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

>Osa12LNT0122500.2

GCTCCTGTTCAAATAGAATTCAAACTATTACATGGATCATGAGAAGAAAATAAAATGGTGCCAAACATAAATAAAAACAACCGTAGCAAATGGAATACAAATACTGTGTCCAGAGAATAGAAGATCTACACACTTGCGTCCAAGTATAAATTTACATCTTGCAGGACTTGGCCCTCACTCGATTTACAAGAGGAAATAATGTCTTTGAAAAATGCACTGCCTTCTGAAGCATCAACATTAGGTGCCTAAGACCGAGGGAAAATCCAAAAGAAGCTTGCATTGAGTGGTTGCCATGGTCAGCAATCTGAGTTGATTTCTTTTGCTGGCAAGTTATCTTCAGGACTTGCATGCATCACAGCACCCCAATCAATTTGCATAATCCAACATGAGTGTAGTTCAAGCCTTAAGATAGTTTAAACTCCAGAGTAGGCCCCAGCCGTGCTCCATCGTCACCAAAGTTCAACTTTCAAGAATTGCTCTCTCACTGTAGAACATCTTCTTTAGCAGAAGAATCCAGAATATGGTTGTGGCAAACATGAACTTTGGAGCATTATAGCCTGGAAAGCTGGACCTCTCTTTCACCACTGCAATTGTGATGTCAGTTTGTCACCCCGTACATAAATATGATGGCCCTGTATGGTCGAGAAGGTTGAGTATGGATTTCAGAAGTCAGAACTACTCCAATCTATCTCATTTCATCCATTTCCGGGACAGAGTCTATGACCAAATATACCTAATTGACAGACATAATAGACTGATATATACTCATCTTAATGCTGATTGCTGTCAGGTCAAGCCGCAAAATTTCTAATATGCAGCTGATGATTACTGAACTAGTTATGCCTGCATGCCACTGTAATCCTTATTTACAGTAGTGCGAGATTTTGTTAATACGGTGACAGTGTGACACCTATCAGTATGGGACCATTTGCCATACTCTGTTGCTTTATCGAATTTGTTACAGGTGAAAAGTTTTGTACCACCACAGAGGTGCACCATCTGTTACCCATCCCCCACAAGAAAAGCTTGCAACTTGTTGCCATCCTGATCCTGTACCCAGCTATAGGCTGGATTTTTCTGTACTTTCCTCGATTTCATTAATTTCCTGATCTTGTTTGCTTCATTCCATCTCCCAGTCTCAGCATACATGTTTATCATAAGAGTATAGTAGCCTGAATGCTCTGGCTTCAATTCAAACAAATGCTCTGCTGCCCATTGTGCTAATTCGATATTTCCATGTATACGGCAAGCCCCAAGCAATGCTCCCCAAACATCGGAATTTGCAGGAAAAGGCATGTCTCTGATAATTTCAGCACATTTAGACAGTTGTCCAGCACGCCCAAGAAGATCAACCATGCAAGCATAGTGCATTTGCTGTGGCTCAATATTTTGAGCAACCATCTGACTGAAGTATTTCTTCCCTTTGTCTACAAGCCCACCATGGCTACATGCTGCAAGCACTGCAATGTAGGATACATGATCATAGTCCAGACCATCACCTTTCATCAGTTCAAACAATTCAAATGCAATATCAATTTGACCATGCATCCCATATCCCAATATCATAGTATTCCATGAAGCAACATCCTTCTTTGTAATCTTATTAAAAATCTTTGATGCAGTGACAAGCATTCCACCTTTAGTGTACAAGTCCAGCAAGGAATTAGAAAGAAAGGGATGGCCACTTAACAATCTCCTAACCAAAACACAATGAATTTCTTTGCCATGCTTAAATACAGATAAGTTGGTACATGCTGATAGAGCTCCCATGAAGGAAACAGCATCATAATCAATTCCAACAGACCTCATCTGCTTAAAAAGAAGAAGAGATTCAAAACACCATGGACTCTGTGAATATCCCAAAATCAAAGTATTGTACGATACATCGTCCTTCTCTGACCTTTCAAAAATATTCCGTGCCAAGCTCAGCTGTCCGCATTTGGAATACATATCAATCAGGGCATTTGATATGAACAAATCGAACATTAAGCCTCTACGGATCGACCATGCATGGATCTGCTTACCCATCTTTAGAGAGGCCATCCTCGCACAAGCTGGAAGCACATTCACTAGTGTGATAGAATTTGGGCATTCCCCACTTTTTTGCATATCTGTGACAAGCCTGAACGCCTCAGTCTCAGCTCCATTTTGCACAAGATTTGCGATCATTGCATTCCATGACACAACATTGCGGTCCTTCATTTGTTCAAAGATGGTAGATGCTTTCTCCAAAGAACCAAATTTGGCATACATATCAACAAGTGAGTTGGCAACAAAAATATCCAAGTCCATTGCTCTCTTTATGCTATACCCATGCACCTCCCTTCCCAAATCAAAACTTCCAAGCTCAACCAATGCAGGAAGCAAACTAGACAATGTGATAGAACCTGGCATGACATTATGCTCTGACATTTTCCTAAACATTCTCAGCACATCACCATAAAACCCTGCATTAAGAAAGCATCCTATTGCAGAATTCCAAGAAACCTCATTTTGTTCCAGCATTCCATCAAACACCTGCATCGATGCCTCAACATCCCCAAACTTACCATACATATCAACCAACGCATTCGCGAGATTCACCATGGTGTTCAAGCCAACTTTCACTGCCAACGCATGGATGCTCAACCCAAACTTCTCCTCTTGCTCTGTGCCGCAGGCAGGCACAACTGACACTAAGCTTGCCACGTTCAAAGGAAACCCACTCCTCATCATGCTCACCAGCGCCCGTCTCGCGTCATGAAACATACCGTTCACCAAGAACGCTGACACAAGCGAGTTCCACGAGACGACGTCCCGCTCAGGCATTTCGTCGAACACCCTGCGCGCGTCGCAGGCCTTTCCACAGGCCGCGTAGAACGCGACGAGGGTGTTGCCCGTGAAGACGTCAGCCAGGTGCCCCCGCCTGAGAGCCGAGGCGTGCAGCTCGAGGCCCTTATCCTCGGCGGAAGCGACAGCCGCGGCGGCGGCGTGGAGGGCGAAGGGAAAGGTGCGGTCATCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.987038
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0122500.2 12 8824127 G C
Osa12LNT0122500.2 12 8823832 G A
Osa12LNT0122500.2 12 8824027 T C
Osa12LNT0122500.2 12 8824399 C A
Osa12LNT0122500.2 12 8824524 G A
Osa12LNT0122500.2 12 8824601 A T
Osa12LNT0122500.2 12 8824754 C T
Osa12LNT0122500.2 12 8825926 A G
Osa12LNT0122500.2 12 8826359 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
Osa12LNT0122500.2 osa-miR815a Cleavage 4.5 7.336 1 21
Osa12LNT0122500.2 osa-miR815b Cleavage 4.5 7.336 1 21
Osa12LNT0122500.2 osa-miR815c Cleavage 4.5 7.336 1 21
Osa12LNT0122500.2 osa-miR1852 Translation 4.0 17.391 1 21
Osa12LNT0122500.2 osa-miR1861b Cleavage 4.0 14.254 1 22
Osa12LNT0122500.2 osa-miR1861f Cleavage 4.0 14.254 1 22
Osa12LNT0122500.2 osa-miR1861i Cleavage 4.0 14.254 1 22
Osa12LNT0122500.2 osa-miR1861l Cleavage 4.0 14.254 1 22
Osa12LNT0122500.2 osa-miR2866 Translation 3.0 14.384 1 20
Osa12LNT0122500.2 osa-miR2878-3p Translation 4.0 18.561 1 24
Osa12LNT0122500.2 osa-miR5081 Cleavage 5.0 16.818 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0122500.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0122500.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0122500.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0122500.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0122500.2 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0122500.2 12 nan Physiological trait Eating quality RM20 RM101
Osa12LNT0122500.2 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0122500.2 12 rv12-2 Resistance or Tolerance Drought tolerance RM491 RM101
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