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2021-10-29 01:48:57, GGRNA.v2 : RefSeq release 207 (Jul, 2021)

LOCUS       NM_023990               2677 bp    mRNA    linear   ROD 26-FEB-2021
DEFINITION  Rattus norvegicus SIX homeobox 3 (Six3), mRNA.
ACCESSION   NM_023990 XM_001059990
VERSION     NM_023990.2
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 2677)
  AUTHORS   Lavado A and Oliver G.
  TITLE     Six3 is required for ependymal cell maturation
  JOURNAL   Development 138 (24), 5291-5300 (2011)
   PUBMED   22071110
REFERENCE   2  (bases 1 to 2677)
  AUTHORS   VanDunk C, Hunter LA and Gray PA.
  TITLE     Development, maturation, and necessity of transcription factors in
            the mouse suprachiasmatic nucleus
  JOURNAL   J Neurosci 31 (17), 6457-6467 (2011)
   PUBMED   21525287
REFERENCE   3  (bases 1 to 2677)
  AUTHORS   Liu W, Lagutin O, Swindell E, Jamrich M and Oliver G.
  TITLE     Neuroretina specification in mouse embryos requires Six3-mediated
            suppression of Wnt8b in the anterior neural plate
  JOURNAL   J Clin Invest 120 (10), 3568-3577 (2010)
   PUBMED   20890044
REFERENCE   4  (bases 1 to 2677)
  AUTHORS   Abe Y, Oka A, Mizuguchi M, Igarashi T, Ishikawa S, Aburatani H,
            Yokoyama S, Asahara H, Nagao K, Yamada M and Miyashita T.
  TITLE     EYA4, deleted in a case with middle interhemispheric variant of
            holoprosencephaly, interacts with SIX3 both physically and
            functionally
  JOURNAL   Hum Mutat 30 (10), E946-E955 (2009)
   PUBMED   19606496
REFERENCE   5  (bases 1 to 2677)
  AUTHORS   Jeong Y, Leskow FC, El-Jaick K, Roessler E, Muenke M, Yocum A,
            Dubourg C, Li X, Geng X, Oliver G and Epstein DJ.
  TITLE     Regulation of a remote Shh forebrain enhancer by the Six3
            homeoprotein
  JOURNAL   Nat Genet 40 (11), 1348-1353 (2008)
   PUBMED   18836447
REFERENCE   6  (bases 1 to 2677)
  AUTHORS   Lagutin O, Zhu CC, Furuta Y, Rowitch DH, McMahon AP and Oliver G.
  TITLE     Six3 promotes the formation of ectopic optic vesicle-like
            structures in mouse embryos
  JOURNAL   Dev Dyn 221 (3), 342-349 (2001)
   PUBMED   11458394
REFERENCE   7  (bases 1 to 2677)
  AUTHORS   Lengler J, Krausz E, Tomarev S, Prescott A, Quinlan RA and Graw J.
  TITLE     Antagonistic action of Six3 and Prox1 at the gamma-crystallin
            promoter
  JOURNAL   Nucleic Acids Res 29 (2), 515-526 (2001)
   PUBMED   11139622
REFERENCE   8  (bases 1 to 2677)
  AUTHORS   Ohkura N, Ohkubo T, Maruyama K, Tsukada T and Yamaguchi K.
  TITLE     The orphan nuclear receptor NOR-1 interacts with the homeobox
            containing protein Six3
  JOURNAL   Dev Neurosci 23 (1), 17-24 (2001)
   PUBMED   11173923
REFERENCE   9  (bases 1 to 2677)
  AUTHORS   Wallis DE, Roessler E, Hehr U, Nanni L, Wiltshire T, Richieri-Costa
            A, Gillessen-Kaesbach G, Zackai EH, Rommens J and Muenke M.
  TITLE     Mutations in the homeodomain of the human SIX3 gene cause
            holoprosencephaly
  JOURNAL   Nat Genet 22 (2), 196-198 (1999)
   PUBMED   10369266
REFERENCE   10 (bases 1 to 2677)
  AUTHORS   Kawakami K, Ohto H, Takizawa T and Saito T.
  TITLE     Identification and expression of six family genes in mouse retina
  JOURNAL   FEBS Lett 393 (2-3), 259-263 (1996)
   PUBMED   8814301
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JACYVU010000163.1.
            On Feb 26, 2021 this sequence version replaced NM_023990.1.
            
            Summary: a homeobox protein that interacts with orphan nuclear
            receptor NOR-1 [RGD, Feb 2006].
            
