2024-03-29 07:13:13, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001309211 5334 bp mRNA linear PLN 30-APR-2021 DEFINITION Zea mays homeobox 3 (LOC542440), mRNA. ACCESSION NM_001309211 XM_008675214 VERSION NM_001309211.1 KEYWORDS RefSeq. SOURCE Zea mays ORGANISM Zea mays Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea. REFERENCE 1 (bases 1 to 5334) AUTHORS Klinge B, Uberlacker B, Korfhage C and Werr W. TITLE ZmHox: a novel class of maize homeobox genes JOURNAL Plant Mol Biol 30 (3), 439-453 (1996) PUBMED 8605297 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from CABHLF010000002.1. On May 21, 2015 this sequence version replaced XM_008675214.1. ##Evidence-Data-START## Transcript exon combination :: SRR3147038.6606.1, SRR3147037.7430.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMN00780084, SAMN00780085 [ECO:0000350] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-292 CABHLF010000002.1 202583757-202584048 c 293-1582 CABHLF010000002.1 202580849-202582138 c 1583-1748 CABHLF010000002.1 202580239-202580404 c 1749-1872 CABHLF010000002.1 202580027-202580150 c 1873-1985 CABHLF010000002.1 202579828-202579940 c 1986-2142 CABHLF010000002.1 202579587-202579743 c 2143-2501 CABHLF010000002.1 202575381-202575739 c 2502-2768 CABHLF010000002.1 202573824-202574090 c 2769-2858 CABHLF010000002.1 202573602-202573691 c 2859-3197 CABHLF010000002.1 202573158-202573496 c 3198-3482 CABHLF010000002.1 202572756-202573040 c 3483-3572 CABHLF010000002.1 202572543-202572632 c 3573-5334 CABHLF010000002.1 202570693-202572454 c FEATURES Location/Qualifiers source 1..5334 /organism="Zea mays" /mol_type="mRNA" /cultivar="B73" /db_xref="taxon:4577" /chromosome="3" /map="3" gene 1..5334 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="homeobox 3" /db_xref="GeneID:542440" exon 1..292 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 293..1582 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" misc_feature 321..323 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="upstream in-frame stop codon" CDS 339..5072 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="CL2032_1; CL2032_1a; cl2032_1(265); ZmHox2a" /codon_start=1 /product="homeobox 3" /protein_id="NP_001296140.1" /db_xref="GeneID:542440" /translation="
MGRKGSEVSPSKRYPLRSAHSSGRVLRSALANNNKDSEPLNAAAATQAAVKKRSGNQLDSPNSTVRLLRSTSKNKDEAHSGPLNDRIIDKPAANKRKHANPSQVGSPSSSVRVLRSAIKNKDMARSEPQSDRTAGEAATNKRKNANSSKVGSLSSGLSVLRSASKAKDETCIKPLNDSAAVEPASSKRKCTSPSKVGSPSNSVRVLRSTSKYKNETCTEPLNDSGAVEPAANRRKGVSRSKEGSPNSSVRVLRSASNNKIDVSIEPLNNSTTGQPAAKRRKNGSSFKSSARVLCSTSERANEASSEPLNDSTAAQPAARKKKGGAMPKTDNPKIGVRVLRSASGKKNETCTEPVNGSTSAEPTVTKKRNCKPSKDRSPKKDYLKICQRIKYILNRMKYEQAFIQAYASEGWKGQSLEKIRPEKELERAKAEILQCKLRIREAFRNMDSLLSKGKLEESLFDSAGQISSEDIFCAICGSKDVTSQNDIILCDGACDRGFHQNCLSPPLLTEEIPPGDEGWLCPACVCKADYIDALNELQGSKLSIHDSWVKVFPEAASTANGSKQVDASDLLPDHIKDSANLALVGTHMVNEIRFSEEDDSKADDLGLPSEDSGDGDFDPAGPDSSEDQNDGLNSEESDFTSDSDYFCAEIAKSCGQDEVSASPLSNVINRTDRMKLRAYSRRSNEENHNHAFMDMELEQDIVLPVPSRRQVERLDYKKLYDEAYEEESSNSSDEEEWSGKELLEGSGTDSLDERLRPVKRCSRRAPAGQQNNELTPQSRPHGSNSEQKTEVLRSNGSSSTGRKYDPEVTQKLKVHFEKDPYPSRETKENLSEELGLTFNQVSKWFSSTRHYSRVASAKKEMHPDSHTCENNDETTVDSMQAKQPNAGVMEKLTGDRNGIVPEKPMVQDNLNQGAMEKLTRDKNDIVPEKPVMQSSLNQCNNEDIPLSGTEIEMESYEQESSDSSDEEWSILSTPRKTRLQDHGKSSVTESLRSAKRCSRRAPAREQNNERIQSEQLHGSASEQQTEFLRSNVSSGKVSKYHFGPIVSQKLKEHFEKDPYPCRATKESLAQELGLTFNQISKWFSGTRHYSRDAVAKNQKRPGENTTVNNNSTTFDDIQVIEPNVGLIDKPAADVNDMISEKLMVQINLNEGIEEDIPPSQYARCEEKITMTPAAISREAGLPGYGPGPGENFLQVSSRNTSCEQSVILAPTAIAREVGPPGYATGENQGNGAPWNTSYERRLFMNPVTSSRAVSPPGYGPEESRGSGISWNTSSEQILFMSPTTISRELGPPGYGPREDQCSGTSWNASCELGVFMSPVTTSREDSPPGYGPRENQENDNMRCELRMFTSPTTISREVGPPGYELTGKNKGNGASCTTNYQQGAFTSPEAFPREACPPGFVSGENQGNDTPWYMSSKQMAFTSPTTNPRVGPPGYGQENQGSRVSWNTSYEQGVFMSSTNISREAGPPGYGPGESQGNITSWISTGGQRMFTGPSTIPNEVGQQGYGPSGIPGTDGSRSMDLKAFPPGYGPAGENQGGGASGSVISPQARSAENVEFSDDARKKAIQRELRRRQKFR"
misc_feature 1752..1910 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; Region: PHD_PRHA_like; cd15504" /db_xref="CDD:276979" misc_feature order(1752..1754,1794..1808,1821..1823,1893..1895) /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="putative histone H3 binding site [polypeptide binding]; other site" /db_xref="CDD:276979" misc_feature 2742..2897 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /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(2745..2747,2865..2867,2874..2879,2886..2888) /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 3453..3611 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /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(3459..3461,3579..3581,3588..3593,3600..3602) /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature <3906..>4619 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="EBNA-3C; Provisional; Region: PHA03377" /db_xref="CDD:177614" exon 1583..1748 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 1749..1872 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 1873..1985 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 1986..2142 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 2143..2501 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 2502..2768 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 2769..2858 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 2859..3197 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 3198..3482 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 3483..3572 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" exon 3573..5334 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /inference="alignment:Splign:2.1.0" ORIGIN
