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

>Osa08LNT0408500.2

AAAAGATCAGCTCATCAAGCTGATAATACATTTGGTTCACACACAAATACCAACACGAAACGTTGCTACCATAGCACATCATATGATAGCAACTGCATAATGATTTATCCTTAAGTGTATTTAATGACTTTGCAGTAACAATGTACCACATGAACAATATAGCTGGAAAGAACATCCACAAGCATGAAGCAGTCATCACCAACTTTATTCATAGCTCTGATCGACAAGAGTACCACCAAAAACAGAATTTCATCCATTCGTTCGTGAAGGCTTCAGTTTCCACGGCAGCAACCAATCCACGGACTTACCTGACGCATCTCAGTAACTGCCCGTATGCAGAATTGCAGATTACTCATTAGGTCAAAACCCTGGGTCTGAGAAGTTAAAGAACTCTCCGTACATATTCTCATCAGACAATGGAAGGGATCATCTAAAATCCCCTTCATAGCCTGGAAGACCTGCCATACCCAGTTCCAAGGGTAGCACTTGTTATGCTTCCAAGACAAGCATCTTCCAAAAGAAACATTACATGACAGGGCTGTACTTATCAAGGCCGAATTCAAGTGTCAATCTTCGCCACTTACTCCCAACAGATTCTCAGCAAATCCTTCATGGTACAAGCTAGTCACACAAGGTAATTGCCAGACCATGCAGATTGTGCTGGTAATTGTTCCGCCAGTGGACCATTTTGCTGGTTCCCTTGCTGAAAATTAAGTTCTGGAAGTTGCTTTGTGGGCCCAAAAAGGTGGAAATCCTGCCACTGTTTTTCATCGCTACCTCTAGGATGCATGCTGAAAGCTTGTTTTCCAGGAAAAGGAAAGGGAGTGGTGAAAGTACTGCTGGCAGTGGTAACATTTGAATGTGCAAAACGCTGATTATTGACATAATCCAGTGATGACCTGTAGCCATCCAACCAGATGCCGTCATTGGTCTGAACATGCTGGCCATTGCCAGCTAAAATGGAATCATCCTGTCGCTTTGGAGGGGCATTGTTAAATCCTGGAGGAGGGCCAACATGTCTTCCAGGACGGCTGACAGGATTTTTCTTTGATACACCATCAGAAGATACTACTGACGGCAGAACTGAATAGAAGGCAGAAGGGATGGTAACTTCAGTATGTTTATACTGACCAATCATTGGATTTGTACTATTCATAGTAGCTTGAGCAGATACCTGAGGCACATTTCCCACAGACTGTAATCCACTGAGTCCACCATTCACTCTTTGATCCAGAAATCCACTTGCACCTATGTTAACATTGTTTAATGCACTCAATAAGAATGAATCTTGCCCAGGGAGTATGGCTGTATTATCTGGGTTACTGAAACAACCGAGTGACGATGGAGGTGTACGCTGATCCGAAATTATATTGGAAAAGCTCGCCATAGGGACTGTATCCAGTGAGCCAACAAGTGGTGCACCAGTGCTTACCCAGTTATGATCAGGTGCTTTCAGAGACTCAAAAATATCAGATGTTGACCTTGCACCAACATCAAGAATCACATGTTGCCCAGCATTGGCTGCCCAACCAAGAGAAGAGATTGGGAGAGATTGAACATAAACATTGGGAGTCAGAACCGGTCCATTGCTCTGAAATGTCATTGGTGGTGGTGCACCATCATTTGACCAATTGACATCAGACACCACCACTGGCTGTAATAACTCATTACTAGTCTGTTCTGAAGTAACTCTCGGAAGCTTTTCAGAAACTGGAGGCTTGAAAACTATTTCTTCATCATCATCTCCATCAAGAAAGAGTTGTGCCTTTGACTGAAGCACACCTAGATCTTCTGCGACAGAACCAATTTTACTGGAGACTTCAGGTTCCTGTTGTATGTGATTTGTTGTCTGCGCATTGGAAGATACAACAAGAGGAACAGAAGAAGCAGGAGGAGGAGGTTCTGAAGCCATAAGGAACTTTTTTGAGGATGCATCAAAATATATTCGCAGCTGATCAATTTGAACGAAATTTAACAGCGCCTTCCCTGCAGCAAGAATCCTTTCTACACGTGCTTTTTTCTCCTTGGTACCTCCATCACTTCCAAAACCTTGCTTGGTGGAGAAGTCCAAGATACCTTGAGCAGGTACCAAAGGCGAAAACCCTCTTAACTCAACATCCTCCCACAACGCAAGCCTGTTCCCAGTTTCACCCTCCTCATATGTGCCCATGTCAAAAAAGCAAGTTTCATCATTATCACCATCGACATGTGCGAGACCAGTCAAAATGAGCTTATTCATAAATGGCACGCATTGACTCCAGAAGAAAGATCTTGCATCGGCTTGCTTTTCATCCATCTCAGAACTAGCCACAAAATCTGGATGGCACGCCAGCCATTCAATGAAGACCAAAATAGCTGGCAAGTAGATACTTGATGCAACATCATGAAGCTCTGCGCATCTTTTGAGAAGGTATCCAACAAATTCAAAGGCTGCAGCAAATGCATTTTGAAGAAGAACTCTGCGTTGCACAATTTCAGCATATGATTGATTATCTGCGTCTTTGTTTGCATTGTGCACTGTGAATATAAGGATAGCAATAAGCTTAACAACAGAAAGCGCGTTTTCAGCAGCCTCAACACCAAAATTAAGCTCCTCGTAAGGACCAGATGAAAGAAGAATTTGCAAATCGCTGATAACTGTAGCAGACAACTCCCCAAATGTTTCCAAGCTTGTCCTTGTGAAAAGAATTCCATTGAGGCGAACAAATCGAATATAGAAAGCCTTCAGTATTTCTTGAATACTGTGCTCTCGCTCCTTTGAATTTTCTTCTGTACTAGAACCTTTGGGCTGAAATCTTGTCTCACCCCTTCCTCTGGCCCTACCAACTGATCTGGATGGCAAGCTCTTAGCGTTGGGAACCTTGCTATTACCTGATAGCTGAGCATAGATATCATGATTCTTGTCAAATGCGAGAATCAAGTTTTCCCTCGCTGCAGAAAAAGGATTATCCACAGCTAAGCTACGGAAGTACCTATAGATAGCTGTTACCTCATCTCCAGCATATGATGCCAGTATTGCAAGCTGATGATGTGGGTTGCCATTCGAAGGGCACAGCGAAGCTGCTTCCTTGTAGTAGATAGAGGCTGCAGCATATTCACGACTTGCATAATCCACATCCCCATACAGACCTTTGTATCGGGTAAGATCTCCTAAATATATCAAACAGCGATAGCATGACAACAAGCCTTTTTTCACCCCAACCACTTTCTTCCCATCTTTATCAGGAACAACAGAACTATCAGGACCCTCAGAGAAGTAGCCCAACGGAAGCCCATAAGTAGACCGAATTTTCAGCATCAAGTCATGATAGAAACCAGTTGCTTCTGAGAGGAAACTTCTAACAGAAGATCTGATCCTCTTGATCCGATCAGGATTGGCATTGTTCTTCCCAGCAGAGACAATATGAGCTCGGAATTCCTCAATTCTTTTGTAGTGCAACTGCCACAGAAGATATTCTATCTCACGTTTTTCAGAGAAGTCATGATCAGCAAGGATTATCTTTTCATAGTTCTCACGCATCTGAAACCATATGTTAGGATCTGATGGCACTTTGGACTGTGCTGACCTTCGCAGACGACTTTCATGTTCAGCGTTCTTCTTTAAGAGCCGCTGTGCAAGCTCCCTTGATGATGGGGAAGCAGTAGCTTTATCCATCGGAACGGTCATCATCCATCAATCACATATGGGGTCAACTACGCTCGTCGAGCAGGAGGATGCAGAGGGGAATTAGGAAGCGGAGAGGAGAGGAGAGGGGAGGGAAGAGAGGGGGGCTA

Coding Potentia
Explanation CPC Score
noncoding -1.22491
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa08LNT0408500.2 8 12724566 A C
Osa08LNT0408500.2 8 12731047 C A
Osa08LNT0408500.2 8 12724685 A C
Osa08LNT0408500.2 8 12725003 C G
Osa08LNT0408500.2 8 12725547 G A
Osa08LNT0408500.2 8 12726056 A G
Osa08LNT0408500.2 8 12726457 T C
Osa08LNT0408500.2 8 12728691 G A
Osa08LNT0408500.2 8 12728891 T C
