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

>Osa02LNT0178400.2

GAATCCTCAACTTCTAGTGTTGATAATAGATAAACAACCAGATCATGGTCGATAGTTCACAGCACCACAATCATTAACGTACACACACTATAGGTCGTTCCGTCTTAGATAACAGGGGGCGACTCAAACCGTCAGACGTTTTCCCCCATACACAAATATTCCCAAACTTAGCAGTAGAACATGACACGTTTGACATTTTCCTTCAGATCAGGAAGCGGCCTTACAGCAACATTCCCAGCAGGCTTAGTGCTGCGTGCACCAGGAAGGGGGCCACCGCCACGGGTATGGGCACCGCTCGCCATCGACCCACTATCTGAAGTATCCGGCTCCATGTAAAATCGAGCTCGAAATGCCGCGAGATGGGCATAATATGCAGGAGGAACGATTGATACGGAACGGGTGCACCTTGCATAGGTGTAGCACAAGTTGTTTGTCAGAGTTTGCAAACCATCAGCAGTGAACTTGTTCTCATCCCACAGAACATGATAATGTGCAGGGCGACTTGTTCCCTGAATGCCCGCATGGCTACACAGGTAGAAATCAAACTCAGTAGGATGGCATATCTTTGAATCAACCACGGTGCCTGGTAGTATATTTCCACTTCTGTCAACAGTGCGCTGGTCCTTGTGGTTATTAGCAAACAGCCTTGTGTGATGACGCTTCTGGACCACCACAAAGGTAACGGGTGGCTGATAATCGGCTTCCAAAGATGCACATGCCTTTCTAATGGCATCAAGCTCATAAAACAGAACCTGATAAAACTGTCCTTCACTGACACCATCCCTGTAAAATATAATCCTCTGGGGTTTCTGTCCAGTTGCCCTCTTGAAAGAAATGAGAAGCTCTCTGATCATTCCACCACTTACAGTTCCTCTTTGAGGATCTTTCCATACTTTAAAAAGATCCTGTATCAATTCCTGACGATGGGCCTGTGCACTCACTAATCCGGCATATTTGGTGACCTCAGGCCAGTCTTGAGAAGCAACAACAGCTGCAATGGAAGGGCTAGAATCTTCTCCAGGATGGGGATGTGTAACATCAGCACCAAAAATGATCGTTGGCCTATCACTCACAAGGGGAATCCTCCTTGTCAAAGCATCAACAAGTACTGTATTTCTTCCTCCCACCTTAACATTGATTTTAAGGGCAACGTTTGCTAAATACTGTTTGCTCATCTTAAAAACATGCTTCGTAAGACAGCATTGCGAGACCAATCCAAGATCAGTCTCACATATCCTTTTGAGATCGCCATAAAGAGAACCATTATTGTCAGGCAATATTGCAATCAGCAGGTCAAGCTCCCCGCCCTGTGGTTTCAGTATATTCATGGCCTCTTGATAGCGTGCCTTGAGCGCTCTTTCCACATGTTCAGGTCTTGCAGTCACTAGAGGAACCACAGGATCAATTGAGAAGTCCATCCCAGATATTTGGCACATAATAGCAAGCTCGCGACAGAAACTCCTAGCAGCATTATCTTGGACATGACGAGAAAAATTGATGCATGTCCAGTTGTTAACTCTACCACCATTGACCATTTTCTTATTCATCATATTCCATTGGCCAATTCTTGGCAAGACATCCTTCTCTCTGCCACTATCGTGGTACTTAAGCCAGGGGGGTGGTAGAACACGAGCTTCAACAGATGCAAGTCGCTCATCGATCCTTATGCCAAACTCCTGTGCATATGGATCCTGATGGTATGCATTGTGATGCACAGTCTGCAAAATGTCCAGCTCACGCTCTTGAGGGCGCTGGCAGGTCACTTTAAGAAGAGCAGTTATCTGCTTCTCATTTAGTCTTTTTGAGTAACGCTGTCCCTCCACAATCTTACAGACCTCCATTGGTAGATAATTTGGCCTTTGTTGATTGCCCACTTGCAAGCAAGGCAAAGTTGTGTGCTTAATGTTAAATCCATATGTCTCCTGGAAGTATTGCACCACCGTCTTCACAGTACCATGATTATCAATGGGAAAAGACAACTCTCGTGTTGCTTGCGAGGTAAGGCCAGAAATGCGATACTTCCTGCGCATATTGCCTCTATGTGTGACCTCAACCTTTACACCCCTTAGGGCCTTCTTGATCTTCACACGATCAGCATCAGATAATGGTCTAACTGAGATGTCTCTGTTCAAAAGCTGTGCAACAAAGTCAATCACAGGTAGAGGCTCAATGAATGCTGTCGATGACATATCAATATTCAGAGAAAGTCCCATCTGCGTGGGTCGTATGCTTTGGTAAAAACCACGCCAACTTTCCAGGCCCTCGCCAAGTTGTTGGCGCCTTCCTAAGTTAGGCGAATAAAATGACCTTGCAACTGGAGAGTACCTTGCAGTAGGCAATTCACGTAGAACAATGTCAAGAACTTGAAGAGCTTCTTGAGGAGCATCCGCTTGCCTTCCAGCTAAAAACATGGCTAAATGGTGGAGATCAGCGCGTGCAGCAAATTTGATCACGACCTTAAATGGTCTCTCACGCCTCTGTGCACCTTGCCCAACAGCAAGGCTCTCTTCCTCATCCTGCAGAATAACGTCAAAGGTCCTAGAAGTAAATGGTAATGGACCAGCTGTGTATAAGCTCTTCCTTCCATCATAGACTGGAAGACGGCCACCCAAATGAGACTGCCTATATTGTGTTACAATTTCTCCAATGACAGCACGATTGACACCACGTGAAGGAACCTCAGGAGTTATAGACACATCATACTGGTGAAGGTCTTTGTCAGGCAATTCAGCAAAGAAATGGTTGGCTTTCACGATGCACCTATCACCAAATGTACCCTTGCCAGGGCGCATTGGAAATCTCACTGATTTGCTCGATGGTGGTGCTGGTTGAATGGCCTGGCTAGTGGGGCTTTGACCCTGGATGGCAAGTTCCTGAAACTGATGTTGGACTTCTTCGCTGCTGGCCTCAACAGGCAGCGAAGATGGGCCAGTTCTTGATGGTGATGGTGCAACCACCGTAGCTTGGTACTGGTCTTGTGAGGCTTGGTGCAGCTCGGGAACTGTTCTTGATGGACTGGCAGGAACTCCATGTCCACCACTGCCACTCCTGTGTTGTGGCATTCCTCCTTGCCGTTGGACACCACGGCCATAGTACTCATGTGCTTGATATTCAACCGGACCACCACCTGGTTGATGTGATGTTGGCCCTCCACGACCCTGGTAACGTCCACCACGTCCCTGGTGTTGTCCACCACCACGACCAGCTTGTTGAGCATATTGAGGATTGGCAGGTTGCCAACCACCACCTCCATGCTGTTGAGCTCTCTCAGGTCGCTGTGAAGGACCCCGTCCAGGAGCTCCAGTGGCTTGTTGAGTTCCAGAACTTTCCCCAGCATTACGGGGTTCAGTTTTTTTCTTTCTCATCATGGCTAAAGCTCGGGGCACCTACCTTACAAATCGAGACGGATGGCCCGACAGGGATTGCTGGGTAGGGGAACGATTAGAGCGCTGGAACCGGTGACTCTCCCCCTTCGTCGGCGCCGGCGCCGGCGCAAGAGCCGGTGCGGACGAGCGCGGGCACGACGCGGCGCGCCGGGCCGATGGAGGAAGACGGGCGGCGGCGGCGGGCGAGCGCCTAGCGGTAGCGGAGCCGAGGAAGGAGGCGGCGGCTGCGGAGGGGGGTCGAGGGCTCGGTGCGGGTGCGGGTGCGCGTGCGCGGCGAAGGGGACTAGGGGTAGGGGAGGCGAGGGGCGAGCGAACCGGGGTGAGGACGAGGGTGACGGGAGAGCGGTTTTGGGCGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.75631