gagtcaatcttggttcatcaaagtaaaaaaggcagaaaacagacacgatgacatctgtttttgacgccttgattaaacacgtggccagcggcctgctacagcctactgcctacagatgcaaatcagtaccaggcgtgctctccgtgagctctacgcctctacctgtgtcttggcgacgactgggcgaccgacgacgcagccgtaggacaggcgaccgacgacgcagccgtaggataggcgaccaggtcttcctgttggctcttgcccttcgccggcgacgagcacccgccagggccacaacgacattgggaacaagtgtatgacatacaaacagtaaaatgggaaggaaagggtcagaagtatcaccaagcaaaaggtatcccttgaggtctgcacatagtagtggtagagttcttcgctctgccttagccaataataataaggacagtgagcctctgaatgcggctgctgctacccaagcagctgtgaaaaaaagaagtggcaaccagctagatagtcctaatagcactgtcaggctacttcgttctacatcaaaaaataaggacgaggcacatagcgggcctctaaatgacaggatcattgataagccagctgcaaataaaagaaaacatgccaatccctcacaggttggaagtcccagcagcagtgtcagggtgcttcgctctgcaataaaaaataaagatatggcgcgcagtgagcctcaaagtgacaggaccgctggtgaggcagctacaaataaaagaaaaaacgccaattcctcaaaggtggggagtctgagctctggtctcagtgtgcttcggtctgcttcaaaagctaaggatgagacatgtatcaaacctttaaatgatagtgctgctgttgaaccagcttcaagtaaaagaaaatgcaccagtccgtcaaaggtgggaagtcccagcaacagtgtcagggtgcttcgatctacttcaaaatataagaatgagacatgtaccgagcctttaaatgatagtggtgctgttgaaccagctgcaaatagaaggaaaggtgtcagtcgttcaaaggagggaagtcccaatagcagtgtcagggtgcttcgctctgcctcaaataataagattgatgtatctattgagccactaaataatagtactactggtcaaccagctgcgaaaagaagaaagaatggcagttcctttaagagcagtgccagggtgctttgctctacctcagaaagggcaaatgaggcatctagtgagcctttaaatgatagtactgctgctcagccagctgcgaggaaaaagaaaggtggtgcaatgccaaagactgataacccaaagattggtgtcagggttcttcgctctgcctcaggaaagaagaatgagacatgtactgagcctgtaaatggcagtacttctgctgaaccaactgtgacaaaaaaaagaaattgcaagccttcaaaggatcgcagtcccaagaaggactacttaaaaatttgtcaaagaattaaatatattttgaatcgaatgaagtatgaacaagcctttattcaggcttatgcaagtgaaggttggaaaggccaaagtttggaaaaaataagacccgagaaggagcttgaacgagccaaggcagaaatccttcaatgcaagttaagaatccgggaagcttttcgaaatatggactctcttttatcgaaggggaagcttgaagaatctttgtttgattcagcaggacaaatttcaagcgaagatatattttgtgccatatgtggctcaaaggatgttacttcacaaaatgacatcattctttgtgatggagcctgtgacagaggattccaccagaattgtttgagccctcctttgctaactgaagaaattcctccgggggatgaaggatggctttgccctgcatgtgtgtgcaaagcagactatatagatgcgttaaatgaacttcaaggaagcaaactctccattcatgactcatgggtgaaagttttccctgaggcagcttcaactgccaatggttctaaacaagttgatgcttctgatctgctgccagatcatataaaggacagtgctaaccttgcattggttggaacgcacatggtgaatgaaatcaggttttctgaagaggatgatagcaaagcggatgacctcggcttgccttcggaggactcaggggatggtgacttcgatccagcaggtccagattctagtgaagaccaaaatgatggattgaactcagaagagtcagatttcacatctgactctgattatttttgtgctgagattgctaaatcttgcggccaggatgaagtctcggcatctccattatcaaatgtgataaaccgtactgatagaatgaaactcagggcctacagtagacgctctaatgaagaaaaccacaatcatgcatttatggacatggagctagagcaagacatagtgctaccagttccaagcaggcggcaggttgaacggttggattacaaaaaactatacgatgaggcatatgaggaagaatcatctaattcaagtgatgaagaagagtggtctggaaaagaactcttagaaggcagtggaacagattcacttgatgagcgacttcgtcctgtaaaacggtgctctagaagagcaccagcagggcagcagaataatgaacttacaccacagagccggcctcatggttctaacagtgagcagaaaactgaagttcttcgctccaatggcagtagtagcacaggacggaagtatgatcctgaagttacccagaaattgaaggtgcattttgagaaagatccatatcctagccgtgaaacaaaagaaaatctatcagaagaactaggcttgacatttaatcaggtctccaaatggttctctagtactcgtcactattcaagggttgcttctgccaaaaaagaaatgcatcctgacagccatacttgtgagaataatgatgagacaactgtagacagcatgcaagcaaaacaacccaatgctggggtgatggaaaagttgacgggggatagaaatggcattgttcctgagaaaccgatggtgcaggacaatcttaaccaaggagcgatggaaaagttaactagggataaaaatgacattgttcctgagaaaccggtgatgcagagcagtcttaaccaatgtaataatgaagatataccgctttctggaacagaaattgagatggagtcttacgaacaagaatcatctgactcaagtgatgaagagtggtccatacttagcacaccacgaaaaacaagattacaagaccatggaaaatcatcagttactgaatcacttcgttctgcaaaacggtgttccagaagagcaccagctagggagcagaataatgaacgtattcagagtgagcagcttcatggttctgcaagtgagcagcaaactgaatttcttcgctccaatgtcagcagtggcaaggtctcaaaatatcattttggccctatagttagtcagaagcttaaggaacattttgaaaaagatccatatccttgccgtgcaacaaaagagagtctggcacaagagctaggactgacatttaatcagatcagtaagtggttctctggcactcgtcattattcaagagatgctgttgccaagaatcagaaacgcccgggagaaaatactactgtgaataataatagcacaacctttgatgacatacaagtaatagaacccaatgttgggttgatagataaaccagctgcagatgtaaatgacatgatttctgaaaagttgatggtccaaataaatcttaacgaaggcattgaagaagatatcccaccgagccaatatgccaggtgtgaagagaaaataactatgactccagctgccatctcaagggaagctggtcttccaggatatggtcctggtcctggagaaaactttcttcaggtcagttcaaggaatactagctgtgagcagagtgtgatactggctcctaccgctatcgcaagagaagttggtccaccaggatatgcgactggagaaaaccagggcaatggggctccatggaatacaagttatgagcgaagactatttatgaatcctgtgaccagctcaagagcagtcagtcctccaggatatgggcctgaagaaagccgaggcagtggcatttcctggaatacaagcagtgaacaaatattgtttatgagtcctacaaccatctcaagagaacttggtccaccaggatatgggcctagagaagaccagtgcagtggcacttcatggaatgcaagctgcgagttgggagtatttatgagtcctgtgaccacctcaagagaagacagtccgccaggatatgggcctcgagaaaaccaggagaatgacaatatgagatgcgagttgagaatgtttacaagtcctacaaccatctccagagaagttggcccaccaggatatgagcttactggaaaaaacaagggcaacggcgcttcatgtactacgaattaccagcagggagcgtttacgagtcctgaagccttcccaagagaagcctgtcctccaggatttgtgtctggagagaaccagggtaacgacactccatggtatatgagcagcaaacagatggcgtttacgagtcctacgaccaaccctagagtaggtccgccagggtatggacaggaaaaccagggcagtcgtgtttcttggaatacgagttatgagcagggagtgtttatgagttctacaaacatctcaagagaagccggtccgccaggttatgggcctggggaaagtcagggcaatatcacttcatggatttcgacaggcgggcagagaatgtttacaggtccttcaactatcccgaacgaagtcgggcagcaaggatatggcccttcaggaatcccgggaacggatggctcaaggagtatggacttgaaagcctttccaccaggatatggacctgctggagaaaaccagggcggtggtgcttcagggagcgtcataagcccccaagctcggtctgcagagaacgtagagttttcagacgacgctagaaaaaaggctatacagcgggagctgagacggcggcagaagttcaggtgatggccgtgatgcgaatttctgatcttgctcatcgaattttgactacggattactactttttaagactacatatccagtcttgatggctgaatgagtgacgaccctagttgtcgagacgcaaaaccttttgttgtatgtgttccttttacagacttccttggcttgtcatgaatttctaatgtgaacttgtgctgtgaacttgttgcaaaacctcttgaacctgaagcattcaacatgatgtgagcttgtgcagttactcttc
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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.
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