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2019-03-23 03:27:20, GGRNA.v2 : RefSeq release 92 (Jan, 2019)

LOCUS       NM_121519               1564 bp    mRNA    linear   PLN 20-MAR-2017
DEFINITION  Arabidopsis thaliana homeobox 3 (HB-3), mRNA.
ACCESSION   NM_121519
VERSION     NM_121519.3
DBLINK      BioProject: PRJNA116
            BioSample: SAMN03081427
KEYWORDS    RefSeq.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
            Pentapetalae; rosids; malvids; Brassicales; Brassicaceae;
            Camelineae; Arabidopsis.
REFERENCE   1  (bases 1 to 1564)
  AUTHORS   Tabata,S., Kaneko,T., Nakamura,Y., Kotani,H., Kato,T., Asamizu,E.,
            Miyajima,N., Sasamoto,S., Kimura,T., Hosouchi,T., Kawashima,K.,
            Kohara,M., Matsumoto,M., Matsuno,A., Muraki,A., Nakayama,S.,
            Nakazaki,N., Naruo,K., Okumura,S., Shinpo,S., Takeuchi,C., Wada,T.,
            Watanabe,A., Yamada,M., Yasuda,M., Sato,S., de la Bastide,M.,
            Huang,E., Spiegel,L., Gnoj,L., O'Shaughnessy,A., Preston,R.,
            Habermann,K., Murray,J., Johnson,D., Rohlfing,T., Nelson,J.,
            Stoneking,T., Pepin,K., Spieth,J., Sekhon,M., Armstrong,J.,
            Becker,M., Belter,E., Cordum,H., Cordes,M., Courtney,L.,
            Courtney,W., Dante,M., Du,H., Edwards,J., Fryman,J., Haakensen,B.,
            Lamar,E., Latreille,P., Leonard,S., Meyer,R., Mulvaney,E.,
            Ozersky,P., Riley,A., Strowmatt,C., Wagner-McPherson,C., Wollam,A.,
            Yoakum,M., Bell,M., Dedhia,N., Parnell,L., Shah,R., Rodriguez,M.,
            See,L.H., Vil,D., Baker,J., Kirchoff,K., Toth,K., King,L.,
            Bahret,A., Miller,B., Marra,M., Martienssen,R., McCombie,W.R.,
            Wilson,R.K., Murphy,G., Bancroft,I., Volckaert,G., Wambutt,R.,
            Dusterhoft,A., Stiekema,W., Pohl,T., Entian,K.D., Terryn,N.,
            Hartley,N., Bent,E., Johnson,S., Langham,S.A., McCullagh,B.,
            Robben,J., Grymonprez,B., Zimmermann,W., Ramsperger,U., Wedler,H.,
            Balke,K., Wedler,E., Peters,S., van Staveren,M., Dirkse,W.,
            Mooijman,P., Lankhorst,R.K., Weitzenegger,T., Bothe,G., Rose,M.,
            Hauf,J., Berneiser,S., Hempel,S., Feldpausch,M., Lamberth,S.,
            Villarroel,R., Gielen,J., Ardiles,W., Bents,O., Lemcke,K.,
            Kolesov,G., Mayer,K., Rudd,S., Schoof,H., Schueller,C.,
            Zaccaria,P., Mewes,H.W., Bevan,M. and Fransz,P.
  CONSRTM   Kazusa DNA Research Institute; Cold Spring Harbor and Washington
            University in St Louis Sequencing Consortium; European Union
            Arabidopsis Genome Sequencing Consortium
  TITLE     Sequence and analysis of chromosome 5 of the plant Arabidopsis
            thaliana
  JOURNAL   Nature 408 (6814), 823-826 (2000)
   PUBMED   11130714
REFERENCE   2  (bases 1 to 1564)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAR-2017) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 1564)
  AUTHORS   Krishnakumar,V., Cheng,C.-Y., Chan,A.P., Schobel,S., Kim,M.,
            Ferlanti,E.S., Belyaeva,I., Rosen,B.D., Micklem,G., Miller,J.R.,
            Vaughn,M. and Town,C.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-MAY-2016) Plant Genomics, J. Craig Venter Institute,
            9704 Medical Center Dr, Rockville, MD 20850, USA
  REMARK    Protein update by submitter
REFERENCE   4  (bases 1 to 1564)
  AUTHORS   Swarbreck,D., Lamesch,P., Wilks,C. and Huala,E.