            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 :: AB030833.1, AI717283.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMD00132279, SAMD00155320
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1176              JACYVU010000163.1  9042161-9043336     c
            1177-2677           JACYVU010000163.1  9039017-9040517     c
FEATURES             Location/Qualifiers
     source          1..2677
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="6"
                     /map="6q12"
     gene            1..2677
                     /gene="Six3"
                     /note="SIX homeobox 3"
                     /db_xref="GeneID:78974"
                     /db_xref="RGD:620909"
     exon            1..1176
                     /gene="Six3"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    8..10
                     /gene="Six3"
                     /note="upstream in-frame stop codon"
     CDS             356..1369
                     /gene="Six3"
                     /note="sine oculis-related homeobox 3 homolog; sine oculis
                     homeobox homolog 3"
                     /codon_start=1
                     /product="homeobox protein SIX3"
                     /protein_id="NP_076480.1"
                     /db_xref="GeneID:78974"
                     /db_xref="RGD:620909"
                     /translation="
MVFRSPLDLYSSHFLLPNFADSHHCSLLLASSGGGSGAGGGGGAGGGGGGGGGNRAGGGGAGGAGGGGGGGGGGSRAPPEELSMFQLPTLNFSPEQVASVCETLEETGDIERLGRFLWSLPVAPGACEAINKHESILRARAVVAFHTGNFRDLYHILENHKFTKESHGKLQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPSKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLQHQAIGPSGMRSLAEPGCPTHGSAESPSTAASPTTSVSSLTERADTGTSILSVTSSDSECDV"
     misc_feature    629..970
                     /gene="Six3"
                     /note="Transcriptional regulator, SIX1, N-terminal SD
                     domain; Region: SIX1_SD; pfam16878"
                     /db_xref="CDD:293483"
     misc_feature    992..1138
                     /gene="Six3"
                     /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:238039"
     misc_feature    order(995..997,1004..1006,1124..1126,1133..1138)
                     /gene="Six3"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            1177..2677
                     /gene="Six3"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
gaatcgctgaatcttgactcggcggtggttggctctcgctctcctctctctccctctccctctccctctccctctctctgcctcgggttctctctctgcgcgcgcgcaccgggccgctctccttcctccctctctatgtggctgcgcgggtgtgtgtgtatgtggatgtgtgtggggtgtgggtgtcccttacgtccttcctcctccccctccttctccttctgctcccccctcctttccatctcctcctcccccctcttctctccctcctcctggtcctcatcgcccctctcctcctcttcctcccctctctcttcctctccctgaattttctcctctcctctcaggtcagtccatggtattccgctcccccctagacctctattcctcccacttcttgttgccaaacttcgccgattctcaccactgctccctacttctggcgagtagcggcggcgggagcggtgcgggcggcggcggcggcgcgggaggaggcggcggcggcggcggcgggaaccgtgcgggaggcggcggtgctggcggagcaggcggcggcggcggcggcggcggcggcggctccagggcccccccggaagagttgtccatgttccagctgcccaccctcaacttctcgccggagcaggtggccagcgtctgcgagacgctggaggagacgggcgacatcgagcggctgggccgcttcctctggtcgctgcccgtggcccctggggcgtgcgaggccatcaacaaacacgagtcgatcctgcgcgcgcgcgccgtcgtcgccttccacaccggcaacttccgagacctgtaccacatcctggagaatcacaagttcaccaaggagtctcacggcaagctgcaggccatgtggctcgaggcgcactaccaggaggccgagaagctgcgcggccgccctctcggcccggtggacaagtaccgcgtgcgcaagaagttccctctgccgcgcaccatctgggatggggagcagaagacccattgcttcaaggagcggactcggagcctgctgcgggaatggtacctgcaggatccctaccccaaccccagcaagaaacgagaactggcgcaggccaccggcctcacccccacacaagtaggcaactggtttaagaaccggcgacagcgcgaccgcgcagcggcggccaagaacaggctccagcaccaggccatcgggccgagcgggatgcgctcgctggccgagcccggctgccccacgcacggctcagcagagtcaccgtccacggcagccagtccgaccaccagtgtgtccagcctgacggagcgcgcggacactggcacttctatcctctcggtaacctccagcgactcggaatgtgatgtatgatagccaaggccgccctcctcctccttcccctcctccccctccaccttcccctcctcctcctagccctgctcctcttcctcctcttctactccatccctagaacaaaccgaaatcaggatacacagccacacacacacacacacacacacacacacaagtccatacacactcccaccccagccaaaaatatatttaaaaaaaacaagaaaaataaattaacctcaaatcatcaacaaccccccaccacctaccaccaccacggccaccccaaaggaccgcgacgccaacagacagtcacaaacgctgatgttgcgggcagaaagcataaaagaggtgacaattgtatactttctaggacaagcacggcttctccttttggttcccacggacccggcaccccacctgcatgacgatttatttgtatctgggaaaatattctctctagtttaaaatgatttaaagagtcgactatacaaaaaaacgccaccatcgccgccgcgacaagacgacaaaagcaaacagacaaaaagaaaaaaaatctgacatctccgttctgaatttgttttttttttttaaaggaaagaaagaaaggaaaaaaaaaactcctcgagagaaatagcaaatgtttcttccttctgttgctcttttctcctttagccctatccatccatctatctatctatctatctatctatctatctatctatctatctatctatctctgttttttaagtccaagtattggtcaaacaagatgcaatcctctgtttttgttcagccgacaatcattttcttcgtaagcacctttttctctccactctgtcactgcctgtgtgggtactggttataaatgtggaaaaagaatagttatgactgtaacagatttttatttttatttcaaaattttatatgaattatgtatatcttaatgatcggtcattttcccagtttgtaatatatgtgtagaaattgcttgtatatgatacctgcttttctcctctcccttctctctctctctcctccctccttccctgcccactcacctctttcctttggggattctcggcgtcgacttggcagtcgaggcttgacgaggtggccagggttagagcgagagagggaccctgtcgctagcaaaagcagagagtgagaccgtagtattcttatgcaaaagctattcaagttttcctagccgctttggaggcccccttcactcccgtagggcgcttttactgttatcttaactgcgtgtttatctatatgtaaaaactttctaaagcaaatacagtattctccattttcttatga
//

by @meso_cacase at DBCLS
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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]