1998)
   PUBMED   9520436
REFERENCE   9  (bases 1 to 2872)
  AUTHORS   Kastury,K., Druck,T., Huebner,K., Barletta,C., Acampora,D.,
            Simeone,A., Faiella,A. and Boncinelli,E.
  TITLE     Chromosome locations of human EMX and OTX genes
  JOURNAL   Genomics 22 (1), 41-45 (1994)
   PUBMED   7959790
REFERENCE   10 (bases 1 to 2872)
  AUTHORS   Simeone,A., Acampora,D., Mallamaci,A., Stornaiuolo,A.,
            D'Apice,M.R., Nigro,V. and Boncinelli,E.
  TITLE     A vertebrate gene related to orthodenticle contains a homeodomain
            of the bicoid class and demarcates anterior neuroectoderm in the
            gastrulating mouse embryo
  JOURNAL   EMBO J. 12 (7), 2735-2747 (1993)
   PUBMED   8101484
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BP310240.1, AK095680.1 and
            BU689444.1.
            On Dec 16, 2010 this sequence version replaced gi:27436930.
            
            Summary: This gene encodes a member of the bicoid sub-family of
            homeodomain-containing transcription factors. The encoded protein
            acts as a transcription factor and may play a role in brain and
            sensory organ development. A similar protein in mouse is required
            for proper brain and sensory organ development and can cause
            epilepsy. Alternate splicing results in two transcript variants
            that encoded the same protein.[provided by RefSeq, Dec 2010].
            
            Transcript Variant: This variant (1) encodes the functional
            protein. Variants 1 and 2 encode the same protein.
            
            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 :: BP310240.1, AK095680.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025082, ERS025084 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-28                BP310240.1         1-28
            29-2193             AK095680.1         1-2165
            2194-2872           BU689444.1         1-679               c
FEATURES             Location/Qualifiers
     source          1..2872
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p13"
     gene            1..2872
                     /gene="OTX1"
                     /note="orthodenticle homeobox 1"
                     /db_xref="GeneID:5013"
                     /db_xref="HGNC:8521"
                     /db_xref="HPRD:08964"
                     /db_xref="MIM:600036"
     exon            1..96
                     /gene="OTX1"
                     /inference="alignment:Splign:1.39.8"
     exon            97..165
                     /gene="OTX1"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    157..159
                     /gene="OTX1"
                     /note="upstream in-frame stop codon"
     exon            166..373
                     /gene="OTX1"
                     /inference="alignment:Splign:1.39.8"
     variation       239
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:373766083"
     variation       249
                     /gene="OTX1"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:368588963"
     variation       265
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372348915"
     variation       267..268
                     /gene="OTX1"
                     /replace=""
                     /replace="ag"
                     /db_xref="dbSNP:34187380"
     CDS             277..1341
                     /gene="OTX1"
                     /note="orthodenticle homolog 1"
                     /codon_start=1
                     /product="homeobox protein OTX1"
                     /protein_id="NP_055377.1"
                     /db_xref="GI:20070107"
                     /db_xref="CCDS:CCDS1873.1"
                     /db_xref="GeneID:5013"
                     /db_xref="HGNC:8521"
                     /db_xref="HPRD:08964"
                     /db_xref="MIM:600036"
                     /translation="
MMSYLKQPPYGMNGLGLAGPAMDLLHPSVGYPATPRKQRRERTTFTRSQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQSGSGTKSRPAKKKSSPVRESSGSESSGQFTPPAVSSSASSSSSASSSSANPAAAAAAGLGGNPVAAASSLSTPAASSIWSPASISPGSAPASVSVPEPLAAPSNTSCMQRSVAAGAATAAASYPMSYGQGGSYGQGYPTPSSSYFGGVDCSSYLAPMHSHHHPHQLSPMAPSSMAGHHHHHPHAHHPLSQSSGHHHHHHHHHHQGYGGSGLAFNSADCLDYKEPGAAAASSAWKLNFNSPDCLDYKDQASWRFQVL
"
     misc_feature    391..567
                     /gene="OTX1"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:28970"
     misc_feature    order(391..405,409..411,460..462,478..480,517..519,
                     523..528,535..540,544..552,556..561)
                     /gene="OTX1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(397..399,406..408,526..528,535..540,547..549)
                     /gene="OTX1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     misc_feature    <1003..1098
                     /gene="OTX1"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:146262"
     STS             277..1341
                     /gene="OTX1"
                     /standard_name="Otx1"
