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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa02LNT0178200.2

GTCCATGGCTAGCTTCCAATTTTTACTATTCAAAGCATCATTCAAAGTATCAGGTTCTGACTCAGCAGTAATTAAATTTGCCCAACGAACTGTACCGTCTGTGTAAACCTTGGGTTTACGAATTCCCTGTTGTAGACGAGTGGCTGGTCGTTGAGGCTGAGTCAGGGCAGCTTCGCTGGATGTGGTAGAGTTGTTCGCCGTAGAGTTGGTCGCCATGGACGATCTTGACGACGAGCTGTCCGAGAGAGGCTCCGACGAGCCCCCGTCGATCGGAACAGCCAAGGAGTCATCGCCGCGTGGAGGAGACGCCGGCTCGGGCGCACTGTCGGAGACACGCGACGAGGAATGGCTGGTGGATGGCGATCGGCTGAGAGAAGAGCCGGCTGCAGCGCCTATATCCCCAGGATGATGCGCCGCAGTTGCGTCAGAAGTCGCAGCGTCGTCAGGGGCTGCGTGAGTGTTAGGAGCCGCGGAGTGCCCGGGCCGCCCGCCGAGCAGAAAACCATGGGTGTTTTGCTCCAAAATTTGCCCTGTTCGCCCAGAAATTTCAGCAGCAGCATCTGCACTCGTAGCAACATCAACTGGAGACTCATGAGCAGGGTTAGTAGAAGAATTAATCACATATTGGTCAACATGTTCGTCCCGAGAAGGATTCAAAAGATGTTCTGGGAGGAGAAGAATTTCAGCCCGGAGACAATGACCAGCATTTGGATGAAGGTCAGAAAATGGGTAGATATGTTCATCAAAAACCACATCACGAGAAATATAAACCCGACCACTTAAACCCTTTGTGCATTACACTGTAACCAAGGAAAACACACCGTTTCAAGCGGAATTGGAGTTTGTGAGAATTGTAAGGGCGTAAATTTGGCCAGCACGCGCAGCCAAAGGTGCGGAGGGAGGTGTAATCAGGTTTGATATGAAAGAGCATTTCTAGAGGTGTGGAGCCTTGGAGAACAGGAGTGGGAAGCCGATTAATAAGGTAAGTACCTGTAAGGAATGCCTCATCCCAAAACTTGAGAGGCATCTGAGCATAGGCTAGAAGGGATAGCCCAACTTCAACAATATGATGGTGCTTACGTTCGGCAGACCCGTTTTGTTGATGTGCATATGGACATGACACACGGTGAGAAATACCGATGCGTTGAAAAAAGGAATTGAGTTTGTGATATTCACCACCCAATCAGTTTGCATAGCTAATATCTTGCGATCAAAGAGTCGTTCTACAGGATTCTGAAAATTATGGAAACATTGAAACACATCGGATTTATGTTTAAGGAGATATATCCAAGAAAATTTGCTGAAATCATCCACAAAACTCACATAATAATTATTCTTCCCAACCGAGGTTGGTGCAGGACCCCAAACATCTGAATGAATAAGCTCTAAAGGAGCACTAGAACGACTCAAAGACTTAGAATAAGGAAGTTGATGACTCTTCCCTTTCTGACAAGCATCACAAACCGAATGCTTGTTTGACTCACTAACACAAGGTAAATTATTATGACTCAAGACTTGTTGAACAATGACTGAGGACGGGTGGCCTAGGCGACAATGCCACTGCGAAGGAGAAAGCTTGATAGCTGCAAAAACTTGTTTATTTGGGAATGATTTCAGAGGATAAAGGCCTCGCTCACATCTGCCTTGGTGAAGTAGTTTCCTCGTTACCTGAACCACTGGCAGTATGAACTTGATCACCTCCATTGTACTTCTCCCGCACCGTCAGCTTGTCAAGATCGCTGGTGATGTGGTCCGTCGCCCCGGTGTCAATATACCAATTGGTACCAACACCGTAGGAGGAGGTAGCAGCAGCAGCACTCTTCTCTTCGCCAGTGAAGGAAGCATCAAACCTCTTGTAGCACTTGACCACCGTATGGCCCAATTTGTCACACAGCTGACACTTGGGGTGATCTCCTCCTTGGTTGTTGGTGAAGCCACCACGGCCGCGGCCTTGGCCGCCGCGACCACGGTTCAGATTTTGGCCCTGGTTTGGCTGACCATGGCCGCGACCTCCTCCATTGCCGCCGCGAGAAGCAGAGTTGGTGGACGACTGAATGCCACCCTGTCGAAGTTCCAATCGCTGCTCAAAAGTAACAAGCTGTGAAAACAACTCACCGACTGAGATTGGCTCAGAACGTTGGGCGACTGCAGAGACAACCGGGTCAAAATCATCATCGAGCCCAGCCAGGATGTCGGAGACGATGTCGTCGTCGTCGAGCTTCTTTCCTGCCGAGGCCATGTCATCAGCAAGACCCCGCATCTTGGCCACGTACTCGGCAACCTTCAGATTGCCCTTCTTCGTGGCCGTCAGAGCCATGCGTGTGTTCATCACACGCGCACGGGAGTGAGATGCAAACATCCCACTTATGGCATCCCAAACCCCAACAGCAGTGGGAATTGAGACCACCTGGATGAGGACATCACGTGAGAGGGAGAGCAACAGGTAGCTGAGAACCTGCTGCTCTTGCGCCACCCACTCGGTATGCGCGGGATTGGTGACCCGCACATCCTTGTCGTCCTTCTTGGTGATGATGGTGGCCGGCGGCTCCTCCTTTGTGCCGTCGATGTATCCAGCCATCTGAGCTCCCCTGAGCGCAGCAAGAACTTGCGCCTTTCAGAGAGGATAGTTGCTGCGGGAGAGTTTCTCTGTGACCGCGTGCGCGAGAGAAGGAGCAGCGCCACCGGCTAGCGAGGATGAAGACGACGCTATAATCACGACGTCGAGGAAGCAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.597158
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0178200.2 2 27297196 A C
Osa02LNT0178200.2 2 27297255 C T
Osa02LNT0178200.2 2 27297863 G A
Osa02LNT0178200.2 2 27298023 A G
Osa02LNT0178200.2 2 27298660 A G
Osa02LNT0178200.2 2 27298762 C T
Osa02LNT0178200.2 2 27299372 T A
Osa02LNT0178200.2 2 27299611 A G
Osa02LNT0178200.2 2 27299690 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0178200.2 osa-miR2866 Cleavage 5.0 19.848 1 20
Osa02LNT0178200.2 osa-miR5144-5p Cleavage 4.5 14.575 1 21
Osa02LNT0178200.2 osa-miR5144-5p Translation 4.5 12.78 1 21
Osa02LNT0178200.2 osa-miR5496 Cleavage 4.5 19.159 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0178200.2 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0178200.2 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0178200.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0178200.2 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0178200.2 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0178200.2 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0178200.2 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0178200.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178200.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178200.2 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0178200.2 2 T2-2tiller Morphological trait Culm/leaf C424 C747
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