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

>Osa11LNT0108500.2

TCTTGATGTGTATAGTTTTTCTTTTCTTTTGTCAAGATTACATAGTCAGAGAGCAATCAAAAGCATCAGTTAAACCCATTACAGTTATACTTAACATGAACCCCCCACACCCTTTTGCCCTTCCATTCCAAACCAAAAACAACGAAGGAAGGCCCTGAATTAGTTACAGAAGTTAAGAACTACTCCGGTAACAAGCAAACCATCAAGCACCCACAAAACCAAAAACATATTTCATAAACATTTCATCACCACTAAACAGGGTGTTAAAAACATAACTGTTCAATCAGTATTTCTGTAATATTATGTCAGGCTAGACATCCTTCTCCTGTGTTGATGCAAGGGAGCTCTCTGAGCTGGTCTAGAAATGAAGCTCTCCCTCCTTCGAGGCGCTGACGCCGCCGTCGAATCGATGCTGTTGTTGCTCATGTTGATCTGATCAGACTTGAGTGGCAAACATTTCATCTTGGGCATGCTAGATGAGAATGCCACTGACCTAGCCTTGGCTGCATTCTTGCAGCTTGAGTAGCTGAAGGAATGGCTCCCACTGAGCTCAGCTGCAGGATACCTGTTCACTGATTTTGTCAGCCTTGTTTTAGTAGCAGAGTGGCTTGCTGAACTATGTCTTTGCCTGCTGCAAACTGTTGGGGACATGAAGTGAGGAACTGATCCATGAGATGCTCTGCTCTTTGTTTTCTCAGTGGCTTGAGGGCTCTCTGCAGAATCAATGTGTCCTACTACCACTAGAGTGCTTCTTGGTGACCCCTTCTCATCACTGAGAGCCTGACAGGCAGATGAAGAGAGCTTCTTCCTCTCTTCAAGTGAGGTTTCAGCTCTCTTTATCTGTTCATTGAGATCCTTGAGCTCTTGCTCGGCGTCGCATATTTCCTTGTCAAGCTCTGCGATCCGCTTCTGCTTCAGCTTCTTTATGTCTTCTGAAAGTTCTTTGCTGGACTCGATTGACCGGGCTCTTTTCGCAAAGCTCAGTGAACAGACTGTTTCACCAATATCATCATCAGAAGGGCTGATATGTACTACCATCAGAACCTTTGACCCATCACCAAGTGAATCACTGAGAATCTGGGTAAGCTTACTGTTTCTGTAAGGAACATGGCTTCTCTTTCGCCTAAGTGCCGCGATGACATCACCAAGGGCTGACAGAGAGAGGTTTATGGCCTTACCCTCATCCATTGTCAACCCAGATGCACCGGTCTTCAGCAGCCGCTCGCTTCCACCAAGATCGACAAGCCATAGCTTGCTGCATTCTTCAGTGGTACCTCCACTACTTCTCTTTATGGTAATTCTTGTCAAGCAATGCGATCGACTCGAAACATCGTTAACATTTGTCCAAGACGTCGACCGTGCACGCCGTCCTCTGCAGTACCACTGGTTGGCCTTCTTGAGGTCTTGAATTGCAACATCTGTTAGACCCTCAACTTCTACAGCTCCACTTTTAGTTGCTAGTATGCTGATGATTGACGATGTGTTGCACTCTGTGGACCTGAAGAGAGGCTGCCTTGGTGTCAATAAGTCCCTGACAGTCCCCATGTAGACCTCAAGCATGCTTATGGAGAAGGAATATGTGGATGAACTGTCTTGAGAAGCATGAGAAAACAGTTCTTGAATCGCTCGGGGGACGATACCGAGCTTACCATTATTTCCTTCCATTGTATAGGTCTTTCCTGTCCCAGTTTGACCATAAGCAAGAATACAGACATTGTGCCCATCAAGTGCAGATCTGAGAATTGGCTTCACTTCTTGGAAAACATCCTCTTGCGTTGACTCCTGATCAAACACCCTGTCAACACTGAATTCTTTCTTGATCCCCACTGCTCGAACCACGATCTTCTCGTTTTCGACGGTAACCGGCGATTTGGTCATGAAGTTGTTGGCCGAAATCGATGGCCGGACCCGGCAGAAAACCCTGATACTTCCTTTCAGGTCTATGAGCTTGTCCAGTGCCTCCTGTCTTCTGTGGTCAAGATGTCTCTGCCTTGATCTTAGAGCTGAAATCTCCTCTTGGAGAGCTGAAATGTCCTTGTCATGGTTGAGCATGATTCCACCATTGTTGAGCTCCAAGCTCAACTTTTCCAGTGGAACAATAACATGTCCCTCCATTGCTGCCTCCTCCACAAAGAAAAGAAGAGATGTTCTTCTTCAGAGGAGGAGATGATTCAAGCAGAAGAAGCCTCTGAACATGCCTGTGCAGAGCTTCATCTGCTTTTTTCCTCACCACTTGAACTTATGATTGTTGAACTCCTCTTTGACCTTAATCTCTTCTTCCAAAACAACTCCTTGAGGAGAACCTGCTGCTTCCTGAGCTTGTCCTTCTCCCTTGAGAAACAGTGTACCCTTTGATCCAAATGCCAGAGCAAGAACAGTAAGGGGAGAAGGAGTAAGCTACAAGAGAATCTCCACAATCCAAATCCAAATGATTGCAGCTCAAGACTTTTCTTTTTTGGCTACTGATCTTTCTTGGATCTTGATGCCGAAAGTTGAGGTAGCAACCAGCAATTACTAGAGTCCAAAAGCCCAGAGCCTGAATATATGCAGCACCTTGGATGTGAAAAAGAAGAGCAAACTCTAAAGCCCCAAGCTTTATTCAACTCAAGGTTGGCACAACACAACACAAGCAAAGCTATACACCAGCACACAAGCACTAAAGCACTACACAACACACTGGAAAGCCTCAAAAAGTGATCTTTCCAAGATCATCACACACTGGAAAACAATTCAGAGGAGCAAGGTGTCCATCAATGCACAGCTCAAGCTCCAAGAAAGAGAAAGAGATAGAGAGAGAGAGAGAGAGAGAAAGAGTGAGGCAGAGCATGTGGCACTATGGCAGTAGAATACTACTAGCAATTGCACAATTTGCATCTGCATG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.506763
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0108500.2 11 25778012 T A
Osa11LNT0108500.2 11 25777721 A C
Osa11LNT0108500.2 11 25776237 T C
Osa11LNT0108500.2 11 25776995 A G
Osa11LNT0108500.2 11 25776185 A C
Osa11LNT0108500.2 11 25776540 T G
Osa11LNT0108500.2 11 25776559 T G
Osa11LNT0108500.2 11 25776628 A G
Osa11LNT0108500.2 11 25776747 T C
Osa11LNT0108500.2 11 25776862 C T
Osa11LNT0108500.2 11 25777015 C T
Osa11LNT0108500.2 11 25777753 T A
Osa11LNT0108500.2 11 25778051 G T
Osa11LNT0108500.2 11 25778324 C T
Osa11LNT0108500.2 11 25778956 T C
Osa11LNT0108500.2 11 25779100 C T
Osa11LNT0108500.2 11 25779102 T G
Osa11LNT0108500.2 11 25779453 A G
Osa11LNT0108500.2 11 25779540 A G
Osa11LNT0108500.2 11 25779811 A G
Osa11LNT0108500.2 11 25778167 G C
Osa11LNT0108500.2 11 25779721 C G
Osa11LNT0108500.2 11 25778550 G A
Osa11LNT0108500.2 11 25776047 A G
Osa11LNT0108500.2 11 25779115 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa11LNT0108500.2 osa-miR5808 Cleavage 5.0 21.138 1 24
Osa11LNT0108500.2 osa-miR156a Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156b-5p Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156b-3p Cleavage 5.0 9.015 1 21
Osa11LNT0108500.2 osa-miR156c-5p Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156d Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156e Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156f-5p Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156g-5p Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156h-5p Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156i Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR156j-5p Cleavage 4.5 9.722 1 20
Osa11LNT0108500.2 osa-miR396a-3p Cleavage 4.5 15.537 1 20
Osa11LNT0108500.2 osa-miR396b-3p Cleavage 4.5 15.537 1 20
Osa11LNT0108500.2 osa-miR156k Cleavage 4.5 9.722 1 21
Osa11LNT0108500.2 osa-miR159a.1 Cleavage 3.5 20.063 1 21
Osa11LNT0108500.2 osa-miR159b Cleavage 3.5 20.063 1 21
Osa11LNT0108500.2 osa-miR159f Cleavage 4.5 20.063 1 21
Osa11LNT0108500.2 osa-miR159f Cleavage 5.0 15.705 1 21
Osa11LNT0108500.2 osa-miR319a-3p.2-3p Cleavage 5.0 19.436 1 20
Osa11LNT0108500.2 osa-miR319b Cleavage 5.0 19.436 1 20
Osa11LNT0108500.2 osa-miR413 Translation 4.5 15.589 1 21
Osa11LNT0108500.2 osa-miR415 Cleavage 5.0 9.722 1 21
Osa11LNT0108500.2 osa-miR419 Translation 3.5 13.849 1 21
Osa11LNT0108500.2 osa-miR529b Cleavage 4.0 21.28 1 21
Osa11LNT0108500.2 osa-miR1857-5p Translation 4.0 4.744 1 21
Osa11LNT0108500.2 osa-miR396f-5p Cleavage 4.0 17.511 1 22
Osa11LNT0108500.2 osa-miR5144-5p Translation 4.0 20.996 1 21
Osa11LNT0108500.2 osa-miR5161 Cleavage 4.5 20.063 1 20
Osa11LNT0108500.2 osa-miR5496 Translation 5.0 19.999 1 21
Osa11LNT0108500.2 osa-miR5498 Translation 5.0 19.799 1 21
Osa11LNT0108500.2 osa-miR5505 Cleavage 4.0 12.836 1 22
Osa11LNT0108500.2 osa-miR5523 Cleavage 3.5 20.889 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0108500.2 11 FON3 Morphological trait Panicle/flower RM4601 RM1233
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