                     /db_xref="UniSTS:507882"
     STS             277..420
                     /gene="OTX1"
                     /standard_name="Otx1"
                     /db_xref="UniSTS:144102"
     variation       298
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:369382436"
     variation       303
                     /gene="OTX1"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:147660988"
     variation       316
                     /gene="OTX1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:150197048"
     exon            374..525
                     /gene="OTX1"
                     /inference="alignment:Splign:1.39.8"
     STS             403..489
                     /gene="OTX1"
                     /standard_name="Otx1"
                     /db_xref="UniSTS:164914"
     variation       486
                     /gene="OTX1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:138715032"
     exon            526..2856
                     /gene="OTX1"
                     /inference="alignment:Splign:1.39.8"
     variation       543
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:376046840"
     variation       585
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:369351862"
     variation       610
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:146221955"
     variation       633
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:373004027"
     variation       639
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:75832508"
     variation       674
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:141612476"
     variation       689
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:376661345"
     variation       724
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:375359674"
     variation       768
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:113447095"
     variation       797
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:369069078"
     variation       815
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200204127"
     variation       852
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199519181"
     variation       862
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:374452924"
     variation       865
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372442766"
     variation       899
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:375731189"
     variation       922
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:111429182"
     variation       952
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:61742369"
     variation       983
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:34233500"
     variation       1007
                     /gene="OTX1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:377736206"
     variation       1011
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:370878093"
     variation       1032
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:373207054"
     variation       1068
                     /gene="OTX1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:17850223"
     variation       1171
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:377143280"
     variation       1212
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:142456387"
     variation       1216
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:370605334"
     variation       1295
                     /gene="OTX1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:142247365"
     variation       1327
                     /gene="OTX1"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:75472776"
     variation       1332
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:140878342"
     variation       1361
                     /gene="OTX1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:367951137"
     variation       1412
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:12613621"
     variation       1421
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:75938487"
     variation       1518
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372345332"
     variation       1573
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:374357286"
     variation       1877
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:187464743"
     variation       1983
                     /gene="OTX1"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:139417747"
     variation       2158..2159
                     /gene="OTX1"
                     /replace=""
                     /replace="at"
                     /replace="ta"
                     /db_xref="dbSNP:148454797"
     variation       2570..2571
                     /gene="OTX1"
                     /replace=""
                     /replace="gtca"
                     /db_xref="dbSNP:72382277"
     variation       2619..2620
                     /gene="OTX1"
                     /replace=""
                     /replace="ta"
