2024-03-29 11:31:43, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS XM_035966096 5373 bp mRNA linear PLN 31-AUG-2020 DEFINITION PREDICTED: Zea mays homeobox 3 (LOC542440), transcript variant X3, mRNA. ACCESSION XM_035966096 VERSION XM_035966096.1 DBLINK BioProject: PRJNA655717 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. COMMENT MODEL REFSEQ: This record is predicted by automated computational analysis. This record is derived from a genomic sequence (NC_050098.1) annotated using gene prediction method: Gnomon, supported by EST evidence. Also see: Documentation of NCBI's Annotation Process ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Status :: Full annotation Annotation Name :: Zea mays Annotation Release 103 Annotation Version :: 103 Annotation Pipeline :: NCBI eukaryotic genome annotation pipeline Annotation Software Version :: 8.5 Annotation Method :: Best-placed RefSeq; Gnomon Features Annotated :: Gene; mRNA; CDS; ncRNA ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..5373 /organism="Zea mays" /mol_type="mRNA" /cultivar="B73" /db_xref="taxon:4577" /chromosome="3" gene 1..5373 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="homeobox 3; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 9 ESTs, 2090 long SRA reads, and 99% coverage of the annotated genomic feature by RNAseq alignments, including 203 samples with support for all annotated introns" /db_xref="GeneID:542440" CDS 381..5111 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /codon_start=1 /product="homeobox 3 isoform X2" /protein_id="XP_035821989.1" /db_xref="GeneID:542440" /translation="
MGRKGSEVSPSKRYPLRSAHSSGRVLRSALANNNKDSEPLNAAAATQAAVKKRSGNQLDSPNSTVRLLRSTSKNKDEAHSGPLNDRIIDKPAANKRKHANPSQVGSPSSSVRVLRSAIKNKDMARSEPQSDRTAGEAATNKRKNANSSKVGSLSSGLSVLRSASKAKDETCIKPLNDSAAVEPASSKRKCTSPSKVGSPSNSVRVLRSTSKYKNETCTEPLNDSGAVEPAANRRKGVSRSKEGSPNSSVRVLRSASNNKIDVSIEPLNNSTTGQPAAKRRKNGSSFKSSARVLCSTSERANEASSEPLNDSTAAQPAARKKKGGAMPKTDNPKIGVRVLRSASGKKNETCTEPVNGSTSAEPTVTKKRNCKPSKDRSPKKDYLKICQRIKYILNRMKYEQAFIQAYASEGWKGQSLEKIRPEKELERAKAEILQCKLRIREAFRNMDSLLSKGKLEESLFDSAGQISSEDIFCAICGSKDVTSQNDIILCDGACDRGFHQNCLSPPLLTEEIPPGDEGWLCPACVCKADYIDALNELQGSKLSIHDSWKVFPEAASTANGSKQVDASDLLPDHIKDSANLALVGTHMVNEIRFSEEDDSKADDLGLPSEDSGDGDFDPAGPDSSEDQNDGLNSEESDFTSDSDYFCAEIAKSCGQDEVSASPLSNVINRTDRMKLRAYSRRSNEENHNHAFMDMELEQDIVLPVPSRRQVERLDYKKLYDEAYEEESSNSSDEEEWSGKELLEGSGTDSLDERLRPVKRCSRRAPAGQQNNELTPQSRPHGSNSEQKTEVLRSNGSSSTGRKYDPEVTQKLKVHFEKDPYPSRETKENLSEELGLTFNQVSKWFSSTRHYSRVASAKKEMHPDSHTCENNDETTVDSMQAKQPNAGVMEKLTGDRNGIVPEKPMVQDNLNQGAMEKLTRDKNDIVPEKPVMQSSLNQCNNEDIPLSGTEIEMESYEQESSDSSDEEWSILSTPRKTRLQDHGKSSVTESLRSAKRCSRRAPAREQNNERIQSEQLHGSASEQQTEFLRSNVSSGKVSKYHFGPIVSQKLKEHFEKDPYPCRATKESLAQELGLTFNQISKWFSGTRHYSRDAVAKNQKRPGENTTVNNNSTTFDDIQVIEPNVGLIDKPAADVNDMISEKLMVQINLNEGIEEDIPPSQYARCEEKITMTPAAISREAGLPGYGPGPGENFLQVSSRNTSCEQSVILAPTAIAREVGPPGYATGENQGNGAPWNTSYERRLFMNPVTSSRAVSPPGYGPEESRGSGISWNTSSEQILFMSPTTISRELGPPGYGPREDQCSGTSWNASCELGVFMSPVTTSREDSPPGYGPRENQENDNMRCELRMFTSPTTISREVGPPGYELTGKNKGNGASCTTNYQQGAFTSPEAFPREACPPGFVSGENQGNDTPWYMSSKQMAFTSPTTNPRVGPPGYGQENQGSRVSWNTSYEQGVFMSSTNISREAGPPGYGPGESQGNITSWISTGGQRMFTGPSTIPNEVGQQGYGPSGIPGTDGSRSMDLKAFPPGYGPAGENQGGGASGSVISPQARSAENVEFSDDARKKAIQRELRRRQKFR"