  CONSRTM   TAIR
  TITLE     Direct Submission
  JOURNAL   Submitted (18-FEB-2011) Department of Plant Biology, Carnegie
            Institution, 260 Panama Street, Stanford, CA, USA
COMMENT     REVIEWED REFSEQ: This record has been curated by TAIR and Araport.
            This record is derived from an annotated genomic sequence
            (NC_003076).
            On Sep 12, 2016 this sequence version replaced NM_121519.2.
FEATURES             Location/Qualifiers
     source          1..1564
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /chromosome="5"
                     /ecotype="Columbia"
     gene            1..1564
                     /gene="HB-3"
                     /locus_tag="AT5G15150"
                     /gene_synonym="ATHB-3; ATHB3; F8M21.40; F8M21_40; HAT7;
                     homeobox 3; HOMEOBOX FROM ARABIDOPSIS THALIANA 7; HOMEOBOX
                     PROTEIN"
                     /note="homeobox-containing gene with an unusual feature: a
                     leucine zipper motif adjacent to the carboxyl-terminal of
                     the homeodomain structure. This gene is expressed
                     primarily in the cortex of the root and the stem."
                     /db_xref="Araport:AT5G15150"
                     /db_xref="GeneID:831367"
                     /db_xref="TAIR:AT5G15150"
     CDS             368..1312
                     /gene="HB-3"
                     /locus_tag="AT5G15150"
                     /gene_synonym="ATHB-3; ATHB3; F8M21.40; F8M21_40; HAT7;
                     homeobox 3; HOMEOBOX FROM ARABIDOPSIS THALIANA 7; HOMEOBOX
                     PROTEIN"
                     /inference="Similar to RNA sequence,
                     EST:INSD:AV552462.1,INSD:AU237853.1,INSD:EH984079.1,
                     INSD:EL081615.1,INSD:EH931061.1,INSD:ES117395.1,
                     INSD:EL226081.1,INSD:ES103022.1,INSD:DR750043.1,
                     INSD:EL322171.1,INSD:DR750718.1,INSD:AU228952.1,
                     INSD:DR750356.1"
                     /inference="similar to RNA sequence,
                     mRNA:INSD:AK229364.1,INSD:U09340.1,INSD:BX831916.1"
                     /note="homeobox 3 (HB-3); FUNCTIONS IN: sequence-specific
                     DNA binding, DNA binding, sequence-specific DNA binding
                     transcription factor activity; INVOLVED IN: regulation of
                     transcription, DNA-dependent, regulation of transcription;
                     LOCATED IN: nucleus; EXPRESSED IN: 18 plant structures;
                     EXPRESSED DURING: 4 anthesis, F mature embryo stage, petal
                     differentiation and expansion stage, E expanded cotyledon
                     stage, D bilateral stage; CONTAINS InterPro DOMAIN/s:
                     Homeobox, conserved site (InterPro:IPR017970), Homeobox
                     (InterPro:IPR001356), Helix-turn-helix motif, lambda-like
                     repressor (InterPro:IPR000047), Homeodomain-like
                     (InterPro:IPR009057), Leucine zipper, homeobox-associated
                     (InterPro:IPR003106), Homeodomain-related
                     (InterPro:IPR012287); BEST Arabidopsis thaliana protein
                     match is: homeobox protein 20 (TAIR:AT3G01220.1); Has
                     11268 Blast hits to 11217 proteins in 570 species: Archae
                     - 0; Bacteria - 6; Metazoa - 8826; Fungi - 177; Plants -
                     2030; Viruses - 5; Other Eukaryotes - 224 (source: NCBI
                     BLink)."
