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

>Osa08LNT0407700.2

AAGATCCAAAATTTGTCATACTACTACATTATTTATACTTCTGCATATAGACTATAAATCAGCACTGTACAAATACAACCCCTGAATTGTACAGGTAGTAAAAGGTATGGCCATATGCCACAATCAACTTCAGCGCCTGTTGAAGACATCTAACATGTAATATTGCTTACAGGATCTCAACACAGTACTCAAAACATGAAAACTATTTGCTCCATCTTTCTTTCCCCAAATCAAAACAGCACGTCAGTATAATACTAGTTGAACAGAAACTGCATGTGCACATTAGTTGATTTACAACCTGGCTGCCATGATGTCATCCTTTCCCATTTTCTGACAGCCTTCTTGCCTAATTGATTTTAGGATCAGCTATGCCATATCTTAATCCATGTCAATGTCCACAGCGAATTAGTGGAGTAGGTTCAGTTGCATCAGAAAGACAAGGCCTGCCTTGTGCCTGCTGGGGGCATCAACATCTCCATCAACCCAATGGCATGAAAACCCCATGGTAACAATGCCCACCATCTTGCAATTGATCACACTCAACACCATCCCAATCAACGTTGATGTTTCCCCCCAAAATTTCAATCTTCAGAAAATCTAGGAGAATTGCAATCTAACAGCTGAGGAGAATATGGTGTTCTTTGTGGAGAGCTTGTAAAATGGCAAATCTCTGAGAGGATGATACGACGCAAATAACCTTTTGAAATTTGCAGCTGGTATTATGGTTCAACAACCATCTTGCATTATCATCCATACATTGGCTCTCAAGGTGCTTTAGTTGATGACCAAAGTGAACCTGTGTATCCATTATCCAGTCCGCAGATAAGAGCTTTGATAGGTCACAGTGCAGTTCTTGTCCATATTGGGTTGTTTTTCCCCCTTTCAATTATAAACATTCAGGGCAATCTGTTGCTGCTGTTGGATACCCCACCCAAGACAGTAGGTGGATGATCATGTAAACTTGAGCAGAAATGTTCAGAACAACCTCTGCTGTTGCTGGATAGCTCCCAAAGATTGACCATGACCAAATGAATTGGAGGGAACTGTTAGGAGATGTAAAATTCATAAGATCAAAGGCAGAATCAGTGGCCACATGTTCTCCCTACTCCCTGTTCATTCTTGGACGGTTCTTGTCAGAACAAAGAAGGTGTGCCCTAAGGTTCCTTGACCACACATCATTCAACACTGGAAGCAGCTTCTTTCTGGCACCAAGGAGCATTAATTCCATTAGATAATATGTTATACATACGATCATCTTTTGTTAAAGCGCCTGAGGACAATTCAGCAGTATGTCCTATATCCTTATCCAATGAATTTACCTCAGAACACCTTGCAATTAGTGTACCATAAGTAATATTGTCAGGAATAACACCTGAGCCCACCATCTCATCGAAAAGCTTGGAAGCTTCTTCACTGTTACCAGATTTAGAGTAAGCATACATAAGAGTAGTGTAAGTAAGCTTATTTGGAGATATACCCCTGGAACGCATCTCCTCAAAGTATGCAACAGCTTCAACCATTTTTCCTAGTTTGCAGTAACCTTGAATCATAATTGTGTAACCAATTACTCCCAGGTCAACATTGTTTTCCCTGGCTTGTGAAAAAATGGTCTTGGCCTCTTCAACTAGACCAGCATGACACATCCAGTACATAAGACTACCATAAGTCACATTAGTTGGTTGTATGCCATTAGACTTCATAGTCTCAACAGCATCAATTGCACCAGAGATGTCACCATTCCTACCATAACCACCAATAAGTGCATTATAAATGAACACATTAGGTTTAAGTCCACGATCCATCAATTCAGTCAAATATTCTTTTGCTTTACGAATATCCTTTGCTTTACAATGACCATCTATTATAGTGCCATATGACACTATATCAGGCTGAAGGCCCTCAGTTTTCATCTGATCCAACAGATGAAAGGTTTCCTCCATTTTACCCAAATTGCAATAAGCATGCAATAAAGTATTAAATGTGAAAAGATCAGGCTTAAACCCTCTTCTGGTCATGTCGCCATGGAGTTTAATAGCTTCCTCCATTTTACTGTCTTTGCAGCAACCTCGAATCATAATGTTATATGTGATGCTATCCAATTCAATTCCCTTATTTAACATGGTCTGTATAACCTTTGTAGCTTCTTTCATGTACTTACCTTCACAAAGACCATGAATTAGCGCATTGGAAGTTGCAAGATTAACACCTAAACCTTTGTTCAATGTCTTGAACCAAATCCCAACTGCTTCTTGATGTTTCCCTCCCTTGCAAAGCTCCCTCATACAAGCTGTCATCAGAGGATCATTTGGGCGCATACCTCGTGTAACCATTTCATTTGTAATGCTTACCACTGACTCCAATCTTCTGGTTCTTTGAAGAAGCCATGCAACCACTGTATTGAACAAACCACAATGAACTGTCATTCCAATTGACAACATATCCTCCAATATCCTCTCAGCCCGCTCCATCTCCCCTTCCTTGCACAGTGCCTTTGCAATCAAGTTATAAGTCACGGCTGTTGGCTTCATCTTCTTTAAAACCATTTCATCAAACAACCTGAGTGCCTGTGAGCAATGGCCCTTCCTACAATGCCAACCAATAAGCTCATTGTAAATAACCTCATTGGGGGAAACCCCTAACTGTTCCATCTCCTGCAATACAATGCCAACCTCCCCAAACCGCTCGCCCCTTGCAAGACCATTGATCAATATACCGAATGTGACCACGCTTGGTGTCATCCCTCCCTGTTCCATCCTCCCTTTCAATCGAAAGGCCTCCTCCACCCTCCCACTCTTACACAGTGCATCCATAAGCACATTGTACGTCACAACCGTTGGCTGAAGCCCAGCCCGCCATAACTCTGCAAGCATCTCAAAACCAGCATCCACCTTTCCAGCCTTGCAGAGCGCCTTGATCATGGCGGTATACGAGTACTCATTCAGAGCGACGTTCCTGCTTTCACGCATTTCGTCGAACACCTCGCGGGCGGCATCGAGCTGACCTGCACGAACAAGGGCTTCGAGGAACGCATTGCAGGTCTTGATGGAGGGCGGCGCGCCGCGCGAGGAGAGAACGCGGAACGCGTCGGCGGCCCTGCAGAGGGAGCCTTGGGCCGGGGAGGTGATGAAGGTGTGGATGAGGAAGTCCGAGGAGGGGGTGGAGGCGGCGTCGGCGACCGCCTCCGCGGCGGTGCGGAGCGGGTGGACGTGGAGGAGTCGTGAGAGGAGGCGGCGCGCCGTCCGGATGGCGGTGCGATCGGCGATGAGGGAGGGCAGGAGGAGCGCCGAGACGCGCGGGGTGAGGAGGTCATCCTCGGAGCGGGAGGAGGTGGAGGAGGTCCTGGAGAGGAGGTGGAGGAGGAGGCGGAGGGCGGAGGCCGCGGGGAGAGGGGAGGGCAGGGACGAGAGGACGGCGGCGAGGCCACCGCCGCCGATGCGACGGAGGAGGGCGTCGAGGTGTCGCGCCGAGTCGGGGGAGGGCAAGGCGGAGAGGGCGCCGACGAGCTCTCCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGAGGCGTGGCGGCGGCGGCGGGGGAGGAGGAGGAGGAGGTGGGGTGGTGGTGGTCTCATGGCGGAGGTTCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.422955
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa08LNT0407700.2 8 11552587 G A
Osa08LNT0407700.2 8 11548590 A G
Osa08LNT0407700.2 8 11549961 A C
Osa08LNT0407700.2 8 11549967 G A
Osa08LNT0407700.2 8 11552177 T C
Osa08LNT0407700.2 8 11553320 G A
Osa08LNT0407700.2 8 11554431 A G
Osa08LNT0407700.2 8 11551538 T A
Osa08LNT0407700.2 8 11549639 A G
Osa08LNT0407700.2 8 11550593 T G
Osa08LNT0407700.2 8 11550610 C T
Osa08LNT0407700.2 8 11550819 T A
Osa08LNT0407700.2 8 11551246 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
Osa08LNT0407700.2 osa-miR5543 Translation 3.5 18.329 1 21
Osa08LNT0407700.2 osa-miR5543 Cleavage 4.0 13.751 1 21
Osa08LNT0407700.2 osa-miR5827 Cleavage 5.0 15.939 1 21
Osa08LNT0407700.2 osa-miR396c-3p Translation 4.5 15.42 1 21
Osa08LNT0407700.2 osa-miR166g-5p Translation 5.0 15.692 1 21
Osa08LNT0407700.2 osa-miR408-5p Cleavage 4.0 18.656 1 21
Osa08LNT0407700.2 osa-miR408-5p Translation 5.0 9.83 1 21
Osa08LNT0407700.2 osa-miR414 Cleavage 4.0 16.738 1 21
Osa08LNT0407700.2 osa-miR437 Cleavage 5.0 6.632 1 21
Osa08LNT0407700.2 osa-miR1442 Cleavage 5.0 15.493 1 20
Osa08LNT0407700.2 osa-miR2093-5p Cleavage 5.0 9.992 1 20
Osa08LNT0407700.2 osa-miR2097-5p Translation 4.0 6.387 1 22
Osa08LNT0407700.2 osa-miR2097-5p Cleavage 4.0 16.736 1 22
Osa08LNT0407700.2 osa-miR2099-5p Cleavage 4.5 23.098 1 22
Osa08LNT0407700.2 osa-miR2924 Translation 5.0 17.595 1 21
Osa08LNT0407700.2 osa-miR5075 Cleavage 4.0 17.621 1 21
Osa08LNT0407700.2 osa-miR5075 Translation 4.0 13.745 1 21
Osa08LNT0407700.2 osa-miR5080 Translation 5.0 14.496 1 21
Osa08LNT0407700.2 osa-miR5491 Translation 5.0 12.016 1 21
Osa08LNT0407700.2 osa-miR5491 Translation 5.0 12.7 1 21
Osa08LNT0407700.2 osa-miR1846a-5p Cleavage 5.0 19.638 1 21
Osa08LNT0407700.2 osa-miR1846b-5p Cleavage 5.0 19.638 1 21
Osa08LNT0407700.2 osa-miR1846c-5p Cleavage 5.0 19.638 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa08LNT0407700.2 8 nan Resistance or Tolerance Drought tolerance RM72 RM331
Osa08LNT0407700.2 8 qDSR 8 Resistance or Tolerance Other soil stress tolerance RM3572 RM404
Osa08LNT0407700.2 8 qALRR-8 Resistance or Tolerance Other soil stress tolerance RG978 C1121
Osa08LNT0407700.2 8 hd8 Physiological trait Flowering RZ562 RG978
Osa08LNT0407700.2 8 dth8 Physiological trait Flowering RG333 RZ66
Osa08LNT0407700.2 8 hsa2(t) Physiological trait Sterility 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