misc_feature 1794..1952 /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(1794..1796,1836..1850,1863..1865,1935..1937) /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="putative histone H3 binding site [polypeptide binding]; other site" /db_xref="CDD:276979" misc_feature 2781..2936 /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(2784..2786,2904..2906,2913..2918,2925..2927) /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 3492..3650 /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(3498..3500,3618..3620,3627..3632,3639..3641) /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature <3945..>4658 /gene="LOC542440" /gene_synonym="GRMZM2G314546; homeobox3; Hox2a; hox3" /note="EBNA-3C; Provisional; Region: PHA03377" /db_xref="CDD:177614" ORIGIN
caaacaaaaatgctattaatgatcgcactcgacttgacactggagtcaatcttggttcatcaaagtaaaaaaggcagaaaacagacacgatgacatctgtttttgacgccttgattaaacacgtggccagcggcctgctacagcctactgcctacagatgcaaatcagtaccaggcgtgctctccgtgagctctacgcctctacctgtgtcttggcgacgactgggcgaccgacgacgcagccgtaggacaggcgaccgacgacgcagccgtaggataggcgaccaggtcttcctgttggctcttgcccttcgccggcgacgagcacccgccagggccacaacgacattgggaacaagtgtatgacatacaaacagtaaaatgggaaggaaagggtcagaagtatcaccaagcaaaaggtatcccttgaggtctgcacatagtagtggtagagttcttcgctctgccttagccaataataataaggacagtgagcctctgaatgcggctgctgctacccaagcagctgtgaaaaaaagaagtggcaaccagctagatagtcctaatagcactgtcaggctacttcgttctacatcaaaaaataaggacgaggcacatagcgggcctctaaatgacaggatcattgataagccagctgcaaataaaagaaaacatgccaatccctcacaggttggaagtcccagcagcagtgtcagggtgcttcgctctgcaataaaaaataaagatatggcgcgcagtgagcctcaaagtgacaggaccgctggtgaggcagctacaaataaaagaaaaaacgccaattcctcaaaggtggggagtctgagctctggtctcagtgtgcttcggtctgcttcaaaagctaaggatgagacatgtatcaaacctttaaatgatagtgctgctgttgaaccagcttcaagtaaaagaaaatgcaccagtccgtcaaaggtgggaagtcccagcaacagtgtcagggtgcttcgatctacttcaaaatataagaatgagacatgtaccgagcctttaaatgatagtggtgctgttgaaccagctgcaaatagaaggaaaggtgtcagtcgttcaaaggagggaagtcccaatagcagtgtcagggtgcttcgctctgcctcaaataataagattgatgtatctattgagccactaaataatagtactactggtcaaccagctgcgaaaagaagaaagaatggcagttcctttaagagcagtgccagggtgctttgctctacctcagaaagggcaaatgaggcatctagtgagcctttaaatgatagtactgctgctcagccagctgcgaggaaaaagaaaggtggtgcaatgccaaagactgataacccaaagattggtgtcagggttcttcgctctgcctcaggaaagaagaatgagacatgtactgagcctgtaaatggcagtacttctgctgaaccaactgtgacaaaaaaaagaaattgcaagccttcaaaggatcgcagtcccaagaaggactacttaaaaatttgtcaaagaattaaatatattttgaatcgaatgaagtatgaacaagcctttattcaggcttatgcaagtgaaggttggaaaggccaaagtttggaaaaaataagacccgagaaggagcttgaacgagccaaggcagaaatccttcaatgcaagttaagaatccgggaagcttttcgaaatatggactctcttttatcgaaggggaagcttgaagaatctttgtttgattcagcaggacaaatttcaagcgaagatatattttgtgccatatgtggctcaaaggatgttacttcacaaaatgacatcattctttgtgatggagcctgtgacagaggattccaccagaattgtttgagccctcctttgctaactgaagaaattcctccgggggatgaaggatggctttgccctgcatgtgtgtgcaaagcagactatatagatgcgttaaatgaacttcaaggaagcaaactctccattcatgactcatggaaagttttccctgaggcagcttcaactgccaatggttctaaacaagttgatgcttctgatctgctgccagatcatataaaggacagtgctaaccttgcattggttggaacgcacatggtgaatgaaatcaggttttctgaagaggatgatagcaaagcggatgacctcggcttgccttcggaggactcaggggatggtgacttcgatccagcaggtccagattctagtgaagaccaaaatgatggattgaactcagaagagtcagatttcacatctgactctgattatttttgtgctgagattgctaaatcttgcggccaggatgaagtctcggcatctccattatcaaatgtgataaaccgtactgatagaatgaaactcagggcctacagtagacgctctaatgaagaaaaccacaatcatgcatttatggacatggagctagagcaagacatagtgctaccagttccaagcaggcggcaggttgaacggttggattacaaaaaactatacgatgaggcatatgaggaagaatcatctaattcaagtgatgaagaagagtggtctggaaaagaactcttagaaggcagtggaacagattcacttgatgagcgacttcgtcctgtaaaacggtgctctagaagagcaccagcagggcagcagaataatgaacttacaccacagagccggcctcatggttctaacagtgagcagaaaactgaagttcttcgctccaatggcagtagtagcacaggacggaagtatgatcctgaagttacccagaaattgaaggtgcattttgagaaagatccatatcctagccgtgaaacaaaagaaaatctatcagaagaactaggcttgacatttaatcaggtctccaaatggttctctagtactcgtcactattcaagggttgcttctgccaaaaaagaaatgcatcctgacagccatacttgtgagaataatgatgagacaactgtagacagcatgcaagcaaaacaacccaatgctggggtgatggaaaagttgacgggggatagaaatggcattgttcctgagaaaccgatggtgcaggacaatcttaaccaaggagcgatggaaaagttaactagggataaaaatgacattgttcctgagaaaccggtgatgcagagcagtcttaaccaatgtaataatgaagatataccgctttctggaacagaaattgagatggagtcttacgaacaagaatcatctgactcaagtgatgaagagtggtccatacttagcacaccacgaaaaacaagattacaagaccatggaaaatcatcagttactgaatcacttcgttctgcaaaacggtgttccagaagagcaccagctagggagcagaataatgaacgtattcagagtgagcagcttcatggttctgcaagtgagcagcaaactgaatttcttcgctccaatgtcagcagtggcaaggtctcaaaatatcattttggccctatagttagtcagaagcttaaggaacattttgaaaaagatccatatccttgccgtgcaacaaaagagagtctggcacaagagctaggactgacatttaatcagatcagtaagtggttctctggcactcgtcattattcaagagatgctgttgccaagaatcagaaacgcccgggagaaaatactactgtgaataataatagcacaacctttgatgacatacaagtaatagaacccaatgttgggttgatagataaaccagctgcagatgtaaatgacatgatttctgaaaagttgatggtccaaataaatcttaacgaaggcattgaagaagatatcccaccgagccaatatgccaggtgtgaagagaaaataactatgactccagctgccatctcaagggaagctggtcttccaggatatggtcctggtcctggagaaaactttcttcaggtcagttcaaggaatactagctgtgagcagagtgtgatactggctcctaccgctatcgcaagagaagttggtccaccaggatatgcgactggagaaaaccagggcaatggggctccatggaatacaagttatgagcgaagactatttatgaatcctgtgaccagctcaagagcagtcagtcctccaggatatgggcctgaagaaagccgaggcagtggcatttcctggaatacaagcagtgaacaaatattgtttatgagtcctacaaccatctcaagagaacttggtccaccaggatatgggcctagagaagaccagtgcagtggcacttcatggaatgcaagctgcgagttgggagtatttatgagtcctgtgaccacctcaagagaagacagtccgccaggatatgggcctcgagaaaaccaggagaatgacaatatgagatgcgagttgagaatgtttacaagtcctacaaccatctccagagaagttggcccaccaggatatgagcttactggaaaaaacaagggcaacggcgcttcatgtactacgaattaccagcagggagcgtttacgagtcctgaagccttcccaagagaagcctgtcctccaggatttgtgtctggagagaaccagggtaacgacactccatggtatatgagcagcaaacagatggcgtttacgagtcctacgaccaaccctagagtaggtccgccagggtatggacaggaaaaccagggcagtcgtgtttcttggaatacgagttatgagcagggagtgtttatgagttctacaaacatctcaagagaagccggtccgccaggttatgggcctggggaaagtcagggcaatatcacttcatggatttcgacaggcgggcagagaatgtttacaggtccttcaactatcccgaacgaagtcgggcagcaaggatatggcccttcaggaatcccgggaacggatggctcaaggagtatggacttgaaagcctttccaccaggatatggacctgctggagaaaaccagggcggtggtgcttcagggagcgtcataagcccccaagctcggtctgcagagaacgtagagttttcagacgacgctagaaaaaaggctatacagcgggagctgagacggcggcagaagttcaggtgatggccgtgatgcgaatttctgatcttgctcatcgaattttgactacggattactactttttaagactacatatccagtcttgatggctgaatgagtgacgaccctagttgtcgagacgcaaaaccttttgttgtatgtgttccttttacagacttccttggcttgtcatgaatttctaatgtgaacttgtgctgtgaacttgttgcaaaacctcttgaacctgaagcattcaacatgatgtgagcttgtgcagttactcttc
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Creative Commons Attribution 4.0 International License (CC BY 4.0).
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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