2024-04-30 00:05:29, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001423107 3741 bp mRNA linear PLN 05-JUL-2023 DEFINITION Oryza sativa Japonica Group homeobox-leucine zipper protein ROC3-like (LOC4349488), transcript variant 1, mRNA. ACCESSION NM_001423107 XM_015757975 VERSION NM_001423107.1 KEYWORDS RefSeq. SOURCE Oryza sativa Japonica Group (Japanese rice) ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa. REFERENCE 1 (bases 1 to 3741) AUTHORS Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y and Yasunishi A. CONSRTM Rice Full-Length cDNA Consortium; National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team; Foundation of Advancement of International Science Genome Sequencing & Analysis Group; RIKEN TITLE Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice JOURNAL Science 301 (5631), 376-379 (2003) PUBMED 12869764 REMARK Erratum:[Science. 2003 Sep;301(5641):1849] COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from AK071939.1 and AB101646.1. On Jul 5, 2023 this sequence version replaced XM_015757975.2. ##Evidence-Data-START## Transcript exon combination :: AK071939.1 [ECO:0000332] RNAseq introns :: mixed sample support SAMD00008650, SAMD00020319 [ECO:0006172] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-904 AK071939.1 2-905 905-3143 AB101646.1 735-2973 3144-3741 AK071939.1 3145-3742 FEATURES Location/Qualifiers source 1..3741 /organism="Oryza sativa Japonica Group" /mol_type="mRNA" /db_xref="taxon:39947" /chromosome="10" /map="10" gene 1..3741 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="homeobox-leucine zipper protein ROC3-like" /db_xref="GeneID:4349488" exon 1..227 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 228..500 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" misc_feature 279..281 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="upstream in-frame stop codon" CDS 315..2963 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="GL2-type homeodomain protein; Protein RICE OUTERMOST CELL-SPECIFIC 3; GLABRA 2-like homeobox protein 3; HD-ZIP protein ROC3; Homeodomain transcription factor ROC3; LOC_Os10g42490; OSJNBa0027L23.2" /codon_start=1 /product="homeobox-leucine zipper protein ROC3" /protein_id="NP_001410036.1" /db_xref="GeneID:4349488" /translation="
MRRMFGDCQVLSSMAAMAGAASSADALFASPLIPNPALAGFMSSSAAMPFHHFSNAAATLIPKEEGLMGGLHVAKDEGMDLEMDMELSGGSGSAHLDGLLSFADVDDDHKPQHSGHDQPPDAAQPSGAAGGNAKKKRYHRHTAHQIQQMEALFKECPHPDDKQRLKLSQELGLKPRQVKFWFQNRRTQMKAQQDRADNVILRAENENLKSDNFRLQAAIRNVVCPNCGHAAVLADMSYEEQQLRIENARLKDELDRLACIATRYGGGGGRQPVLSTSALSCISAPPPVLMPPLDLDMNVYSRHFAEQAPVMGCGDLIPPPVVPQHDGAAAYMGAMMAPVQEQDKQLVVDLAATAADQLARMCRAGEPLWVRQRGAEVMAVEEHARMFSWPVDGAKQGDGGAVARAEGTRDNAVVIMNSINLVDAFLDANKWMELFPSIVCKARTIQIINHGAASGHLGSGTLLLMQAEVQFLSPLVAAREVVFFRYCVHNADEGSWAIVDFPAEGFEEGLLQASVVRCRRRPSGCIIQDMPNGYSRVVWVEHMEMVGEEKPLQPVFRDYVASGAAFGATRWLSILQRQCERLASELARNIADLGVIRTPEARTNMMKLSQRMITTFCANISASGTQSWTALSDSTQDTIRVTTRKNTEPGQPSGVILTAVSTSWLPFTHQQVFELLADEQQRCQLEILSNGGSLHEVAHIANGSHPRNCISLLRINAASNSSQNVELLLQESSTHPDGGSLVVFATVDVDAIQVTMSGEDPSYIPLLPLGFAIFPATSPSPAAAPTISSSTTTTTGNGNGETSSTPPRNSSSNNNNADELLPPNGCLLTVGMQVLASAVPSAKLNLSSVTAINSHVCNAIHQITAALKSSAGGAGGEPASDQ"
