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

>Osa02LNT0186700.2

ATAGTTACATACTACACTATTAATACATGGTCCCACCTATCATACACACTGTGTCTTGGAGTCCGTGCTACAGCTGGCTACAAATCTATAGCCCGCTGCTCTTCTCTCTCCTCATTTATCTGTTTACAGCTGGCTTATAGTCTGCTATTATTGTAGCTGCTCTAAGAGCCAATGGGTAAATGACGCCGATATAGTCCAATATGCAAAGGCTATAACGACGATCTGTCAGACAATTTAAACTCCGCCAACAAGAGACGGCATCGGAATATGCATTGCTTTTAATGAATTTATCATGCTCATGTCCACTGGCCAGGATTGGACCGTCTGCTGCCACCTGCCATCAAACACAAGGTCTCGCTCACTCGCTCCCAAAATATAACCACCTAACACGAACTCTTCTCTACACTATGCCATCACTCAACAGATCGAGGTTCAAAGAACCCGATCTTCAAATAACAGTACGTATTTTTGTTTCCCCCTCATATACAGATTACATTACAGCTGCAAAATGAACACTTCAGATTACAGACATTTTGCAACGCAGAATTAACATATTTAGTAGTCACTGTTGAAGGGAGAGACCTGGGAGGTTTTCCTATGGGACAACTACTACCTACAAAATCTTAAATGGCAAGCTGTGTGCAACAGCCATGCCAAATTAATGTATAACTACTAGAACATCATTTTGGCTAATTATCCATATCTGGATCTCAATAATATACCATTTCTCCAACAGTCATCGGTGGTTTCGTCCAAACCAGCCGTATTCATTTTTATGGGAGCCGTGCCAGTACCTTAACATAGCCATGAACTGGACTCTTTGTCTGGTTCAGTATGGTTTCTTTGGAACCACATATGAACACCCATACAGTTTGGTAACCCAACGTTGAGCTGCCAATGTAATAAAAAGGCAGCTCATCTTTTCAAGATCAATATGTACAGTTGAGATCGGGATCTAACACTTGGCAAATCAGCTCACTGAAGATGGTTAAATTCTTAAAAGAGACTTAGTCCTTCTGATAAAAGGAGAGAACTAGGTCTGTATGTACTGAGAACAATTGCGTGTCCACAAAGAGCTTCATAAAGGGCCTCTCACGGGTCGGGAAAGAACCGATGAAGCTCTCTCTTAAAAGCAAGGAAACCTTGTCATTGTTGGATTGCACATTAGTAATCGTATGAGATCTCAAGTTGGAACACAGCGAATCAAGGTAGGATCTAAGCACTGCCAAGAAACCTTTGGCAGCTTCCACCTGGGCATCTGTACATTCATAAACGGGCCTCTTTCTTGCTAGAAAACTCTCTCCCACTAGTCTGGAATGGTATGGACGCAGGGCAGAAAGCAACTCCTTCTGCTGCGGGAGTTGCGGGACAGAAGTAGACTTGATCTGATTCTTGTTGGCATCAATAACCACGGCGTTCACTAGCCTGGAATGTACATCGGATGTCTTGTTCTGCACACCAACTATGTATGGAACAGGTGCATCAAGAAAGTCCATCATGTCGTTTGGCAAGACCGGTATGAGTAGACTCTGCCACTGATATGGGCGTATCAGAGGTATGATGGACAAAACTGAAGCAGAAAGCATTCCCAAATTAGAACAAACAATAATAATCTGTTTCTCCAGCAGTGCTGCAGCAAAAAGTGTCATTACATGCTCCAACCTGAGGCATCCACAAATGGATGCCACAGCCCATGTTGATAAAGCAGTCGATTCCTCCTCGGCAAATAGCGCATTGCGCATCTCAGCCACCTCTAAACTTGTATCACATGACCGCAGATCAATAGTAGAACCAGCAATATGAAGAACTGTTTCACCTGGCCGGTGAAACCTTAGAGGATGAAGGTGATCCAACGGGTGAAAAGTAAGGGATGAACCCCTGGCAGGACACTGCAGCTGATAGTACTGAGAAACAACTTGCAGAGATCCATATTTTTTTGCCTTAGCCCATTGCGATATATTGTTGTGGCCAACTAAGTCTCCATGACCAATTGATGATGGCTCCTCCAAATCCGATTCATGGCTATCGCTTCTGAAATTTATGCCTTCAGAAGGAGAGTCCTGGGAACCTGGAGATAATTCAGAACCTTCACAAAGGCGAGAGCGCATGAGAGGTAGAATAGTATCATTAACAAAGATGTCAAGCTGTTCATCGTTCACATCATCCTGTAAAGAATAGCCACAATTTTCTGTGGTATCAGATTCCTTCAGGATAACTGGTACAGAATCCAGTTCATGAAGCTCAATCCCAGATTGATCGGCAGTTGTATCTTCTGATAAACAATTGTCAGGCCTTTCAAGAGTATCACACTGAGGAGCTGTTCCTGTTACAAGATCATCCTGTACTACACATTCCTGTTGAACTTCTTTGCAGTTTAAGTCCAATTGGTTATCTCTACATTCAGAACTGCTGTCAGTGTCAGACAGCTCCTTTGAACAAACTCCCACACTTGATTCAGAGGATTTTTCCAGATCTACTGCATGACCATCGAAATATTGTTTTTCTGTTGCAAGTTCAGTTCCTTCGCAGACAACATCATCCTCACAGGTTTCCTCAGGTGATAATGATGTAAGCAAGCTAACCCCATCAGTGAGCCATTCGAGACGCTCTTCCATAAGAATACTCTGTAGCACCCCAAAGTGCAGTTCAAAGAATGGGAGCCTGGAAAAGATGCAATAGCATCGCGGTGTAGTTATTACATAACGACTCCGGCGTGGAAAGACAGGTTTTTCACTTGTGAGCATAGAAACCAGCTTCGAAGGTCTCTGTACAATCTCTTCAACTAACACGCAGCATCCATATAGTGTAGAGTCATCAGCAACCTGTAAACGGAACACGAAAGACTGGTTGCTTTCTTTAAGTTGCTCCTGTCCTAGGAGGATTTCATTCAGCTCACTGAATGAGGGGGTCCGTTCAACCGCATGGACCTGTACACCTCCAGGAAGACAGAACGAGAGGATATCCTTGTACTTGAGTGGTAGAGGCCTCTCTGGAGGGTATGCAAAAAGAACCTGAGGTTCCAAATTTGACAATGCATGAACTTGGTGGTGATTGTTACCGAATATATTTCTCGGTTTCTTTACATCTTCCTCATTGCTCCCTAGTGCAATGTTTTCTAGCTCATGGATATCTGCCTGAGGAGGGAGTCCAACAATCACAATGCTCTCGAAAAGATGTGATGGTTCTCTGATGCACCTATTACCCAGCGACTTTAGTTGGAACCTGGACCACTGGCGCTTTTGTGTTGTGAGAACCTCCGGGTTGTAAGATCCAGACACTTCAGGTGACGTTGAAAACCCTTTCAGGATCTTCGAAAATTGTTGTTGCAGCTTCTGCATTGGGCTGCCACTCTCTTCTCTGGAAGAGTACACCACAGATGGTCGTGTTGACTGTACAGTGGCTGCAGAAGCTGCAGCAATAAATGCTCTCGCTACCTCTTCAGTTGTTTGCATCAGGTGTGATGTGTTGAATTTGAGCCCTTCAGATCCATCGTTCTTGTCCACCATTCTAAATGCTTCCTCACCTGACGCGGCGGCGGAGGGGAGGGCTTTGAAGCTTCACCCCGCGAAGATCTCCTCGCCTCGGCTCTCCTCTCCCCGCTGCGCGCGCGCGCGCCGCCGCCGCCGTCGAAATGGACCCGCCGAACTAGCAACGAATGGGATGGCGGCCTCCTCCCCTTCCCCTCTCCTCCTCCTCCTCCTCCTCTCCTTTTTTTTTCCCCTTCGGATTTGTGGTTTAATGCGTCGATCCGTTCGATTAAAACCAGAGGCGATTCGTCGCGGAAAAAAAATTAAGTGGCGTGATTTGGTTCGGCGCTTGGGCTGGACTGGACGAGGGGGGAGGAGAGATTTTGAGAAGGCGAGTTTTTCGTGGACGAGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.778793
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0186700.2 2 32861087 A T
Osa02LNT0186700.2 2 32858449 A G
Osa02LNT0186700.2 2 32858487 C A
Osa02LNT0186700.2 2 32860190 G T
Osa02LNT0186700.2 2 32863545 G A
Osa02LNT0186700.2 2 32864241 A C
Osa02LNT0186700.2 2 32866714 C T
Osa02LNT0186700.2 2 32859612 A G
Osa02LNT0186700.2 2 32869160 C T
Osa02LNT0186700.2 2 32859602 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
Osa02LNT0186700.2 osa-miR5528 Cleavage 5.0 15.923 1 21
Osa02LNT0186700.2 osa-miR812t Translation 5.0 17.493 1 24
Osa02LNT0186700.2 osa-miR812u Translation 5.0 17.493 1 24
Osa02LNT0186700.2 osa-miR818f Translation 4.0 16.02 1 21
Osa02LNT0186700.2 osa-miR1861o Translation 4.0 16.049 1 22
Osa02LNT0186700.2 osa-miR166a-5p Translation 3.5 20.618 1 21