Osa08LNT0408500.2 8 12729406 G A
Osa08LNT0408500.2 8 12729473 C T
Osa08LNT0408500.2 8 12729869 T C
Osa08LNT0408500.2 8 12730798 T C
Osa08LNT0408500.2 8 12731442 G C
Osa08LNT0408500.2 8 12731531 G A
Osa08LNT0408500.2 8 12728353 A G
Osa08LNT0408500.2 8 12731073 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa08LNT0408500.2 osa-miR5528 Cleavage 5.0 15.529 1 21
Osa08LNT0408500.2 osa-miR5790 Cleavage 5.0 15.146 1 24
Osa08LNT0408500.2 osa-miR169i-5p.2 Translation 3.0 12.305 1 22
Osa08LNT0408500.2 osa-miR169i-5p.2 Cleavage 5.0 12.947 1 22
Osa08LNT0408500.2 osa-miR171g Cleavage 5.0 13.917 1 21
Osa08LNT0408500.2 osa-miR172a Cleavage 4.5 16.705 1 21
Osa08LNT0408500.2 osa-miR172b Cleavage 4.5 16.705 1 21
Osa08LNT0408500.2 osa-miR172c Cleavage 3.5 16.705 1 21
Osa08LNT0408500.2 osa-miR166g-5p Cleavage 5.0 13.917 1 21
Osa08LNT0408500.2 osa-miR166i-5p Cleavage 5.0 13.917 1 21
Osa08LNT0408500.2 osa-miR172d-3p Cleavage 4.5 16.705 1 21
Osa08LNT0408500.2 osa-miR395w Cleavage 5.0 14.868 1 22
Osa08LNT0408500.2 osa-miR1428a-5p Translation 3.5 21.014 1 21
Osa08LNT0408500.2 osa-miR169r-3p Translation 4.0 20.258 1 21
Osa08LNT0408500.2 osa-miR1850.2 Cleavage 1.5 14.192 1 21
Osa08LNT0408500.2 osa-miR1860-5p Cleavage 5.0 21.213 1 21
Osa08LNT0408500.2 osa-miR2275a Translation 4.5 17.35 1 22
Osa08LNT0408500.2 osa-miR2275b Translation 4.5 17.35 1 22
Osa08LNT0408500.2 osa-miR5147 Translation 5.0 13.137 1 21
Osa08LNT0408500.2 osa-miR5161 Cleavage 3.0 12.236 1 20
Osa08LNT0408500.2 osa-miR5339 Translation 4.5 14.895 1 21
Osa08LNT0408500.2 osa-miR5488 Translation 5.0 14.386 1 21
Osa08LNT0408500.2 osa-miR5499 Cleavage 4.5 16.079 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa08LNT0408500.2 8 hsa2(t) Physiological trait Sterility nan nan
Osa08LNT0408500.2 8 qALRR-8 Resistance or Tolerance Other soil stress tolerance RG978 C1121
Osa08LNT0408500.2 8 qDSR 8 Resistance or Tolerance Other soil stress tolerance RM3572 RM404
Osa08LNT0408500.2 8 hd8 Physiological trait Flowering RZ562 RG978
Osa08LNT0408500.2 8 dth8 Physiological trait Flowering RG333 RZ66
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