                     /db_xref="dbSNP:72298697"
     variation       2658
                     /gene="OTX1"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:75162241"
     variation       2666
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:114310934"
     variation       2686
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:367962319"
     variation       2688..2689
                     /gene="OTX1"
                     /replace=""
                     /replace="gc"
                     /db_xref="dbSNP:71862991"
     variation       2717
                     /gene="OTX1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372188590"
     variation       2803
                     /gene="OTX1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:1061384"
     polyA_signal    2837..2842
                     /gene="OTX1"
     polyA_site      2856
                     /gene="OTX1"
ORIGIN      
acatacccggggagggcagtagaaaggtgatcaatcttcatcaggctacatttccaatcacctaaacaaccgagcaagacaagccactccgacaaggttggctgcccggcgggtctctgtgagagatccaggtagatggtgaacggccccggcagctgagggcaggccaggcccccagacgcatcagaccctgaaggactgcgtggtgggagccctgcaccgctcctggccccgggccccctggatccgtcggggcgcctccacccagctgttagcatgatgtcttacctcaaacaacccccatacggcatgaacgggctgggcctggccgggcccgccatggacctcctgcacccatccgtgggctatccggccactccgcggaagcagcggcgggagcgcaccaccttcacgcgttcacagctggacgtgctcgaggcgctcttcgccaagactcgctaccctgacatcttcatgcgggaggaggtggcgctcaagatcaacctgccggagtctagagtccaggtctggttcaagaaccgccgcgccaaatgccgccagcagcagcagagcgggagcggaaccaagagccgcccagccaagaagaagtcctctccagtgcgggagagctcgggctccgaaagcagtggccaattcacgccgccagctgtgtccagctctgcctcgtcctctagctcggcgtccagctcttccgccaacccagcggctgcagcggctgcgggactaggtgggaacccggtggcggccgcgtcgtcgctgagtacaccagctgcctcatctatctggagcccggcctccatctcgccaggctcagcgcccgcgtccgtgtcggtgccggagccattggccgcgcctagcaacacctcgtgtatgcagcgctccgtagctgcaggcgccgccaccgcagcagcctcttatcccatgtcctacggccagggcggcagctacggccaaggctaccctacgccctcctcttcctactttggcggcgtggactgcagctcatacctagcgcccatgcactcacatcaccacccgcaccagctcagccccatggcaccctcctccatggcgggccaccatcatcaccacccacatgcgcaccacccgttgagccagtcctcaggccaccaccaccaccatcaccaccaccaccaccaaggctacggtggctctgggcttgccttcaactctgccgactgcttggattacaaggagcctggcgccgctgctgcttcctccgcctggaaactcaacttcaactcccccgactgtctggactataaggaccaagcctcatggcggttccaggtcttgtgagcccaggaatgaaagaggagaagaaacgcaactacctgcgccctccgtggtcccgatcctgttgctgctgctgcaccgcccgcctttgcctcgtcttctccaaaactgaattttcaccccccaaaaagatgtccattgcctgcactgccgcccccatttttgtgccacttgcttggggggatgtgcaaacccaccctgccccttggatggggggaccggtgcttcggcttggcctacacattctatacaggagagatgtattatttccccccttcagcccctactaaactcttaagcctccccttccagtctttctggacagctattaagcacttgcagccttcggaggctctgcgctctgatccgctgtttgagcccaacactttaatttattctttctggacactggagtcactaactggcgtgtttctgcccattggagcacccgcacactactccaaatcaaaaccactaagagttcctcccgcgcagactgctgccccttcagctgccctcgattttgctccacgcctgccggccagagcctcccggcgtttcttccgccccagcggagtgcgctggggcgcgccagggctaggcccgccggaggagcgcgtccccagccttccgcgcacagagccgcatcccgccccgccctgcgctggactggttcaagcttccgcctcggcgggaacgctgtacatagtcaggtccgttccagggaccacttaaactttttagttgctgttggttggttgaactgaacatatcttgtcttagcacccaggaaacagaactttaagatatatacagcacatatatatatatatacatatatatatacacatatataaaaaacaaaagcaaaaaatattttccctctgtccgtcccccttctgctcttcctcaatcaatggcgctttttctttttcagttgttgcaaagctgccctgccctcttcacatcttctccctctgtgtatttattgaagagaaccgcttggtttcaggaagctgggcgcgggatatccgaagtgtggaggaaacagacaagtcagggtacagaggtgggggttgggcaggggcgcagggctgaccccctcacccggtctaagcacagggtcgcagttccagtttacaaacctaaaacaagaaaaccaaaaccagggaacaaaacaacaaaacaaaacaaaatccgtaaaagtacagcattagggaaaaacaaacaaacccaggccccaaacccagttccaactcctctgtcggcttctctctttcaacacccttgttttgtctagtgagtttttagtgcaccttcgttctccgaaatctgcggagagcccgcgcgcctgtgtatcaattttggctttggccgcttcgtccagtaggtgggaaagtaatttgtaaatttgatttgtctgatgtgaagatcacaaattacttgttgaaatgtaaggcagtccccctcctcctctttatctacattacttcccgaaaataaatgcaaattaatgaaaaaaaaaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:5013 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: NAS
            GeneID:5013 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:5013 -> Biological process: GO:0006355 [regulation of transcription, DNA-dependent] evidence: NAS
            GeneID:5013 -> Biological process: GO:0006357 [regulation of transcription from RNA polymerase II promoter] evidence: IEA
            GeneID:5013 -> Biological process: GO:0007275 [multicellular organismal development] evidence: NAS
            GeneID:5013 -> Biological process: GO:0009952 [anterior/posterior pattern specification] evidence: IEA
            GeneID:5013 -> Biological process: GO:0022037 [metencephalon development] evidence: IEA
            GeneID:5013 -> Biological process: GO:0030901 [midbrain development] evidence: IEA
            GeneID:5013 -> Biological process: GO:0042472 [inner ear morphogenesis] evidence: IEA
            GeneID:5013 -> Biological process: GO:0048852 [diencephalon morphogenesis] evidence: IEA
            GeneID:5013 -> Cellular component: GO:0005634 [nucleus] evidence: NAS

by @meso_cacase at DBCLS
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