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

>Osa09LNT0431700.2

ATCACAAGAACAATATCAAAATTAACAAATATAATAATGGCGTCCAACAAATACACAACCAAACTGAGATCAAGGACGGTCTGTCACCACAATCTCATTAACATTTTTGAGATTGGTGAACATATACATAAATACTGCGGTACTCATTTGTTTGCTGTAGGGGGACTGTACAATTTTCCGGCAAAATTGGAGATGAAAATCTCCAGATCATACACTCGGCCTGCCAGCAATGTGAAAGATGGATACCTGAATCTACCTCCTGCACTCAATTCAATCAACAAGAGGTTTTCACATAGAACAGGATTCAAGCCATCAAAGACAGTTGAGTTCTTGTTCCAATGAAGCAAAGTCGAACCCGTCCCAGTTGAGTTCTGCATTGAGGTCGAACTTCAGATCTGTGATAGGCAGCGGCAGGTGGCTGATGTCTGCAAGGCCAATGTAATCATCGCCCAGTGGCACATCTGCCATGCCGATAAAATCACTAACTGGGAACGCATCTGCAAGCCTAGTGAAATCATCAGGTGGAAATTCATCAATATGGCCCACACAGTTGCTCACAGGAATCTCATCTATCCTGCCAAGAACAGCGCCCATCGAAATCTCTTTGCCTTTAGGCGTGGACGGCAAGTTCAGCAAGTGCTCATCCTCAGTCTCATGGCTAATCTTCACTGACACTCTCTTCTGCACTTCTGGCTGTGCCTTAATCTTCTGAGCTTGTGGCTGTGCCTTAAACTTCTGCTCAACGGTCTCACGGTTAACCACCACTGACACTCTCTTGTGTTCTTGTGGCTTTGCCTGAATCTTCTGGTCACATGACTGAGATGAGGACACGCAGGATATAGTAACAGAGCTTGACAAATCTTCCTGCTCTGATACAGAAGATTGGATTTTCAAGGCCATCAACTCTTCATGGAACTGGTTTGATTGTGCAAGATATGCCGCAGCGGCCTCCTCCTCACTGTTAAATGTGCCAATCCATTTCCTTGATTTTCGCACAGGGTCACGTATTTCTGCAGCCCATTTGCCCCACGCCCGCCGGCGCACACCCCTGTATTTGCTCGTCGGTTCCTTCTCGGAATCCTTTACAGTCTTTGTGCCACATTGAACAAGGGTCTTAACAGGTTTGGATGCCTTGGAGTTTTCCATTGGAATTAGTATTTCCCTTGAAAATCTCCTTTCCTTCTTATTCTGGTCATCTTCATCAGAGGAGTCAGTGGCATCAGGATCAGAGCAGAAAACACGGACTTTCCGTGAAGAGGGCACCATCATCTCAACGTGCAACCAGAACAAGATCAGAGATTATTGGATTACAATTGGCCTTGATTGCAGTCAGGTAAGAGTTTAGATGAATCAGGACAAAAGTTTGTTGTCTGCTCTCTAAGCTTATCGCAGAAACTCAAAAAACCAGAAACAGAGCCTTTGTCCAACTTCTGTTTAAAACTGGAGCAAAAGAGAGCTCCTGTGTGTACAGAGATGTCCGAGAGAAATCTCAAATCTGGCCGACTTTGTGAACTAGAAGAATGTCAGGTTGCAAAAGTTCGGATTCTGTACTTGATCCACTCAAGCCAAACCAAATCTTAAGGCAATTTGGGGGCTATCTTCAATTGTCACCAGTCTAAATGAAGAAAGCCAAAGTATTTCACCCCAAATCCAAATCTGGAGATCGTGAAGGGATTTTGCTGTGTTCTTGCGCCCCTCGTATACCAATTTTGAAGGAGGAGGATGAGAAGGGAGCAGGAAGAAACCGTTGGCGGCGACTGGAGCTCAGAACCATGGAGAAACGGGGGTAGAGCAGGCGACATAAATCAACAGCGAGCACCAGCTGCGGCGGCGGAGACGACGAGCTCTACTCCTCCTCTTCCTCTAGGCAGCTGAGGCGACGACGCGATCGATGGCGCGAATGACGTGGCAGGAAGTGAGTGAGTGAGGAGGCGGTGGCGGTGAGATGGCGAGGCGGAGGAGGAAGAAGAGGAGGAGGAGGAGGGGTTTATTAATGGTGGTGGTGGGGGGAGGGGAGGTTTTTGGGGGAGAAATTGCGGGCGATTTGGAAGCGAAGCGAAGGAGAGAGAATGAAGAAGACGAGCGGAGGAGGGAGGCGAAACGTGTGATGTGT

Coding Potentia
Explanation CPC Score
noncoding -1.16286
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0431700.2 9 8201088 A G
Osa09LNT0431700.2 9 8201938 A G
Osa09LNT0431700.2 9 8200182 C T
Osa09LNT0431700.2 9 8200391 C T
Osa09LNT0431700.2 9 8200538 A G
Osa09LNT0431700.2 9 8200547 T C
Osa09LNT0431700.2 9 8201275 G A
Osa09LNT0431700.2 9 8201594 G A
Osa09LNT0431700.2 9 8201784 T C
Osa09LNT0431700.2 9 8202401 G T
Osa09LNT0431700.2 9 8202730 G A
Osa09LNT0431700.2 9 8202745 C T
Osa09LNT0431700.2 9 8202797 T 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
Osa09LNT0431700.2 osa-miR5526 Translation 4.5 19.215 1 21
Osa09LNT0431700.2 osa-miR5536 Cleavage 4.0 21.047 1 22
Osa09LNT0431700.2 osa-miR6254 Translation 5.0 22.768 1 21
Osa09LNT0431700.2 osa-miR2097-3p Cleavage 3.5 10.28 1 22
Osa09LNT0431700.2 osa-miR396f-3p Cleavage 5.0 18.689 1 24
Osa09LNT0431700.2 osa-miR2118f Cleavage 4.5 21.429 1 22
Osa09LNT0431700.2 osa-miR2118h Cleavage 3.5 21.429 1 22
Osa09LNT0431700.2 osa-miR2118h Translation 5.0 16.876 1 22
Osa09LNT0431700.2 osa-miR2118j Cleavage 4.5 21.429 1 22
Osa09LNT0431700.2 osa-miR2118k Cleavage 3.5 21.429 1 22
Osa09LNT0431700.2 osa-miR2118k Translation 5.0 16.876 1 22
Osa09LNT0431700.2 osa-miR2118m Cleavage 4.5 21.429 1 22
Osa09LNT0431700.2 osa-miR2918 Translation 4.0 17.135 1 21
Osa09LNT0431700.2 osa-miR2922 Translation 4.0 19.92 1 20
Osa09LNT0431700.2 osa-miR2929 Cleavage 4.0 18.903 1 21
Osa09LNT0431700.2 osa-miR5501 Cleavage 5.0 21.383 1 21
Osa09LNT0431700.2 osa-miR156b-3p Translation 3.5 16.623 1 21
Osa09LNT0431700.2 osa-miR2096-3p Translation 5.0 13.285 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0431700.2 9 apd9 Others Others CDO590 G103
Osa09LNT0431700.2 9 nan Morphological trait Root C711 G103
Osa09LNT0431700.2 9 nan Resistance or Tolerance Drought tolerance R1164 R79
Osa09LNT0431700.2 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0431700.2 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0431700.2 9 qAC9 Physiological trait Eating quality RM4413 RM5122
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