Osa02LNT0186700.2 osa-miR166e-5p Translation 3.5 20.618 1 21
Osa02LNT0186700.2 osa-miR171i-5p Cleavage 4.5 19.597 1 21
Osa02LNT0186700.2 osa-miR439a Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439b Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439c Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439d Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439e Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439f Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439g Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439h Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR439i Cleavage 5.0 21.724 1 21
Osa02LNT0186700.2 osa-miR1861a Translation 4.0 16.049 1 22
Osa02LNT0186700.2 osa-miR1861b Translation 4.0 16.049 1 22
Osa02LNT0186700.2 osa-miR1861c Cleavage 3.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861d Translation 3.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861e Cleavage 4.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861f Translation 4.0 16.049 1 22
Osa02LNT0186700.2 osa-miR1861h Translation 4.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861i Translation 4.0 16.049 1 22
Osa02LNT0186700.2 osa-miR1861j Translation 4.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861k Cleavage 4.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861l Translation 4.0 16.049 1 22
Osa02LNT0186700.2 osa-miR1861m Cleavage 4.5 16.049 1 22
Osa02LNT0186700.2 osa-miR1861n Cleavage 3.5 16.049 1 22
Osa02LNT0186700.2 osa-miR2092-5p Cleavage 3.5 16.709 1 21
Osa02LNT0186700.2 osa-miR2101-5p Cleavage 4.5 20.053 1 22
Osa02LNT0186700.2 osa-miR2863a Cleavage 5.0 16.112 1 21
Osa02LNT0186700.2 osa-miR2868 Cleavage 4.0 16.045 1 20
Osa02LNT0186700.2 osa-miR812n-3p Translation 5.0 17.493 1 24
Osa02LNT0186700.2 osa-miR2873b Cleavage 4.5 15.444 1 21
Osa02LNT0186700.2 osa-miR5515 Cleavage 5.0 13.877 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0186700.2 2 sk1(t) Morphological trait Seed nan nan
Osa02LNT0186700.2 2 nan Morphological trait Seed C747 C1445
Osa02LNT0186700.2 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0186700.2 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0186700.2 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0186700.2 2 ss2 Physiological trait Source activity RM240 RM213
Osa02LNT0186700.2 2 Hd7 Physiological trait Flowering R3393 R2511
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