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

>Osa02LNT0189700.1

TTCGGGCAGGGAGGCTGGTCATTTTTCTTTCATTAATTTTCCTCAGTCACTGATGCACACAGCACACCAGGCGTGAACTGATGAGTACATTGGTATCTTGGTGATGAATCTGAATATTTCACATTGTACCTTTCTACTACTATACAATATATAGGAAGAATGAATGAGAAAATAACTATTTTTGATCAACCAACCCCTCCAAGGGAGACAGAAAACAGAAAGAACCACGTAGAACAAGGTACGCAAATGGAGAGGACTATCACGACAATAATGTAACAACAAAATGGCACTGACCGAGCAGTACTATAGTCCGGCAGGAAAATTGCTCACTTGGCCTTGTTCCAGTCTGTCCTCACCATTCACTTTGTATGACATCCGGATACGCATTGCAAGTGGTTTCTGCCCATGTTGGTTATTGGTGACACTGAACCCTTGAGTAACTGAACCATTGCCACTAGCTGGAACAATGTTGCCACTAGCTGGATCCAGTCGCAATTGGATAAACTTTGGAACAGCTGCCTGAAAAACAAAATCCGTATAAGAACTGGATGTCAAATTTGTAAAAGTAGCATGGACGGTAGTCTCGTGTGGTTTCTCAGGCTGCTTTTTGAAATTGAAGTTGATCTTCAAGGTTGCACTCTGGAAAGCTGTTATTGATGAGTGATTAACAGGTCCAGAAACAGATGTATTTGATGGCAGACCATCAAGCAAATCCATATCTTGAGGTACTGCAGGAGCGGATTTGGTCCCAGAAACAGATGTACTTGATGACAAACTACTGAGAACATCCGTAGCTTCAGGTACAATCGCACCGACTTGGGCAGGAGTAGAGTCTGCTGCTGGCGGGCCATTCTGTGATGGAGATGATCCGATAGATAGAAGATCAATAAGAATATCTGTGCTTGCGGATGAAGGTGCAGCTGCAGGTGATGAACTTATCCCACCAATACCCAGAAGGTCTTGTAGGAAGTCGTTAGGTGCTGTAGTGGTAGAAGCAGTGGTAATGGCTGGCACATCATCAGAACTTAAGTCAAGCAAATCAACTAAAGGACTGGTGGCAGGTTTTGCTACACCATTTGGAAGCTTAAGGCCTCCGGGAGTGACTGCTGGGGTAGGCTTATCAGCTGCAAGAGTTGCTTGTGTAGCACTAGCCCTCCTCAGCAAATAACTAGCTTCATCCAATGCAGGCATACGCTCAAGCAAAGATGGCCTGATAGACTGATGTCTTTGTATGATGGAACTGAATTCAATTGATCTTTGCTGTAGTTCAAGCACAATATTCTTTTTATTCTGGGAAACTATTTGCTTTATCCTCTCTGATGTCGATGGAAATCGTGACGAGAGCTTCAAAAGAGCCACAAGACACATAGCTCGAGTTGTCACATCAGCAGAGTAACGGTTAAGAGCGAGTTGTACAGCATCCACAGCATCAGATTCTGTTACCGTAATAGGTTCCTCCCCTTGCAGCATGCCAACATTGTTAACTAGCATTTCACCATATTCACCGATGCACCAAACAGCCACTCTTACTAAACTTCCCTGATCGACAAATGCTTGTAGAGCCATGTATAATAACCTCACTGAATATCCTTGAAGTTCTGATGCATTGCTTATTACAACAACGAGGGCATGCCACACATCATCCTTCACATGATTTCCAGCCAAGGATAAAACCTTGAACATCTGATCAAGGTACCATAACTTCTCTTGAGAAAACTTTTCAACTATTGAGCATATCTTGGCAGTGAGATCTTCTTTGAAATCCGGATCAGCTGAATCTAAGTAGTCGACAAGCTCTTTAGTCAAAGGCTTTACATTTGTATCGTTGACTAACAAAAAAACAAGTTCAAGGGCCCTCTTGCGAATAGAAGCATCTGCATCCTTTACACACTCCAATATTGTCGTCCTGTGTCTCTGTACTGCCTGTGTATCTACAGTAATGGCCCTCATAAGCATGTTCAGAGCAACGTATCTTATATTATTATCACGATTCGACAAGAATCTACCCAAAATATTGATCGCAAGCACACGTAAACCACTAGTAGCTTCAATACCCATTATAGTCTGAACACATTCATACAGAATGGCATTAGCAGCATTCTTATTTGACTCATTTTTCGTTGCAACCTGAGCAAGAATATCATTCATATATTCACTGCAGTCTGCATCTCCTTGACCCAAAATGCGCATCAGTTTAAGAACTCGAATATGCAAGAAAGGGTCTGATATGCCAGCAACGTCATACTCAGGAGCATAAGAACTATTGGAGACATCTCTCAGTATGCGCACCAATCCTTCAACGCAGTTCTTTCTCAGGTACTCTAGTGCATCTTTGCTGGCTTTACACAGTTCCGTGCATAGTTGAACTGCAGATATCAGAATCCCATGATGTTTCTCCTTCAATAACGATGAAGCAAGACCCATGAAGTTTTCTGCCAAGTCTGGGACTTTTCTCACAATCCTTATAGCACACAAAGCAGCCTTTTTCTTTGTGTTAACGTCCCTGCTACGCATCAGCCTCTCCACTTCAGGCGACAGATCCCGTGCCATTTCAGCGGAGCAGATATTCCCAAGCGCACACAATGCAAGCCCCACGATGAACTGGTTCGAGTGATTGAGATCTTGTTTGAGGGAGTTGGTGACGAGCATGAGCACCTCCTGCCGCTCGTCGAGGAGCAGCATGAGGCCGAGGTAGCCGATCCGCTTCTCCGGGTATCCCGCGGCGGCGATGAGCTTGAGGCACTCCATCTGGCCGAAGTGGGTGGGGTATCCGAGCATATGGATGAACATGAGCTTGGCCATGTTCCGGTGCCGGATCTCCTGCTGGTTCTCGCCGATGGCCTCTCGTATCTCCGCGCACTCCCGCCGCACCACCGCCCGCTCCTCCGCCGCCGTCTTGCACGCGCGTATCGCCCGTATCATGTCCCGGAGGCGCGTGCCGGAGGAGAAGGGGCCCATGGCGATGTCGGAGGCGAAGTCCTCGACGATCTTCTCGACGGTGTCCATTGCCGGGGGGCGGGGATCTCGTGGAGGGGGGAGGAGGAGAGCTCGCGTGGATCTGGCTCCCGCGCGAGGTGGTTGGAGCGGGAAGGCGAGGCGAGGCTGGCAGAGGAGGAGGACGAAGGCTCGCCTTGGATGGATCTGAACTTCTGAAATCTGAACT

