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

>Osa08LNT0408000.2

GTACAAATCATAGAGGGTATTATTAAGTGGCAAAAATTCTCCACATGCTACAGCAATTACTACCAAACGAAGCTTTTGGTTAATTGCAGGCATAATTTAACCCCAATTGAATCGAATTTCTACAGATAGGATAGTAAAATAACATTACAACCGATCCGCAGGAAATGGGCAAAAAAAAAAAGATGGTGCCTTGACTAATGAACCGGATGCCAACTATACACTGCCAAATAATAATAATCCACTGCCCTCAACTCTGTCAAGACATTCATGACAGTCCATCCTCGCAGTGAGAATCGGCAAAATTCTCGGCTTATCTTGCAAAACGGTGACCCCGGAGGACATGAAGATCTTTATCACTCACTTGTTCTTTGCCTTTTAGAATTAGGTCCATCAACTGGATCACGGTTATGTTGATGTGAACTCCTGGAATGACTTGGACCAGCTCTTGCAGTATTCAAGTTCCCATGTGCAGCCTGTGAAGGGGTGCTGCTACTGACTGCTGAGGCACTTTGATGATGTGACTCAACTTGGGAAATAAATGGCATAATTTGGCGAACTAAGCTAGCGAACCGTAGACCCTCATCACTGACTCCTGACACTTCTGGTGCTCCATGATTTCTACCATCTACCTGCTCAGCAGAAGCCGGTGCATGCTGATTTGTGCCATTTACTCGAGAATTTTCCCCAGAAAAGAGTGATGCAATCCAAGGGATACTATCCATCAACTGAGAAAAAGGCCCCTGGCCATTCTGCTCCCCAGGGGAAGTCTGAGTGCCGTTTTCCGCATTGATATCAACAGGAGATCCTAGAGTACCTGCTTCATGATACTGAGATGTCTGTGGATTCGGTATCTGATTAGCACTATGGGCAACTTGAGCGTTAGTGTATGCTCTTTGTTGAATTCTGGCAAACAGTGGGTAGATAATACCAACTCCACTAGAAGACATTGAAGGAGGATGACTGATGCCAGCAGGCACAGCAACCACTGTTCTATGCGGCACCAGCCTAACTCCAGATTCAACAGAAAATGGAGCACCAGCTGTAACCCCTGCAAATGCTTCACTACTGTTTGCAGGTGAAGCATTTGCACTTCTATCTGTACGATCTTGTGTTTGATGTTCCTCAACCCGCTCAGGTGGGTTAGTACCAGTTAAAGACACAGACCCACTCGTGCGGACATGGATGTCAATATCTCTTGGGTGCAGAACAGAGCGATGTGAAGTAAGACTAGAAAATATTGGGCCCACTTGAACAGATCCTGTTCCTGGAACAAAAGGAGCAGGTTGAACCATAAGAGGATTTGGTCCAGATGGAGAGATAAAAAGAGCTGGTCCAGAATTGACAACCGCTTCTGAAGTTGCAGGATTTATACGCAGCATCATTGTCGTGCGGCCAAGTTCTAGAAGTAATGAACCAAGGTATTGGATGAGAACTCCATATCTGACTACACTGTTTTGAAGGTTCCTCCGTGTTGTAGCATCAGTTACATTCACAATATCTCCTAGCTGGTTTGGTAGTTGCTGCATTGAAATAACTCATCTTAACTTCAGACACGCTAGTAACGTATAAAACCGAAGTTAACAACTCAACAAAGCAGATAAGCAGCAAACCAAACTAAAGAAACAAATTTCAGCATCTATGGGAGTCAGTTGACTACCAAGTAATCATAATGAAGTGATCACAGCACAATAATATAATTAACACAGGAAATGAACTTATCCTGCAATTAGTTTTTAATTGCATACATGAATGGTTACAAAAATTTCCATTTCACTTGTTCTCCACTTAAAACAAAATAAAGTATAATGGTATCCGCGTATTCCTCAATATTATGTTATATACTAACACAAAAAAAAAGATAGTTTAGAAATGAAAAACTCAACAGACATGATGTGTACACGTTTTGTACATTTTACAAGGTTATAGTACCATGACTCTTGGTGGGGAGTATGAACATTAGCTGGATAATTTATAAGAAACAGGGTTTAATTGAGTGCAACTATGAATGTCGGAATCTATGAGACAATGGAGGGTGATTGGACCTGCCAAACTCATATGTTGTACCCAATGAAACATTTACCATATTACCCTCAATCAAATAGCTCAAATTGATATATCTAACTTCACTAATACTTTCCCTATCATTGAAGAATAATAGCTACATGCATAGTATTCTCAACTCAGCAAGAACAAACAGAAAAGAGATCAAACTATTCATGAAGCTAAAACATAACTGTTATATTAGCTAATTCATAACGAGAAAAAATAAAAAAATGGCACGGACAGATAGCAATGCTCCAGCATGCTCAACAAGAAGTTGTCTAGTAGAGTGCATAGTTTCAGCAAGCAATGCTGCAGTAGGAAGCCCATGCGCCGAAGCTGAATCAGGCTGGCTTTCATGATTTTGAGTACCACCTCCATGGGCACTTCCTGCAGTTCCATGGTCAGCATTATTCAGAGTTTGTCCATTTTCGAGGAAGCCTTCCCTTCTAAAGGAGTCTCTCAAAAAGTTAATGTACTGAGAAATTGTGGTCAACGAATCAGGAATGACGTTTGGTTCTGATAACCCAACTGACGTTTCAGACTGGAAAAGTGGAGGAACCAGCATTTGATCAAGTACAGCCCTGACACCATTTTGCGTTGAAGATTGTGCACCTTCTGAAGGTCTGGCATCAGAAGGTGCTGGTCCACTCGAAACTTGTGTGCTACTAGGAGCTCGAAGCAGGCTTTGGAGCAACTGTGCAACACTGAGTTCACTCCCCTGACCCACATTAATAGCCTCAAGTACAATACTGCGAGTCATAGTGGGACCACGACGACGAGCAGGATTTGATGTGGTACCTTCATTTCCAGCATTTCCTGATGTAGCGGATTGTCCTGGTTGTCTAACCACGAGATGCAATGTATGGCCATCTTCCACGTGATACGCAGAGAGGAGTTCATCATCCTTTAGAACTCTCCCACGGCAAATCAGACGTTGTTGCTCAGACAATATTCCAGTTACAGTGGCAATTTTTTCCTTTAGCAGAGGCACTGGCACGCGTTTATTGACACGCAAATTGTATGTTTGAGAATCCAATGTCTTTATTTTGATCTCGATTGTACTCTCACTATTCAAGTCCTCAGCACAATGTGACATTTGAACATCTGAAGAACTACTCTCCATGATCTCCAGGATCCCCCTCCCCTCCCCTGCTCTGCTCGTCGGATGGAGATCGGCGCCCCTCCCCCTCCCCTGTTCAGCCGCGAGATGGCGCAAGGAGCGGAGGAGACGAGACGGGGAGATTTTTCTTTTACGCCAACAAGGGAAGGGGGGAGAAACTCGGGGGGCGCCTAATGCGCGCCTGGTTCGCTGCGGGCGCGCCC