                     /codon_start=1
                     /product="homeobox 3"
                     /protein_id="NP_568309.2"
                     /db_xref="GeneID:831367"
                     /db_xref="TAIR:AT5G15150"
                     /db_xref="Araport:AT5G15150"
                     /translation="
MYMYEEERNNINNNQEGLRLEMAFPQHGFMFQQLHEDNAHHLPSPTSLPSCPPHLFYGGGGNYMMNRSMSFTGVSDHHHLTQKSPTTTNNMNDQDQVGEEDNLSDDGSHMMLGEKKKRLNLEQVRALEKSFELGNKLEPERKMQLAKALGLQPRQIAIWFQNRRARWKTKQLERDYDSLKKQFDVLKSDNDSLLAHNKKLHAELVALKKHDRKESAKIKREFAEASWSNNGSTENNHNNNSSDANHVSMIKDLFPSSIRSATATTTSTHIDHQIVQDQDQGFCNMFNGIDETTSASYWAWPDQQQQHHNHHQFN"
     misc_feature    order(710..718,722..724,773..775,791..793,830..832,
                     836..841,848..853,857..865,869..874)
                     /gene="HB-3"
                     /locus_tag="AT5G15150"
                     /gene_synonym="ATHB-3; ATHB3; F8M21.40; F8M21_40; HAT7;
                     homeobox 3; HOMEOBOX FROM ARABIDOPSIS THALIANA 7; HOMEOBOX
                     PROTEIN"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    710..871
                     /gene="HB-3"
                     /locus_tag="AT5G15150"
                     /gene_synonym="ATHB-3; ATHB3; F8M21.40; F8M21_40; HAT7;
                     homeobox 3; HOMEOBOX FROM ARABIDOPSIS THALIANA 7; HOMEOBOX
                     PROTEIN"
                     /note="Homeodomain; Region: HOX; smart00389"
                     /db_xref="CDD:197696"
     misc_feature    order(710..712,719..721,839..841,848..853,860..862)
                     /gene="HB-3"
                     /locus_tag="AT5G15150"
                     /gene_synonym="ATHB-3; ATHB3; F8M21.40; F8M21_40; HAT7;
                     homeobox 3; HOMEOBOX FROM ARABIDOPSIS THALIANA 7; HOMEOBOX
                     PROTEIN"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    875..991
                     /gene="HB-3"
                     /locus_tag="AT5G15150"
                     /gene_synonym="ATHB-3; ATHB3; F8M21.40; F8M21_40; HAT7;
                     homeobox 3; HOMEOBOX FROM ARABIDOPSIS THALIANA 7; HOMEOBOX
                     PROTEIN"
                     /note="Homeobox associated leucine zipper; Region: HALZ;
                     pfam02183"
                     /db_xref="CDD:280364"
ORIGIN      
cagatatgtaaatgaagtggaaaatgtatgtacgtatccataatccatgtgctatttaatttcaattttaatttcccaagtgtcctatacaaattgaatcaaaagaaaaatcagcatatgccctaaaagcttaaatggtataaagggtgggtcctatacaaacctcccatgaactgatctcttccttcttctccttcttcttctcttctcactaattttccttcagaaaacttcaacgatcttgtgatattgatatctaaacaagttcttgatctaagctacgaaagttgatctgctcagaattcataataagagttgatcatttgtgggctttgagggtgtgtatacatacatattaattatatatatgtatatgtatgaggaggaaaggaacaatatcaataataatcaagaaggactgagattggagatggcctttcctcaacatggcttcatgtttcagcaactccatgaagacaatgctcatcacttaccttccccaacctctctcccctcttgtcctcctcatctcttctatggaggaggaggaaactacatgatgaacagatcaatgtcgttcacgggagtatcagatcatcatcatctaactcaaaaaagcccgacaacaacgaacaacatgaatgatcaagaccaggtaggcgaggaagacaacctatcagacgatgggtcacatatgatgttaggagagaagaagaagaggctgaatttagagcaagttagggcattagagaagagcttcgagctagggaacaagctggagccagagaggaagatgcagcttgctaaggctttaggattgcagcctaggcagattgcaatatggtttcagaacaggagagctaggtggaagacaaagcagctcgagagagactatgattctctcaaaaaacagttcgatgttttgaaatcggacaatgattctcttcttgcccacaacaagaaactacatgctgagttagtggcattgaagaaacacgaccgtaaagaatcagcaaagatcaagagagaattcgcagaagcttcatggagcaacaatggaagcacagaaaataatcataacaataatagttcagacgctaatcatgtgagcatgatcaaagatcttttcccttcttcgatccgatccgcgaccgcgaccacgacctctacccatattgatcatcagattgttcaagatcaagatcaagggttttgcaatatgttcaatggtattgatgaaacgacgtcggctagttattgggcatggcctgaccagcagcaacaacatcacaatcatcatcagttcaattgatcatattgtctaagaacaacatcatactcatcttgatatcattattatcatcaaaagaaaatttcgtagatttttttaataagtattttcaaattatttggcacgtttaaaattaattaaattgggttattatgttttttttttctctcctttgggtttgtagagaattggtgtataggggatactcaacaaatttgtagtatgatattttcttgttacttgtattgaatgaataaatttttctttcatatc
//

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]