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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa04LNT0259400.1

TAGCATTAAACATCATTCATTTGAAGCTACGCAGATAGACAAACCATATTCTTTAATCAATTGTACAAAATGCGAATCTAGCTTATACAATGTACCTAACCAAATTAGGAAACCCACTTCGAGTGCAGATTCAGTACCAAATGTGCAAAATTTCAAGTACATGACCAATTCATCTAGAGAATGAACATCCAATACCCAACTCTAAAGTATAAACCATCAGAAGCAAATGCTGAGAAAGAAAAAGTGTAGACAAAGCTTAAACCGTCAAAAATCAGACACCATGGTCTCTATGGACCATGTGATCGTCAATGGGGGATGACCATCATTGATGGGTCAAGGTTGATTCCGCCGGCGCCTAGGATCTGAGCAGGCATTCAGATTATCACTTGGGAGCTTGATGCGTACATGGGGGACATGGTCACAGTGTTCCTTCTGTCCTGCCCTGATTCCCTTAAAGCAAAAGAAACCAGCAAAATGACATGTATACAGTCCAAACTGCTATCGTCAGAAAAAGAATTGAGATCCGAAAATTTAGAAATGATTGCAGCTTCAATACAGTAACATGAAGATATCTGAACCTCATCACCAAAGTTTATCAAAAAAAACAAAACCCTAATTCATGTATGGCCCTAATATCACTGTACCAGCAAAATGGCTAGTGGTTTCACTGGAGCACAAGCACCTTTTGATAAAATCACAATCTATAGATTTGGAAAGATCGAAATGTATGATGCAGCTAGAGATAAAAAATTTCACCAGAACTGTATAACAAAAGGAACATAAGTAAAACCACAATCTAAGACAAGCAAATTAAACAGACCTCATCCACCATCCATTTGAAGAGAGGAGATCAAGGCTATGGCTATGGCAGGTCCCATCTTAAAGATAACTGCCAAAGCCTGCACTCTCTGAAGTAGAGATATGTGGTATTCTTTCCAGAAAAGAGATAAAAACTGAACTGAACACATGCACTGTGAATTTCAATGGACAGATAGAGGACCCTTTCCAAGTGAAATTAATAACAATATTATAGCCCGCTTGCATAAGATTACCTGAAGCCACTCTAAATATCTTTTTCTTGCCAAATCTGAAGGCAGAACTCTATGACTTAATATATGACATGTTTCTCCTGTGTGGGCCTAATGTAATGCATATGCCTAGTACTGAATGGAATGGAATAGATTTAATAGAAATAATCTATATATGAAAGAAGGTGCTGATTATGGAAGTGTTGAATGCATGGGAACTGGGAGCAATTGATCATCTTACTCCAGCTAAATTTTAAAAAACATAAATATATTTATAGATGAAAGAGGGGAAAACATATATACAAGGACAAAAACTGACCAGATCTTCATGTAGTTGATATGGTTTTATCCAAGGGATTAGACAACTGCTGCTTATGTTGTGTGAACTACACAAATCAGCTACCTCTTCTTCAGGAAAGTATACTCATACATCAACTGCAACACATGCAGTATCTGCAATCGTGTTAATAAATGCATCACCGAGAAAATCATATGCCTAGAAGTATATTATACTGGAGAGGTAGATGGCATGAGGGATGAGTGTTATCCAGCTGGGATTGATTCGCAGCCACCGGGGAGAGATTGGAGAGGCGATGCGGCGTGCGATGGTGGTGGAGGTGGTCGAAGGGGAGAGAGCGGAACGGAGATGCGGAGGGAGGCGTCTGCTTTGAAGCTGCTCAATCAATTTATCCCAGGTAGAGGTGCACGGGAGGGGGAAAGCGGGTGGCTCCCGTCGATCTGGCGGTGGCGCAGGTGGAGCGGCGGCGCAACCGACGGCTCCCTATGACAGCGCAGGTCGAGCGGCTGGCGGCTCCCGTCGATCCGGCAGCTGCGCAGCCGATGGAGGAGGTCGATCGGTGGTTCCCGGCGATGGCGCAGGTGGAGCGGCCAATGGATCCCATCGATCCGGCGGTGGCGTAGGTTGAGCAACAGCGCAGCCGATGGAGGAGGTCAGAGTGGGTAAAATTTCAGGTCAACGTGTCCCTCATCTCGAGAACAGACGAATCGAAAGTTGTCTTCTCGTTCTCAATCCTGCTCCTGGGTGGGGCGTCGGCGGCGGAGGCGGAGGCGGTGGACAGGGAGGAATGTTTGTGACGGCGACCACGGTGGCGCCGATCTGGCTGAGGACAGATGCGACGACGGCGGAGGGGTGGTGGCGTAGGAGGCGGCGGCGGGAAGCGGCGGGCGCATAGGAGGCGGCGATGGGTGGCGTAGGAGGCGGCTCCGGCGGGAGACGGCGGCCACAGGCGGATCCGAGGCGGCGACGGGGTAGGGTGAGCGGCTCCGGCGGGCGGGCGTGCGGCGGCGGCGCCGACGGACCAGGCGCGTGATTAGCGTTGCGGAGGACGCGTGCGAAGGAGAAGGGGAGGCAGTTTTTTTTGCGAAATGGAAGCAGTTTTTTTTTTGG

Coding Potentia
Explanation CPC Score
noncoding -1.16639
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0259400.1 osa-miR5528 Translation 4.5 15.37 1 21
Osa04LNT0259400.1 osa-miR414 Cleavage 4.5 19.478 1 21
Osa04LNT0259400.1 osa-miR528-3p Translation 5.0 20.419 1 21
Osa04LNT0259400.1 osa-miR1423-3p Translation 5.0 21.324 1 21
Osa04LNT0259400.1 osa-miR2094-5p Translation 4.5 16.449 1 21
Osa04LNT0259400.1 osa-miR2930 Translation 5.0 18.459 1 22
Osa04LNT0259400.1 osa-miR1862f Translation 2.5 7.574 1 20
Osa04LNT0259400.1 osa-miR1862f Translation 5.0 11.332 1 20
Osa04LNT0259400.1 osa-miR1862g Translation 2.5 7.574 1 20
Osa04LNT0259400.1 osa-miR1862g Translation 5.0 11.332 1 20
Osa04LNT0259400.1 osa-miR2873b Cleavage 4.5 14.558 1 21
Osa04LNT0259400.1 osa-miR2873b Translation 5.0 11.06 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0259400.1 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0259400.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0259400.1 4 nan Morphological trait Root RG449 RG788
Osa04LNT0259400.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0259400.1 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0259400.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259400.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259400.1 4 nan Morphological trait Panicle/flower RG788 RZ69
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus