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

>Osa11LNT0090100.1

GTGAGTATGAGAGGCTTGAAGCACATGCCAAGAAACACGCTGGTGATCACCATGCTCAACTGCAGTTACCTTTTAAACAAAAGACACTACTGTTTGAACTATGAATAGCAATACATCACAACTAATAAGTGGCATATACTACCACCAAAAAGCTAATTAAGCAGTCGAGACAGTCTTATAAAAGGATAATTCAAGAAAAATAACCAGCTCCAACAGCTAGACGGTCTAAACAACTCATTATATCCCAGTTCTTCCTACTAGTGGAACTTAATATGAATCTCATTGACAAAAGGCAGAGTTCTTGTCACTGCAAGTTTAAGCCTTGCATTCCTGAATATTCAACAGGTACTTCATCTAGAGGATCCTTCATCATGACTTGAACTCGAATTTCCTTCCTCGAAACTGAAGAGATTTGTCGACCGATCCATCCTTCTGATAAGAACCACTACATCCAATGTACTCAAGAACTTCACAGTTTCACAGACCCCTTCATCAACTTCTTTACAGTGGACTTTCACTACCTTAAGATGTTTGGATATTGCAGCTGGTTTCACCAATGCACTGTAATTTTCTACTGCCCCTATCATAGGTTTTGTTTCCTTGGAAATTTGAAGAGTGAGTTTCAGTAGAACCGGTGAGTGTTCGAGAATACAAGCTAGTGCCCAGAAATTATTAGCAACACACCACTCATTGAGTAACAAAGACTTCAACTTGCTAAACAAAGGGCACCATCTTAAATCACTTCTGAAAATACGCATTTCAGGTCCAGCTATCAATTCCAACTTCTTAGCTTCTGATAAACCTCCAAGGAGCACGCATTTGGCACTGTCATTGCCAGCATTATCTACCATACCATAACAACCATGACAGTATTCATCTTCACAGTTACCAGAGTAAGTATTACTACACAAGTCATCACTATCTCGGTGGGGTCTGACAAATGCTGCAATTAATGACGGCATGCTTTCCAGAAATGGAACTCTGCCCCAACAATCATCAAGACGGAGCGTAATGAGGTTTGGTGCATAAATGTGAGTGCGGTGATGTTCACTGAATTCAGGGAAGTCGAATGTAAGATATTTTACTGACTGGGACAAGATCTTCTCGACAGAATTAAAACAGCAACTCGCAGAGAAATATATATATTCCAATGCAGGACAGCTGGAGAAGTTGAGGACAAATTTTCTGAAATCCAGACCAGAAAGATTGAGCTCTGTCAAGTGCCTCGAGAAGAGTGAGAAGCCATCGTCCATTTCAATGTATGCATGCATATTTTTTATTGTAAGCACCTGGACTTGGCACATTAGAGCATACATGACCCACATGATGGCACAATGGAATGGATTACTGTCGCCGGACATTATCATCCAGTGTGCACATGAATTGATTTTGATCTCAAACTTGTGTAGAGGCGAGCTGCCACGGAAGAGCACTAGATGGTTGACAAGCTTGATGAAGTCCTTGGGGCTCCTCCATCTCTCTGTATTGGTGATGCACAGGATGGGCGTCAATTTCCAGAGATGGCGCCAGCGCCGGGACAGGACACAGGTCTTCACGGCATCCTCGGCCGGCAGGAAGGACAGAATGTGCTGGAGGAGAGCATCCGGGAGGACGTCGATCCCGTCCTCTTCGCTGGCCTCAGCCATTCTCTTGCTCCTCAAGCTCTTTTGCTTAGGAGACATTCCGTCGAACAGGTGGCGGGCGACGCGGGCACTACCGCGCAAGAAGCGAAGAGCCGACTCACCAGGTGCAATGCGAGGTCCTCGCTTAATCAATCAGACGCGCGGCGCCCATGGCGGGGAGGAGGCCCAGCCAGCCGGGTGGCTGGCCGTGTCGGCGGTGCCTTCGACTTTGCCGTGGTCGGGGCCGGGGCGACGCTAGGACGATGCACCTTGCAGGGACGAGGCGAGGCGACGCTCGTGCCGCACGTGGGGAGGGGGACGCGGCTGCAGTAGCGCGGATCTGAGGAAGATTCGCCGGCGAGCTCGCCGGAGACGGCGGGGTCGTGGCGGTGGATGTAGCCAAAGACACGCTTTCAGGGCTCACTGCTCTTCTTCCACTCTTTTTGGTTGCCTTAGGGCCTGCGCTAGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.754529
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0090100.1 11 5557429 A G
Osa11LNT0090100.1 11 5557646 T C
Osa11LNT0090100.1 11 5557683 T C
Osa11LNT0090100.1 11 5557782 G T
Osa11LNT0090100.1 11 5558729 T G
Osa11LNT0090100.1 11 5558981 C T
Osa11LNT0090100.1 11 5559874 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa11LNT0090100.1 osa-miR812v Cleavage 4.0 8.369 1 24
Osa11LNT0090100.1 osa-miR397a Cleavage 4.0 23.255 1 21
Osa11LNT0090100.1 osa-miR397b Cleavage 4.5 23.255 1 21
Osa11LNT0090100.1 osa-miR168a-3p Translation 5.0 17.586 1 24
Osa11LNT0090100.1 osa-miR419 Cleavage 5.0 7.262 1 21
Osa11LNT0090100.1 osa-miR426 Cleavage 3.5 17.159 1 21
Osa11LNT0090100.1 osa-miR2095-3p Translation 4.5 21.601 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0090100.1 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0090100.1 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0090100.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0090100.1 11 qRRE-11 Resistance or Tolerance Other soil stress tolerance C496 C410
Osa11LNT0090100.1 11 fer11 Resistance or Tolerance Cold tolerance RM3701 RM552
Osa11LNT0090100.1 11 dc11 Resistance or Tolerance Cold tolerance RM552 RM3137
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