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0178400.2 2 27330587 C G
Osa02LNT0178400.2 2 27334297 G C
Osa02LNT0178400.2 2 27334450 A G
Osa02LNT0178400.2 2 27334763 C T
Osa02LNT0178400.2 2 27334832 T C
Osa02LNT0178400.2 2 27335017 A C
Osa02LNT0178400.2 2 27336602 A G
Osa02LNT0178400.2 2 27337497 C G
Osa02LNT0178400.2 2 27337951 C T
Osa02LNT0178400.2 2 27338615 A G
Osa02LNT0178400.2 2 27335484 A G
Osa02LNT0178400.2 2 27331835 G T
Osa02LNT0178400.2 2 27331991 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0178400.2 osa-miR5796 Translation 4.0 20.456 1 21
Osa02LNT0178400.2 osa-miR169a Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR168a-3p Translation 4.0 23.467 1 24
Osa02LNT0178400.2 osa-miR169b Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169c Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169e Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169f.1 Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169g Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169h Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169i-5p.1 Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169j Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169k Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169l Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR169m Cleavage 5.0 21.973 1 21
Osa02LNT0178400.2 osa-miR444a-5p Cleavage 4.5 16.313 1 21
Osa02LNT0178400.2 osa-miR530-5p Cleavage 3.5 22.916 1 20
Osa02LNT0178400.2 osa-miR1440a Translation 4.0 13.361 1 20
Osa02LNT0178400.2 osa-miR1861b Cleavage 4.5 14.87 1 22
Osa02LNT0178400.2 osa-miR1861f Cleavage 4.5 14.87 1 22
Osa02LNT0178400.2 osa-miR1861i Cleavage 4.5 14.87 1 22
Osa02LNT0178400.2 osa-miR1861l Cleavage 4.5 14.87 1 22
Osa02LNT0178400.2 osa-miR5497 Cleavage 4.5 10.413 1 21
Osa02LNT0178400.2 osa-miR5497 Translation 4.5 18.407 1 21
Osa02LNT0178400.2 osa-miR5514 Cleavage 4.5 17.548 1 21
Osa02LNT0178400.2 osa-miR5517 Translation 4.5 24.033 1 21
Osa02LNT0178400.2 osa-miR5793 Cleavage 3.5 11.382 1 21
Osa02LNT0178400.2 osa-miR6251 Translation 5.0 21.482 1 21
Osa02LNT0178400.2 osa-miR1846c-3p Translation 3.5 11.209 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0178400.2 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0178400.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0178400.2 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0178400.2 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0178400.2 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0178400.2 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0178400.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178400.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178400.2 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0178400.2 2 T2-2tiller Morphological trait Culm/leaf C424 C747
Osa02LNT0178400.2 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa02LNT0178400.2 osa-MIR168b 100.0 106 1 106 5.55e-51 196
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus