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

>Osa11LNT0091000.1

GCCAACACAGTTCACGCGCCATTTATTACTCTAGAGCACAGGAAGACAATAATGCTACTGGGCATACTTGAACACAAACCCTCCCTCCTCTTGTTAAAAGCTATTCTACACCCATGAAAATAAAACCATAGGAGAGAATGCAGAAACACAATACACGATTTACAAGGGCTACTCTGCAGACGACTGACTGACTATACAGGGGATTGGTGAGACTTGAGAGGTACAAAGAATTAGTTGGCTTAACCAGCCATCATTATAATAAGATCCTACAACAACCCCTACTAATTTACACAATCTACGCGAACCCGCCGCTTGCCATAGACGGTAGCAGCGCTCTAGCACTATAGCAACAAGACTAACACTACCAAATACTGACGATGTTGATGGCATCCATCCTCATCTTCGTCGATGTTGGGCCATCTTTGCCTGAGCCTGCTTTATCCTATCCGCATACATCGGGAGGCGCGTGATCTCATGGATCTCTTCTAGAAGCTTCTCTTCGGTGATATTATCTGTGATGCTCCTCATTACCTTGCGGTATGTGTTGATATCATTTGGAGTTGATTTATCAGATCTAATACGCATGCAGACCCAGCAGCCCTCTTCCTTATTCCAAGAGCACTCTACAATCCTCCCTGAGATAGAGGATGGATCTTCATTTGGAAATGCTATGCGGGAACCATCCATAAGTTTCTTTTTGCCTCTCTCATAAAGGAAAACAAGCTGACGATTGTCACCCCCAACCTCAAACAAAAAGTCAACAGAATTCATTGAAGGGTATTTCCACTTGAGAAGACCTTCATGGGTACGAGTTACATATGGATCATCCCAGCCCTGAAAAATAAGACCATCAGCATCATGTGAAAGTGATGGAATAAACTCCTTAAGTAGCTTCGTTACTGTAGAAAGAAGCCAAAAATCCTTTCTCCTGACCGAAAATAGTTCCATATCATATTTGTACATTGGGTTGCTCTTAACGCCACTCTCAAACTGTTTTTTTTCATAATAACGTGGACGAATTATTTCATCTTCAAGCAGCCTCCATCTTTCAGAAAATGGCAACTTGGTTTTTGACACGGCATCAAGTGCCATCAGATCATATGCTAAATACCTCCTCTTCAATCCTGAATCTGGTACTGTGTCTATAATCATTTCTCCATCAATCAAAGTCATCTCATGTAGTCCTTCATTAAGATTCCTATGGGGAAAGCGCATTTGAACTCTTCTGAAGCAAAAATTCCGATCAATCAAGAAACAGCCATCCCTCATTATAAGCATCATATATCGGGTTCCATCAGCTTTCCATGTAGCAAAGTAGTATCGCTGTCTGAGTAGTTGCAAATTCTCACTGTTAAGAGAGACAGGATGTGATCCAGGAAACTGTGCATGCCCTCTCACAGGGGGCATTTCCAGCAAGCGATAACATACGACACGCAGAGCATCTTGCTGATCATATGGTACAGCATCTCCTAGCACATCATCATTAGTGATAACTTTATCTTCCACCTCATTATGTACTGGTGCAAGATCACCATTCTCATCATCATCATCTTGCTTGGCTTCACCATTTAAATCAAGATCGGATGACCTTTTCCATTCTGGTGTTGAAGGGCATGTTATCATATGCTCAGGAACCTCATGATAAAATGAATACAGTGCTTCAATGTAGTCCCTCTTATATATACCAGGCGGTCTCCTTTTTGCAAATATGTTTATCGCCTCAGCGACGCAGGATACTTGTGTTCGCATAAGGTAATGGATAATCATGAAACCAGTACGATTATGACCATGGGTACAGTGAACAAGAATATATTTAGGATTCTTTGACTGCTTCTGTCGGTCAAGAAACATCATCACCTCATAGACAAACCAATTAACAGATTCATTATCAGGTACAGCATCTCTTCCCTTGCATGGAATCTTGACATGCTTAATACCTTGCCTTGTCCATTCTGCAGGTGAGTAATATCGAGTAGTATTTGTCAAATCAATCACCAAACCTATTTCACGACCAGCTTTTCTTTGTTTATTAACTACTTGTTTGGAAGAATATCTTTTCCCAGGAGGCACCAAGTCATTGAATGTTTCATCAAGAGGAACCTTGGAAGGTATGATTTTGTCTATTGGCTCACCAAATGCTGGACAATTCATCCAACCATCAGGTGCCTCTTTTATTCGACCTCTACCAGCTCTGTTATAAGGTGCATAATCGTTCCTAATCTGCTGAGAATGTAATCTTGAGCCTTCATCTTGTTGCTCTCTCTTTAATTTTTTGCGTCTCTCTTCACGCTCCCTTCGCATTGTAGCAACAGCAGACTCAACATGCTCCTCCTGTGCAAAATCAACCTCGACCTGTTGTTCATAAGGCTGTTCATCTTCCTCAGGCAATGGTGAGGCATTTAAATCCATTGAGAAGGTCATTCAACATCCACTACTTCATATATCCTCAATAACGTTTTGAGATTTGCACCTCGCGCCGGAGCGGGGGGGTGCGGTGGTGGTGGTGGTCAGGGAGGGGGCGCTGTCGTCCCTCCCTCCTCCCGCCGAGGGAGGGGCGCGTGCGGGACGGCGGCGTCGCCGGCGAGCGGCGGAGAAGGGAGGGGGGTTTGGGCGGGGGTTGTGGTGGTGGGGGATCTGCGGACGAGGGTGGTTAGGGTTTGGGGGGAGCCATGGGATGGAGTGGAAAC

Coding Potentia
Explanation CPC Score
noncoding -1.09383
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0091000.1 11 6119832 C A
Osa11LNT0091000.1 11 6120296 A C
Osa11LNT0091000.1 11 6117147 C A
Osa11LNT0091000.1 11 6117677 T C
Osa11LNT0091000.1 11 6123513 G A
Osa11LNT0091000.1 11 6115103 G C
Osa11LNT0091000.1 11 6115192 T C
Osa11LNT0091000.1 11 6116576 A G
Osa11LNT0091000.1 11 6117122 A G
Osa11LNT0091000.1 11 6117585 G A
Osa11LNT0091000.1 11 6117663 A T
Osa11LNT0091000.1 11 6117770 T C
Osa11LNT0091000.1 11 6118518 G A
Osa11LNT0091000.1 11 6118563 T C
Osa11LNT0091000.1 11 6118619 C G
Osa11LNT0091000.1 11 6118763 T A
Osa11LNT0091000.1 11 6119751 A G
Osa11LNT0091000.1 11 6120094 T C
Osa11LNT0091000.1 11 6120213 T A
Osa11LNT0091000.1 11 6121055 G T
Osa11LNT0091000.1 11 6121429 G C
Osa11LNT0091000.1 11 6122375 G A
Osa11LNT0091000.1 11 6122405 A G
Osa11LNT0091000.1 11 6124406 G A
Osa11LNT0091000.1 11 6124576 T G
Osa11LNT0091000.1 11 6124594 A G
Osa11LNT0091000.1 11 6124610 T C
Osa11LNT0091000.1 11 6124611 A G
Osa11LNT0091000.1 11 6124758 A G
Osa11LNT0091000.1 11 6125122 T C
Osa11LNT0091000.1 11 6125173 A G
Osa11LNT0091000.1 11 6125897 A G
Osa11LNT0091000.1 11 6126481 A G
Osa11LNT0091000.1 11 6126673 G A
Osa11LNT0091000.1 11 6117755 G C
Osa11LNT0091000.1 11 6115949 G A
Osa11LNT0091000.1 11 6122792 C G
Osa11LNT0091000.1 11 6122819 A G
Osa11LNT0091000.1 11 6123867 A G
Osa11LNT0091000.1 11 6123915 G A
Osa11LNT0091000.1 11 6124304 T C
Osa11LNT0091000.1 11 6124405 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
Osa11LNT0091000.1 osa-miR168b Cleavage 5.0 12.52 1 21
Osa11LNT0091000.1 osa-miR172b Cleavage 5.0 14.429 1 21
Osa11LNT0091000.1 osa-miR166g-5p Cleavage 4.0 16.955 1 21
Osa11LNT0091000.1 osa-miR1440a Translation 5.0 19.481 1 20
Osa11LNT0091000.1 osa-miR1853-5p Translation 4.5 16.692 1 24
Osa11LNT0091000.1 osa-miR1882e-3p Translation 4.5 12.669 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0091000.1 11 fer11 Resistance or Tolerance Cold tolerance RM3701 RM552
Osa11LNT0091000.1 11 dc11 Resistance or Tolerance Cold tolerance RM552 RM3137
Osa11LNT0091000.1 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0091000.1 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0091000.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
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