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

>Osa11LNT0096000.2

GTCGAAAGAATGCAGGCAAACACGAAAATTATCGTCAGAGGTAAGCACACACAGCGCTCTGGATTACATACGCAGAGACATTGCATGACATTTCTATGTTCATTCACCCCAGTGCTAACCGAACTAAACAAGCTGAAATAGGAGACATTGTATGGCATTTCCATGTTCATTCACCCCAGTGCTAACCGAACTAAACAAGCTGAAATAGGAAGCCTAGGTTTTCTTTGGTAGATAGTATATCAAGCTTCTAGATAGTATGTACATACGAAGTGCACTTATGCTGGATCATATTTACAGTAGAATAGTGACCATGCTGCTTTTCTTTCTTGATTACAGCCTTGGACCTCTGAGTGTAACCTGAAGTTGCATGGCTGCTGAATAAAGCAAATAACATAACCATTTAACTATAGTCAATCTAAAATAGGAGTGCTCAACCAAGTACGTTCAAAGAGTAAAGTGTAATAACACTATATTTTTCTTTCTTTCCTCCATTAGGAACAACAGCTTCTTCCTACTGAACACAAGAGCTAATGTGCTATAAATATTGCTCACAATTTCTATGTGGCTGCTGTAGTGCCAAATAAATAACTGAGATAATAGGCACTATTAACATGACAACTAAATTGTAATAGAAATTGATTGGGGTGTGAATTTAATACTAATATGTACTGGAACTGACCACAATTAATAGATTTTGAGTGTCAAACTATAGTTAAAAGTAATACAAACTGAAACTATAACTATAGTTCGAAATACACATACTATGGAAAAAACGTGATATAATACAAATATGTACTTGTACCTGATACATAAACAGAGTTAGGAAACAATTGCATCAATGCAAAATAAAATAAATCAGGAAATGTAAGTAGGAACATTACTTTGGTATCGCAGTCACTGAGGAGCAACCACCAGAATAGCTAGATCAATATGGACTTGCTGTCCTATGATAGTGAGAGCATGATAAAAACTAACACGGCTGAGATGGGCTTTATTTTGCAACAGCTGAGCTGGCAGACTACAAAGCAAATTTTGAAAAAAAAAAAGAGAAAAAAAAGTGACATGTACAAGTCAAAAGCATTGTGTTGTTCAATGAATTTTGTTGCAACATTACCTCAGTTTCCCATGGATCGATATTCTTCAGCTCAGCTACTGTTTTCTGTTCCACTCAAGCCAGACACCGTGATGCGCCAAAAGATTCAGCCATGTGGTATGTCAATTACTGGCGTAGTCCTCCACGGTGATGTTCTTCTGGTAGTGGTAGACTGGTAGCACACCTCGCAGCCTCCGACCATCTCGTTCAGCGGCTCTTAGATTGACCCCAGCATGGCTACGTGATATACGGTGACCCACCATTGCCCGTGAGAACACTGGTTATCTTCTTAGCCTACGATAGGCCTAGATTCCGAGCCATGGCTCACAGGAAGTCAGGAACTTGGAGGTCACTTGCCTCCGGGTGGTGTGCCTCCTAGATCGGCCGCCCGCCCCATCGACCTTGGCTCCAGATTCGCCACCATCCTCAGATCCTCTTCTTTCCACCACGCCATTGGCTACTTGCATCTAATGCCGCAAGATGAGTCGAAGAGGGTGGCTATTCAACCTTGACGAAGTCAGCATGCCAATTTTTTAGGTCGAGACCAACACCTCAGCAGCGTCATGTTGCTCCTTTCCAGCTCCTCCTCACCACACTGGCTGCTGGCCTGCATCAGCATGTCCTCCGCCGCCCTAGAGTGAGGGCTGCCAACGGCAGCCATCATCTTCTTCACCAATACCATCACCTTCTCGAATGGATCTGCTCCTCCTTCCCCGCGATCGAGGGAGACCGGGACAGCAATACACACAGATAAGATCATATATACACCTTCTTTGAGCCACCAAACAGCAAGCATGTGATAGCTTTCTTGACATCAGAATGACCATAAATTCAAGGGCCAATCATTGAGCAAATCTTGGCATACGCATTTGACCTCTGTACAAATTCTTAGAATTCCATTTCCTCATCAAGTGTAAAATTTGAGGGACCATTTGAGTTGGCATCTAGGGAGGTACCGTTTGTCTATATGGAATAATAAGATTTATTAGTACAAGGACCATTTGAGTTGGCATGGAGGAACATGGACTCATGGAGTACAAGGACTTCACCTTGCAATGAGGCATTAAGGACCAATGATGTTTTCTCAACAATTGAATATGTATATTCTGTTTTATCCATCCAACATATAAAGCTGCCATATTGAGTTTATATTGCTTACAAGTTATACCCAAACTCCGTACAAGTTACTAAACAGAATATGTACAGGAGGCGCGTTGTTCTAATCTCTACAATAATAAGTGACTCAAACTGCACATTGATTGATTAAAAAGAATTGAAAGCTTTCAGCAAGCAAGCAGATCCTATAGATAATTGTTACCTTCTGAAAAACTGGATATCCAGCTTTAAATCTTATGCAAAGGAAGACCATTATTGGCTAGAATGGCCCAGCTCTTGTCACAAGAATGGGTTGCATAGGAATGTTAATATCTCAAAATCTTAGTGCAAAGCTTCTCAGCTTGCTTGTAATCTTTTTAGCTTCAACTTGCATGCAACATTGTTCAAGTCACGAGGCGGAGGCGGAGGCGGCGACGGGCACGCGGCGGTTGTGGCGGCCGTGCTCCGAGATGGGGTCGGCACGAGGCGGAGGTGGCGGCGCCGGAAGAAGGAGAGGGAGAAGGTGAGTCGGGAAGGAGGAGAGGATGACGACGCGAGAGGGAGGCAGAGGTGGCGGCGCGAGACGGCGGCGGCGGCGCGAGGCGGAAGAGGGAGAGGAAGAGGGGGAGGCGGTGGCGGCGCGAGACGGCGGCGGCGGCGCGAGGCGGCAGAGGGAGAGGGAGAGGGAGAGGGGGAGGCGGAGGCGGCGGCGCGAGGAAATGGGGACGGCGCAAGGGGGAGGCGGAGGTGGCGGCGCGAGGGGTGGCGGCGGCGGCGGCGCCGGAGAGGGAGAGGGAGAGGGTGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.772796
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0096000.2 11 11871761 A T
Osa11LNT0096000.2 11 11872322 T A
Osa11LNT0096000.2 11 11872676 G A
Osa11LNT0096000.2 11 11874004 G A
Osa11LNT0096000.2 11 11874150 T C
Osa11LNT0096000.2 11 11874185 A C
Osa11LNT0096000.2 11 11874904 T C
Osa11LNT0096000.2 11 11876069 A G
Osa11LNT0096000.2 11 11876245 T C
Osa11LNT0096000.2 11 11876276 A C
Osa11LNT0096000.2 11 11878139 C A
Osa11LNT0096000.2 11 11878674 C A
Osa11LNT0096000.2 11 11871531 G A
Osa11LNT0096000.2 11 11877549 A G
Osa11LNT0096000.2 11 11877794 T C
Osa11LNT0096000.2 11 11877818 A G
Osa11LNT0096000.2 11 11873488 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa11LNT0096000.2 DTM_#DNAt_MULE_japo_Os0205 Chr11 - 11877117 11878135 1018
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa11LNT0096000.2 osa-miR5828 Cleavage 5.0 19.916 1 21
Osa11LNT0096000.2 osa-miR5837.1 Cleavage 4.5 14.27 1 21
Osa11LNT0096000.2 osa-miR6250 Translation 4.5 15.361 1 22
Osa11LNT0096000.2 osa-miR169n Cleavage 4.5 19.64 1 21
Osa11LNT0096000.2 osa-miR169o Cleavage 4.5 19.64 1 21
Osa11LNT0096000.2 osa-miR820a Cleavage 5.0 20.037 1 21
Osa11LNT0096000.2 osa-miR820b Cleavage 5.0 20.037 1 21
Osa11LNT0096000.2 osa-miR820c Cleavage 5.0 20.037 1 21
Osa11LNT0096000.2 osa-miR169r-5p Cleavage 4.0 19.64 1 21
Osa11LNT0096000.2 osa-miR1859 Translation 4.0 18.511 1 22
Osa11LNT0096000.2 osa-miR1860-3p Cleavage 4.0 15.165 1 22
Osa11LNT0096000.2 osa-miR1861c Translation 4.5 23.572 1 22
Osa11LNT0096000.2 osa-miR1861e Cleavage 3.5 23.572 1 22
Osa11LNT0096000.2 osa-miR1861g Cleavage 3.0 23.572 1 22
Osa11LNT0096000.2 osa-miR1861k Cleavage 3.5 23.572 1 22
Osa11LNT0096000.2 osa-miR1861m Cleavage 3.5 23.572 1 22
Osa11LNT0096000.2 osa-miR1861n Cleavage 3.0 23.572 1 22
Osa11LNT0096000.2 osa-miR2099-3p Cleavage 5.0 13.507 1 20
Osa11LNT0096000.2 osa-miR3979-5p Cleavage 4.0 19.091 1 20
Osa11LNT0096000.2 osa-miR5837.1 Cleavage 5.0 13.48 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0096000.2 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0096000.2 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0096000.2 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
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