Coding Potentia
Explanation CPC Score
noncoding -1.241
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa08LNT0408000.2 8 11870038 A T
Osa08LNT0408000.2 8 11870313 T C
Osa08LNT0408000.2 8 11870945 A G
Osa08LNT0408000.2 8 11871789 T A
Osa08LNT0408000.2 8 11871792 C T
Osa08LNT0408000.2 8 11873085 T A
Osa08LNT0408000.2 8 11874211 A G
Osa08LNT0408000.2 8 11874747 A G
Osa08LNT0408000.2 8 11875472 T A
Osa08LNT0408000.2 8 11875874 G A
Osa08LNT0408000.2 8 11875914 C T
Osa08LNT0408000.2 8 11876970 A G
Osa08LNT0408000.2 8 11878252 A C
Osa08LNT0408000.2 8 11876551 T C
Osa08LNT0408000.2 8 11871129 C T
Osa08LNT0408000.2 8 11877801 A G
Osa08LNT0408000.2 8 11873700 G T
Osa08LNT0408000.2 8 11873811 T C
Osa08LNT0408000.2 8 11873713 G T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa08LNT0408000.2 DTM_#DNAt_MULE_japo_Os2081 Chr8 - 11873482 11873863 381
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa08LNT0408000.2 osa-miR166a-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166b-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166c-5p Cleavage 5.0 16.574 1 20
Osa08LNT0408000.2 osa-miR166c-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166d-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166e-3p Cleavage 4.5 15.585 1 21
Osa08LNT0408000.2 osa-miR166f Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR167a-3p Translation 4.5 22.295 1 22
Osa08LNT0408000.2 osa-miR172c Translation 4.5 15.591 1 21
Osa08LNT0408000.2 osa-miR166g-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166h-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166m Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR166j-3p Cleavage 5.0 15.585 1 21
Osa08LNT0408000.2 osa-miR1423-5p Translation 4.0 18.632 1 24
Osa08LNT0408000.2 osa-miR1428a-3p Cleavage 4.5 21.237 1 21
Osa08LNT0408000.2 osa-miR1850.2 Translation 4.0 22.4 1 21
Osa08LNT0408000.2 osa-miR1873 Translation 4.5 17.699 1 24
Osa08LNT0408000.2 osa-miR1877 Translation 5.0 13.235 1 24
Osa08LNT0408000.2 osa-miR2105 Cleavage 4.5 11.679 1 20
Osa08LNT0408000.2 osa-miR2864.2 Translation 4.0 10.257 1 21
Osa08LNT0408000.2 osa-miR2931 Cleavage 5.0 19.049 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa08LNT0408000.2 8 qDSR 8 Resistance or Tolerance Other soil stress tolerance RM3572 RM404
Osa08LNT0408000.2 8 dth8 Physiological trait Flowering RG333 RZ66
Osa08LNT0408000.2 8 hd8 Physiological trait Flowering RZ562 RG978
Osa08LNT0408000.2 8 hsa2(t) Physiological trait Sterility nan nan
Osa08LNT0408000.2 8 nan Resistance or Tolerance Drought tolerance RM72 RM331
Osa08LNT0408000.2 8 qALRR-8 Resistance or Tolerance Other soil stress tolerance RG978 C1121
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