Coding Potentia
Explanation CPC Score
noncoding -1.01508
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0189700.1 2 34337286 T C
Osa02LNT0189700.1 2 34336842 T C
Osa02LNT0189700.1 2 34337081 A G
Osa02LNT0189700.1 2 34338376 C T
Osa02LNT0189700.1 2 34339354 C T
Osa02LNT0189700.1 2 34339356 C A
Osa02LNT0189700.1 2 34339439 G A
Osa02LNT0189700.1 2 34339892 C G
Osa02LNT0189700.1 2 34339899 T C
Osa02LNT0189700.1 2 34339982 A G
Osa02LNT0189700.1 2 34340131 G A
Osa02LNT0189700.1 2 34340969 A C
Osa02LNT0189700.1 2 34341291 G T
Osa02LNT0189700.1 2 34341607 T C
Osa02LNT0189700.1 2 34342634 A G
Osa02LNT0189700.1 2 34342712 T A
Osa02LNT0189700.1 2 34343197 C T
Osa02LNT0189700.1 2 34343301 T G
Osa02LNT0189700.1 2 34339371 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
Osa02LNT0189700.1 osa-miR5530 Translation 4.0 22.346 1 21
Osa02LNT0189700.1 osa-miR5543 Cleavage 3.0 11.282 1 21
Osa02LNT0189700.1 osa-miR5543 Translation 5.0 11.02 1 21
Osa02LNT0189700.1 osa-miR5802 Translation 5.0 19.541 1 24
Osa02LNT0189700.1 osa-miR426 Cleavage 4.5 18.759 1 21
Osa02LNT0189700.1 osa-miR530-5p Translation 5.0 17.671 1 20
Osa02LNT0189700.1 osa-miR530-3p Cleavage 4.0 18.198 1 21
Osa02LNT0189700.1 osa-miR530-3p Cleavage 4.5 16.493 1 21
Osa02LNT0189700.1 osa-miR1441 Cleavage 4.5 15.538 1 21
Osa02LNT0189700.1 osa-miR1441 Cleavage 4.0 12.528 1 21
Osa02LNT0189700.1 osa-miR1855 Cleavage 4.5 21.311 1 21
Osa02LNT0189700.1 osa-miR3979-5p Cleavage 4.0 10.548 1 20
Osa02LNT0189700.1 osa-miR5073 Translation 4.0 6.225 1 23
Osa02LNT0189700.1 osa-miR5150-5p Translation 4.5 20.034 1 24
Osa02LNT0189700.1 osa-miR5511 Translation 4.0 24.821 1 21
Osa02LNT0189700.1 osa-miR5519 Translation 4.5 12.957 1 21
Osa02LNT0189700.1 osa-miR530-5p Translation 4.5 20.997 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0189700.1 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0189700.1 2 ss2 Physiological trait Source activity RM240 RM213
Osa02LNT0189700.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0189700.1 2 nan Morphological trait Shoot/Seedling RM250 RG256
Osa02LNT0189700.1 2 gn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0189700.1 2 gw2.1 Morphological trait Seed RM250 RM208
Osa02LNT0189700.1 2 pl2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0189700.1 2 sn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0189700.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0189700.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0189700.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
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