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

>Osa11LNT0092100.2

AGACACACAAGTCGTTCACGATAAAATGGGTAAAGCTCCACGGCCAAGATCACATACAATTTTCAAGAAAGATGAAAAGAACGGTGCTTTAGGTAGCATAACATGATTACAGAAAGGTTCGCTTCCTCGAAAAAAATTACAGAAAGGTTCAGCTATGACAATCCGTTCCTTTGCTTTAATCTGATCTAAGTGTAGAAACAGAACAGAACATTAGAAAATTGCATGTTAATTGAACTATAACAAAAAAAATGCGTTAGAAATCAACTTAGTCGTTGGTCATCTCTGGAGAGGCAAAAAAAGAACCTTCTTCCATGCACTCATTATGTTCTACCATGGCAGGTATAAAGCATCAACCATGATATGCAAGGCAAAACTATGGCAAGGCAAAACCATCTTCCATGCATTCTGTCCTAGTCTCCTGCATGAGCTGCTGAAGAAGGGAAGGGTTGCTTGTGACAATGGCATCAACATGTTCATACAACATCCTCTTCATGGAGTCGGCATCATCAACAGTCCACGCATAAACCTTTTTGTCATTTCTGTGCATAACCTTCATGAGCTTCTCGTGGATCAGGCGATGATATACACCAGCAACTTTGGACCCTGTTATCCTTACTAACTCAGTAGTTCTACCAGTGGACTTATCAACCATAACAATATAGCCAACCGTTATATCTTTAGACAATTTAATTACATCCCTTCCCACATTGTCACTTTTTGCCCAGACAAGACAATTTTTACATTGTGTTCTGCCTATAGTAGACAGCACATCTTCAGCTAAATCTTTCTCAAATGAAGGAGGACCAACTTTGACATCCAGAATAACCTGCCTTACGGATTGTGATATCAACGCTAGAACATCTTGTGCTTTAGGGACTTCCTGGTTCTGGACTTTTTTTGACAGTTGAAACCTTGTGCTTAGAGCTTTAATCTACAAAAAACTCATCCGAGCTCCAGTAGCCAACTTTTGCTGTAGAATTACCAGACATTCTTTGCAGATCCCTATCGTGAAGCACAAAGAGCGCGCCATCGGAGGACCTCGAGACGTCCACCTCCACGCAGTCGACGCGCGCGTCCAGAGCCAGGCGGAAGGCGTCCATCGAGTTGGGGAACGCGTTGGTGGAGTCGCCGCCGTGCGCGCACACCATCGGCGGGCTCGCGATCCACCCGCACCTCCTCTCCCGCATGCGGTGGAAGCGGCGGAGGCGGAAGTGGAAGAAGGCCGGGGGGATGAGGGAGAGGGCGGCGAGGAGGAGGAGCAGGCGGAGGAGGCGGTTGGTGGGGAGGATGCGGCGGAGGAGAGCGGAGGAGGAGGAGGAGGAGGACGGCGGGGAGGCCCTCTTCGTCGCCGGCGGCGGGAAGAGCGGCAGCGGCGGCGGCTGCTGCTGGCGGCGCCTCCCGATCCCGAGAAGCCTTCTCATTGCTACTCTCTCGTCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.635628
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0092100.2 11 7251546 T G
Osa11LNT0092100.2 11 7251681 A C
Osa11LNT0092100.2 11 7251462 C T
Osa11LNT0092100.2 11 7252099 G A
Osa11LNT0092100.2 11 7252227 T C
Osa11LNT0092100.2 11 7253422 C G
Osa11LNT0092100.2 11 7253838 A C
Osa11LNT0092100.2 11 7254102 T G
Osa11LNT0092100.2 11 7254260 A G
Osa11LNT0092100.2 11 7254432 G C
Osa11LNT0092100.2 11 7254402 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa11LNT0092100.2 DTM_#DNAt_MULE_japo_Os0098 Chr11 - 7251727 7252095 368
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa11LNT0092100.2 osa-miR5544 Translation 3.0 11.22 1 22
Osa11LNT0092100.2 osa-miR5791 Cleavage 4.0 16.993 1 21
Osa11LNT0092100.2 osa-miR172b Cleavage 4.5 11.923 1 21
Osa11LNT0092100.2 osa-miR2931 Cleavage 5.0 11.442 1 20
Osa11LNT0092100.2 osa-miR2931 Translation 4.5 15.494 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0092100.2 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0092100.2 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0092100.2 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0092100.2 11 fer11 Resistance or Tolerance Cold tolerance RM3701 RM552
Osa11LNT0092100.2 11 Tid1 Morphological trait Dwarf nan nan
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