misc_feature 624..746 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="propagated from UniProtKB/Swiss-Prot (Q336P2.1); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" misc_feature order(717..731,735..737,786..788,804..806,843..845, 849..854,861..866,870..878,882..887) /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:238039" misc_feature 723..884 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="Homeobox domain; Region: Homeobox; pfam00046" /db_xref="CDD:425441" misc_feature order(723..725,732..734,852..854,861..866,873..875) /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 1344..2054 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins; Region: START_ArGLABRA2_like; cd08875" /db_xref="CDD:176884" misc_feature order(1428..1433,1458..1460,1536..1538,1542..1544, 1575..1577,1587..1589,1599..1601,1608..1613,1626..1631, 1716..1718,1722..1733,1740..1742,1749..1751,1755..1757, 1761..1763,1812..1814,1866..1868,1872..1883,1887..1889, 1923..1925,1929..1931,1935..1937,1941..1943,1947..1949, 1959..1961,1977..1979,1983..1991,1995..2003,2010..2015, 2022..2024) /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="putative lipid binding site [chemical binding]; other site" /db_xref="CDD:176884" misc_feature 2658..2774 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /note="propagated from UniProtKB/Swiss-Prot (Q336P2.1); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" exon 501..766 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 767..884 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 885..1073 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 1074..1598 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 1599..1706 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 1707..1922 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 1923..2097 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 2098..2366 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 2367..2462 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" exon 2463..3741 /gene="LOC4349488" /gene_synonym="GL2-3; OsJ_031281; Roc3" /inference="alignment:Splign:2.1.0" ORIGIN
ggttactcctcttcctcgctcgctcgctcgctgccttagccttgacctccatcgatattgcaaccataaagaggaggaggaagaggaggcgagaaagagagagagatcgtcttcttctccagccagccagccagccgtgattgatctcaagggggaaggcagctgcagggatcaagaagaaggagaagaagtgatcaaggaaggaaggccacggaacaaccgacagggcaggagggcgctggccggatcgccggagaaggaaccactagctagctagctagctactcctattgaagatatcgccggccggacatatgcgcaggatgttcggggactgccaggtcctgtcgtccatggccgccatggccggggccgcctcctccgccgacgcgctcttcgcctcgccgctcatccccaaccccgctctcgccggcttcatgtcctcctccgccgccatgcccttccaccacttctccaacgccgccgccaccttaatacctaaggaggaggggttgatgggcggcctccatgtggccaaggacgaggggatggacctcgagatggacatggagctcagtggcggctccggcagcgcccacctcgacggcctcctcagcttcgccgacgtcgacgacgaccacaagccgcagcacagcggccatgaccagccgcccgacgccgcccagcccagcggcgccgcggggggcaacgccaagaagaagcgctaccaccgccacacggcgcaccagatccagcagatggaggcgctgttcaaggagtgcccgcatccggacgacaagcagcggctgaagctgagccaggaactgggcctcaaacctcgccaggtcaagttctggttccagaatcgccggacccagatgaaggcgcagcaggacagggcggacaacgtgattctgcgcgcggagaacgagaacctcaagagcgacaacttccgcctccaggccgccatccgcaacgtcgtctgccccaactgcggccacgccgccgtcctcgccgacatgtcctacgaggagcagcagctccgcatcgagaacgccaggctcaaagacgagcttgaccgcttggcctgcatcgccacccgctacggcggcggcggcggacggcagccggtgctgtcgacgtcggccctgagctgcatctcggcgccgccgccggtcctcatgccaccgctcgacctcgacatgaacgtctactcgcggcacttcgccgagcaggcgccggtcatgggctgcggcgacctcatcccgccacccgtcgtgccgcagcacgatggcgcggcggcgtacatgggcgccatgatggcgcccgtgcaggagcaggacaagcagctggtggtcgacctcgccgccacggcggcggaccagctcgccaggatgtgccgcgccggcgagccgctgtgggtgcggcagcgtggcgcggaggtgatggccgtggaggagcacgcgcggatgttcagctggccggtggacggcgcgaagcagggagacggcggcgcggtggcgagggcggaggggacgcgtgacaacgcggtggtcatcatgaacagcatcaacttggtggacgccttcctcgatgcgaacaaatggatggagctgttcccgtcgattgtttgcaaggcaagaacaatccagatcataaaccacggagctgcgtctggtcacctcggcagtggaactctcctcttgatgcaagcagaggtgcagttcttgtcgcctctggtggcggcgcgcgaggtggtgttcttccgttactgcgtgcacaacgccgacgaggggagctgggcgatcgtggatttcccggcggaagggtttgaggaggggctcctccaagcctcggtggtcaggtgccggcggcggccgtccggctgcatcatccaggacatgcccaatggatactccagggtggtgtgggtggagcacatggagatggtcggggaggagaagccgctgcagccggtgttcagggactacgtcgccagcggcgccgccttcggggccacgcgctggctctccatcctccagcgccagtgcgagcgcctcgccagtgagctcgcccgtaacatcgccgacctcggagtgatccgcacccctgaggcaagaacaaatatgatgaagctgtcgcagcggatgatcaccactttctgtgctaacatcagtgcttctggaacccaatcttggacggccctctcggattcaacccaggacactatcagggttacaactcggaagaacactgagcccggacagcccagcggtgtcatcctcaccgctgtctccacaagctggcttccttttacccatcagcaggtgtttgagcttcttgcagatgaacaacagcgctgccagcttgagattttgtcaaacggcggctcccttcatgaggtggcacatattgcaaatggatcacatccaaggaattgcatctctcttcttcgcattaacgctgcaagcaactcgtcacagaatgtggagctcctgctgcaggagagcagcacccaccctgatggtgggagcctggtggtgttcgcgacggtggacgtggacgcaattcaggtgacgatgagcggcgaggatccttcctacatccctctcctccccctgggcttcgccatcttccctgccaccagcccatcacctgctgctgcacccaccatcagctcaagcaccaccaccaccactggcaatggcaatggcgaaaccagtagcactcctccaagaaacagcagcagcaacaacaacaatgcagatgagctgctgcctcccaatggctgcctcctcaccgtcggcatgcaggtgctggccagcgccgtaccttctgccaagctcaacctctcgagtgtcactgcgatcaacagccatgtctgcaacgccattcaccagatcacagctgcactcaaaagttcagcaggtggtgctgggggtgagccggcgtccgatcagtagcaaaggagacctggaggagaggggatcggagcaacatgggatcagacaccaaaatgcctcccaatttatttcgctaacatcgcagtttgtttttctgttagctctcggtctggctggttcatcaggtgcaagggagggtttgacaagaagccaacactaacagctactcaaatctctcctctcttcccgccatatttctgcctctcaaaatgacgaaaatacccccaaccagccaacaagcaaagccatggggggcattttgatcattttgggaagctacttctgctgagaaagaaagaaagaaagaaagggtcttgtcaagctctcacttgcaccaaccagctgattcatgaatttgctgacatcagctctgcaggcattttggtcgtgcatcggtttcttgctactccatccatccctctttaggttcttcctccctttcctcatcaaaagtgagaactgcatgtgaagaaggttagctccttgttttgaatttttgtaataataagatggaagaagaagacttggtagcttgagtgtgtggtttgtgttaagatcgagctagactttgtgtaaggttgaagaagaagaagacattaagcagattgttattaggagatgagataagagaaaggaggagaggagaagtcaagagcgaaccagttgtgacccttcttcacactagaagggggtcttggttcgggaattgacttgttacctctctgcactctttgtctgtaacctttgccctatcttattattactactagtattgttc
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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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