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

>Osa04LNT0251700.2

TAAAATGAGATATGATTAATATTAAAGAAAAGAATGATATCACGAGTTATTACATTATTAATTACATAGCCACATGGCTAAAAATAACATCCCAAATTTTCCATCTTTCGAAACCATGCAAAAGGGCAAATCCATATTTCTTTCTCACCTATGGTATAGAGACACTGGACAGCTTCGACAATCAACCCAACACTTTTTGGTTGGTACCCCCGTGCCAAAAAGGTCATCATCTCTCTGGTGCTTATGTCATGTGATTTTATTGTGCCCAAGGATCGACATCTAACTTGCTGCATGCTGAAGGATAGAAGCACTGAAGCAGCTCGTCGACCCATGACAGGCTCGCTGTGCTGGACATTCTGTAAATCTCATCTACTGGAGGAAGCTCTCTCTTATTTATACATCAATGGGTACATGTGCTTCTCAATTTTGTGCAAATGTACTTAAAAAATGGTCATGGTCAGGTCCGCGACTCCTTGCCTTGCTATAACAAATTAAATCGACCAATAAGAATACCTGCTGTTGACGTGCTCTTATTGCAGAACTCTTGGAAATCAATGGATTCAGTAGGATAATTTTATCCGCCGATGCAACTGGAGAGAAGGTGACACAGCTTCAGCTCCCCGTCCACCTTGTCCCTTGTATGTAGGAGACAACTAAACGAATCAGTATAGATATCACACATATATAGAAGTGAAAATCACAAAGCAGTTTCCAAAATAGTATATCCACAGTGCTCATTGATAACATATAGAACACAACATAGGATGTGTGGCAATGTGCCATGTTTCGGAAGACCCATAGAATAATTAACCATGATATAGAACATAATGAATCTAAACCCCGGAAACTGATCACAGATGCATGACAATATTAAAAATATAAAGGACCAAAATAAATCTGATGGTCTCCACTTCACCTCTTCAATTCACAACTCACAACTACTTATCATTCATGCCCGTACCTTAATTTCTCAGTAGTATAAACTATTCAAGTACAGTTCACTAATTAGAACTCAAAACAAATGAATCCGTCATGCAATATTAACAGTTTGGAATATTGTGAGGGAAAAAAGTATGAGCCAAGAATTGCTATTGTTGCAAACCTCAGACGTTTAGCAAAAAGCAAACATAACCATTGCACCCATCCTAATCATTCTCTGTTTCTTCCACTGAAACAGACAGCCTTTATACTGGCATACCTTTTGTGTCATAATGGAAATTCAGAAAAGCAAAATCCAATTATAGAAGTTATATCATGTAGATAGTGCAATTAAGCATTTATTTCATTTATAATGGCCATGATCAAGGGATAATTCATCAGCTGAACGAAATTCTCCATTTCTGAAATAACCACGGGACAAGGTTTCCAATACTCACCTTGGAGAGAGCAGAGAGCAGGATGAGACTGATGGAGAGTGGTGGTGATGGGGAAGATCTAATTTTGATTTGGAATAAATTTAGCACAGTATCGACAATTAGAGTTCGGTTCTTCAGTAGTTTAGCTCGAAGGTCTGAGAATCACCGTACTTCAAGAATTAGTTGCAGATCAAACACTCTCCTATCGGTGGCGGATGGGATTTGGTTGGCGGCGCCGGCGCTTGATGCGTAGGAGGTGACAGCACGTTGGTGGAGGAGGCAGCGGCATGACCGGCTTGGCGACGACGAGCCCGGCGACTCCGGCCAATGGTGAACTGGTGACGCAGAGGCGGGCGGCCAGGCGGAGATCGGTGGCAGCGAAGTTGTGGGTGTTCCGGCGGCGCCGATCGGTGGCGGATCGGTGCGATGGGCGGGAGGGTGGCGCGGATGAGATCGTCGTTGGTGGGCGGAGGCGCAGCGGGCGGCGCCCCGGGGGGGAGGGGGGTGCTGCCGACAGAGGGCGGGGAAACGGGATCGCGGGCTCGCGGCGGTTCCTCGGATGGGAGAGGAGGGGGCGTAGAGGCGCGATCTGTGGAGGCTGATCCGGGAGTGGCGTGGGGGAGAGACGCGATCAGGATGAGGCAGT

Coding Potentia
Explanation CPC Score
noncoding -1.22695
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0251700.2 osa-miR5079b Cleavage 3.5 11.45 1 22
Osa04LNT0251700.2 osa-miR167c-3p Cleavage 3.5 23.266 1 23
Osa04LNT0251700.2 osa-miR167h-3p Cleavage 5.0 24.578 1 21
Osa04LNT0251700.2 osa-miR414 Cleavage 4.0 22.381 1 21
Osa04LNT0251700.2 osa-miR444b.2 Cleavage 5.0 13.708 1 21
Osa04LNT0251700.2 osa-miR444c.2 Cleavage 5.0 13.708 1 21
Osa04LNT0251700.2 osa-miR444f Cleavage 5.0 13.708 1 21
Osa04LNT0251700.2 osa-miR1850.1 Cleavage 4.5 11.638 1 21
Osa04LNT0251700.2 osa-miR2099-5p Cleavage 5.0 17.686 1 22
Osa04LNT0251700.2 osa-miR5079a Cleavage 3.5 11.45 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0251700.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0251700.2 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0251700.2 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0251700.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0251700.2 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0251700.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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