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

>Osa11LNT0095000.3

TAACTAAAAGAACCCATCAATAACTTTTACTGAATAACCATGAAATAGAAGGTAATTTACAAAGCTATTAGTTGTCATGAACTGGCAATAATTTCACAGATGCACAGCCAAAAGACACTCAAAATGGCATTCACTAAAGATCTTGGAAGCGCGCTAGGTGATGTCAGATTCCAGAAGGACAACACAAGATGCGACTAGCATCCCTCAGGTATGAATATCTGGGTATGGCGCACAACAGCAGCAGAGACATCAAAACCATGCACTGTTAAAAATACATCAAATCTATGAACACTAATGTTCTAAAAAATTCTTATCATTCTAAAAGTTCTAAAGGAGTTAAACGTCTCCAGACCAAATTAAATCTGAACTCAGAGGCACTTTGCAATCCAGATATGGGGTGGGATGCGTCGAGCATATTCAGCTGCCAGTAAACATTGTGCTCTCCAAGCAGCTATCAGCTACTGTTAGTACATCAACATGACATCATTGGCAGTGCTTTCCAGGAATGCTGTCTTCGGTGATTCCTTAACCGGACAAGAGTGAAGATATATCGGACAACACATCAATTCTGTTATCTAAGATGGCTTAGTCCTAGACATCTTTCCAACACTCCTCAAACATTGCTGCATTTTACTCAGTTCCTTTTGTGCCATGAAAGCATGAGCAGAGGAAACCTGTTGTATCAGAAGGCAGCTAGTATACATTATCCATTTATCCTCCTACCAGTTCCAAACATTTTGGTGAAACGACAAGATATCCCTCAAGATTTTTCTTCTTGCCCATGCACAGCTTAAGGAAACTATATCTGGAGCATAATTACATGGTTTCCAGACACTGCACCATTTACTCTTCATTGTTGGTGCAAATGAGCATCTTGCATAAACTGAGATCTCTGCCATTGCGCTACTTTCACTGCCACCATCTGGGGAAAGGTCAGGGCCATGCACCTTAAGATTCCATTTTTATGGTCCTAGCTTAACTTGGACACACAGAACCTCCATCATCAAGTTTAATTTTCTTATGCTGAGGTCTTCCATTTACTTTATCATCCCAATTTGCCACGTCAACACTTCTTTTACGTACACCACCAGAAACATGTGAAATAGTATGCACATTGCTAGAGCTTACTCCAGTAGCATTCACACTGTCACCATCCATCAGGTGCTCAGCATTGTCCATTTTGTTATTTGTGCTCTCATTACCTTTTCCATGGATTACGGAGAAAGAACAAGTATTTAGCTTCATATTCACATCAAAATTTACATCACAACCATTACCCACAGAAGGATATCCCATTTTCTCTTTCTGCTCTGAATAAGCAAGTTTAAGGTCTTTTCTTGTCGGGACAGGGAGAAAATCATCAATAGCACTACTGTTATTTGTTGGAAACATTGCTGTGATTGAATCATGAGACTGCCCGTCTAAAGGATTTCCAACCAAAGGATGAAATAGAGATTTTACACCATTCGAGCACCCCTGATTATTATCATCGTTTTCACCCCTACTCAGATCCAGTCAATAGATCCATCACAAAATTAGAACTCACATATGGGTAGATCAGGTGGAAGGTTGGCATCTTTTCTTCTAACTCTAAATACACCCCACAGAAAATGGAACATGTTCCATCGTTGGAAGTTATTTGGTAGGGTGTTTGAAGCAAATATGAGCAATTCAGCTGTTTCAATATTTCCTCTGAGTGCTAAATCATCCTTTAGCATATTTTCTACCAACTTCCTGTAGTGAATCTCATAGCTTTCAGTATCTCTCGCAAAGAAGAAAAGAGCAATGCTGTCAATCGTAGGGCCATTATCATGAAATTGTGGAGGCCATAAATTCTGACGAGGAAGTTCCTCAAGCTGGACGTTAGAAGGGAATTTCTTTGCTACTTCCAGCACTTTAGGTGATGCAAAGCATGATAAGTGGGCTTGCAAACCCTCACAAAGCACAGGTGATCTTACAGTCCTTGACAGCTCAAAACCACCTCGCCAAATATAATCCAACTCTGGAATAGTTGAAGCTATATGTTTACAGCTAGGTGAAAAGCTTTGACTGGAAAACGTTATTTTTTTTTCCTTCATATCCTTTGACATGGCAGAGATGCTGTCCACAGATCTTCCTCGCATGGAAGGTACAGTCTGGTGATCTCTCAATGATGCGCTGCCAGGAATGGACACACTGCTAGAATTACTAGGTACCAAGCTAGATGGGCTCTTTATTTGATCATCCAGATGTGATGAATCTGGAACCTGAATTGTCTTTTTCTGTGCACCTGAACCAAGCATACCTATGTTGGCATGTCCTTTTGTGTGAGGAGGTTTCTTTATACCACAATGTCCAAGAAAACTTCTAGCACCTTCACCGCCAGAAGTGCCTAAAATATTTGAATCAGCCATTCTATTTCCTTTATTGAGATGTTGTGCTGAAGACTGTGCTTTCGAATGAACTGGGACAGTCACTGATCCAGTAAGGGAGCGGGACCCTAATATTGAAGTCAATATATCGTTTCTTGCATTTTCGCTCACAAGTGGATTCATCACCGTGGAAGGCTTTGCCTTATTTACTGGCTCAAAACATTTAGGTTTTTTAAATGATGCTGACTTAGCAAGTATTCCCATTGGCCCCTCTTTTCTCATAGGAGTGGACAAAGAGTCCTTGAAAGTTTTGGGCTTCTGAGGAACTTCATTCAGTAGCTGTTTCACCTTAGGGACCTTTGAATTGTTGAAAGAAGTGGATTTGGAGAGTTGACCGCGAAGAGGTGCCATTTGATTCTTAGGATAATTAGATGTCAACAAGGTTGAAACATGTCCAGCAGGGTCCTTTCCTTTCTTTCCATCCAGCTTGAATGAGCTTTCACGTGACACTGGATTTTGTCTCACCAGTGAAGTAATCCCTGCATCCCCATCCTTCCTCTTGTTGACACTGTTCATTTCATTTCCTCTGTTTGACATATTACTTCCCACATTTTCAGCATCCACACCATTCTCAGAAGAACTTGGTTTGTTCATTGGTCCTTTGGAACCACCAACCTTTAATTCGGATGTTTCTATTTTGTTCTTTCTCTTTTCACTCTCTACTTCACTATGGCATGTTTCACATAGCCACTTAGCCTTTGGAACCTCTTGCATCATCACTCGCATGCAGTAAATATGCTCAGCACCGTCATTGCATCTACTGCACACAGCAAGCTTCTCCTCAGCACCAATATCTCCACATATGTCGCAGACTTTCACATCTTCAACCTCTTCAGAACTTTTAACCTCACTCTTTATAGAACTTTTATTCTTTACAGCCATATTAGATATGTCATGAGCCACGGATGTAAATGGAACATCATTATTGTGGCTTTGCATATGCCTCTCTCCATCTAGTATCTTCAAATTAAAATCATCATTTCTCCCACTGGATGTCTGCTCTTCGTTTTTATTAGCAGCCTCACTGCCACCAATGCATGATCTACCGTCTTCCTCCTTTCCTGTAGAAGTACAGCCACTAGGGACAATCCCTTCCTCTGCATCTTCTTTTGTACTCTTACTGGATATATTACTCACATTTAGGTCTTTACTACTCACATTTGCAGCCTTCACCTTACTCCCTACAGAAATTGTACTAACCTTCACTTGAGATTTCTCAAGTATGCTCTTTTCTTTTTCAATCTGCATCTCAGTTCGGCACTCTTCACAAAACCAATCACCCTCTGGAACCTCTGGCATCATTACCCTCATGCAGTAAATATGTTCAGCACCATCATTGCACCTACTGCAAATAGCAAGCTTCTTCTCCTCACCAACATCTCCACATATGTCACATATTTTCACCTGTTGATCTTCACTTTCTTCAGAACTACTATCCACATAGGTGACATTGTTCTCTTGTGCGTTTGACACTAGATCATCCATCCGGCGTCGCATGTCTCTGATTCAGGTTTGTCAAGAAGGTTCTGGCTCACCGATGTGCTTTCTTTCTCAGAGTTGAAAATCACCCTAACAATGAGAACATACCAATGAACGAAAATAGTATTTCGATGCTTGTTTCAGTTACGCGTCACATATGATGCTATCGGTGAAAACAGGATGCGGCGGAAGCAGCATGACGAACGATGGCGCCCTGCTCGCCGGCGCCTCGCGGGATGGATGGGGATCGGCGGCGGCGGAGGCGGCGGCGGCGGAGGGCAAACTGATGGATAACTCACGACAGAGGACAACTA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.873839
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0095000.3 11 10650744 C T
Osa11LNT0095000.3 11 10649984 C A
Osa11LNT0095000.3 11 10650271 T A
Osa11LNT0095000.3 11 10650635 A G
Osa11LNT0095000.3 11 10648129 A G
Osa11LNT0095000.3 11 10648693 G C
Osa11LNT0095000.3 11 10648697 A C
Osa11LNT0095000.3 11 10649708 T G
Osa11LNT0095000.3 11 10649863 A G
Osa11LNT0095000.3 11 10650012 G C
Osa11LNT0095000.3 11 10652403 A C
Osa11LNT0095000.3 11 10652987 T C
Osa11LNT0095000.3 11 10653232 A G
Osa11LNT0095000.3 11 10653244 T G
Osa11LNT0095000.3 11 10653392 C T
Osa11LNT0095000.3 11 10653517 G C
Osa11LNT0095000.3 11 10653544 A T
Osa11LNT0095000.3 11 10654156 G C
Osa11LNT0095000.3 11 10654449 T C
Osa11LNT0095000.3 11 10656197 T A
Osa11LNT0095000.3 11 10652669 T 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
Osa11LNT0095000.3 osa-miR5532 Cleavage 5.0 19.547 1 22
Osa11LNT0095000.3 osa-miR5801 Cleavage 5.0 21.817 1 24
Osa11LNT0095000.3 osa-miR530-3p Cleavage 4.0 14.861 1 21
Osa11LNT0095000.3 osa-miR530-3p Cleavage 4.5 15.777 1 21
Osa11LNT0095000.3 osa-miR395o Translation 4.5 9.818 1 21
Osa11LNT0095000.3 osa-miR529b Cleavage 4.5 6.829 1 21
Osa11LNT0095000.3 osa-miR1853-3p Translation 4.0 8.732 1 22
Osa11LNT0095000.3 osa-miR2118a Translation 4.0 23.374 1 22
Osa11LNT0095000.3 osa-miR2874 Cleavage 4.0 6.034 1 24
Osa11LNT0095000.3 osa-miR2874 Cleavage 4.5 6.45 1 24
Osa11LNT0095000.3 osa-miR395x Translation 3.5 21.381 1 21
Osa11LNT0095000.3 osa-miR5144-3p Translation 5.0 18.936 1 21
Osa11LNT0095000.3 osa-miR5508 Cleavage 4.0 12.242 1 21
Osa11LNT0095000.3 osa-miR5508 Translation 4.5 14.749 1 21
Osa11LNT0095000.3 osa-miR5143b Cleavage 5.0 11.093 1 24
Osa11LNT0095000.3 osa-miR5143a Cleavage 5.0 11.093 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0095000.3 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0095000.3 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0095000.3 11 nan Morphological trait Seed RM332 RM229
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