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

>Osa12LNT0118100.2

GACAAAATAGAACTAAGATTAACATTCATAAGATTCCAATCCTACTCGCCTGCTCGGTAAGGCAATAGCCGCAAAAGGTAAGCAAACACTACTAGTTCATTACATCGCTAAGGCTAATTTATTATCTCATCGTCATGTCATATATATTTTGGCAGAAGGACAACCAGCACATGTATTAGATGGGCACAAAATGAAGCTAACAGAAGAACCTAATCGAGCAATTCAGACATTGCGTTCTTCCTGTTGAATGGATCGGTAGCAGCAAGCAAAGACGCCACAGCCCTATTGGGGAAAATGTCATCAGCCTTCATCCTCTCCTTGAATCCATAAGGTGGGGTCTTTGCATTCAGATATGCCTCAAGAAGCAGCTGATACTGTCTAATCCTCCCAGTATAACCCATCTGCCGCACCTTGCTGAACAATTTCTCTGCATTATGGACGTCTCCTTTCTTGGAATAACTATCAAGCAGCATCAAGTATGTGGTGTACATAGGCTTAATCTTGTTCTTATATGATAGCTTATGCAATATGGAATCAGCTTTCTCCACCTCTCCTGCATCCGAATAGAGCTTCACAAGTGAATCCAATGTATAGGGCCCTAGTCTGCAACCATCATCACCCATCCGCTTTGCTAGCTCCTTCCCCTTGTCAAAAAGCTTTTTGTTGGCATACACCTTCAGCATAGCATTGTAGTATTTGGACGAAAGTGTCTTCCATGTCTTGAACATATTGTCAAATATCTCCTCAGCCTTTTCAACATCCCCAAGCTTACCAAAAGCCTCTATTGCAGACATGCACTCATCTAGACGAGCATTGGCCTCACAAACCTTCCAGATCCTTTCAACATCATCATTTTTGCCAAGAAAAGCATACAGGGGTAAAACAAATTTGCAAGCAGAACGGTTTTCATTGATATCATCCCCCACCATTTGCTCCAAAATTGCCTCAGATTTCTCACGATAACCACCAAATATGTAGTGCCTTGCAATTGTGGCTTGAAACAGAAGATCTGGTTCAATTCCATCCGCTTGCATTGCCTGAATGACCTTTTCCATATCTTCAATATCTCTAGCAGCACCCTTGGTATCTACAAGGAGCTTATAAGTGAAGAGGGAAGGCTTCACATTCTCCTTTTCCATCATTGTGAGAACATCACCAAGCTTCTTCTTGTCCACTCTCTTGTAGAGTAGCAGAAGCTGATTGCAAGAAAATACGCTAACTGGAAATCCAAGGTCCTTCATCTTATTGAAGACTTGTTCTGCTTTTTTCACATTGGCTATAGCCACACAGTTAGCCAAAAGAGTCCTGTATACAATCTCACCCCTATGAGATGCAGGAACATTCTCAATGTACTTTTCAGCTTTGTAAATACTGTGGGTTTTAGCTACCAAATCCACGCGTGAAGCATAATCACGTTCTCCAAGATCAATTAGTTTGGATTCTTCAACATACTCCAGAAGCTGCAAGGCTTTGATGTAGAGCTTCCGCCTCCGAAGAATAAGAAGGACATAAAAGAGCTCACTTCTATCCAATGTATTGCCATCATTAAGCCATTTTTTCAATGCTCCAGCGACATCAACCCTTGGAGATTCCAGCAAAGCCTTAAGAAGAGTGGATTGTGACTTCTTTATCGGCTCCTCAGGTTTTGCATCAGCCTCCACTTCAGACAAGCCAATTGCATCAATGGTGTCCTCATCAGAACTCTCATCGGATGTCAAATCTAAATCCTTTTTATGAGCTTCTGGTGGAACCTCCAGATCAGAAAACCCTTCCTCCAACTCATCCTGCTTATCACCAGAACTTGCACCGGCCTGAGAAGAGAAACCCCTACTCCACATGAAACGGCCTGATGAGAATGATGGTTGGCAGACCAATGGCTTTGGTTGATGACAGCAATCCAATTTCTGACAGTCCCCCTCATGATGCTCTTCCACATTCTTTGCATCTGCATTTAGAATTACTTCAAGGTTTGCACAACCACGGGCACTCAAAGCTTGGTGGGCACGGACCCTGAGGGGGTTGCCCGCGCGGCGGAGCGCCCACATGGCGGCGGCGGCGGACGAGGAGACGATGCAGTGGCGGCTCTAGGATCGATTCGTTGGGTGGTCCTACTATGAGGAGCTGTTTAGGGCTTGAGGCATAGACTCGTCGTCGTCGTCGAGCTCGAGCAGGACTGCAGGAGGGAGAGGGACCCGACGCCGCCGATGGGCGACGGCCGGCGCTGTGGGCCTGTGGCGCAGAGCGAGAGCCGAGAGGAGGCGAGGAGCGCAGCGGAGGGAGAGGCGGCGCGTGCACGGGGCTTTGAGCCCTCTCCTCTGCCGGCTAACCCT

Coding Potentia
Explanation CPC Score
noncoding -1.21238
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0118100.2 12 3567800 G A
Osa12LNT0118100.2 12 3568920 C A
Osa12LNT0118100.2 12 3568991 A G
Osa12LNT0118100.2 12 3571105 T C
Osa12LNT0118100.2 12 3571940 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
Osa12LNT0118100.2 osa-miR5826 Translation 5.0 21.702 1 24
Osa12LNT0118100.2 osa-miR7693-3p Translation 3.5 13.237 1 22
Osa12LNT0118100.2 osa-miR159a.1 Cleavage 3.0 10.937 1 21
Osa12LNT0118100.2 osa-miR159b Cleavage 3.0 10.937 1 21
Osa12LNT0118100.2 osa-miR159c Cleavage 2.0 10.937 1 21
Osa12LNT0118100.2 osa-miR159d Cleavage 2.0 10.937 1 21
Osa12LNT0118100.2 osa-miR159e Cleavage 2.0 10.937 1 21
Osa12LNT0118100.2 osa-miR159f Cleavage 3.0 10.937 1 21
Osa12LNT0118100.2 osa-miR166g-5p Cleavage 3.0 18.014 1 21
Osa12LNT0118100.2 osa-miR417 Translation 3.5 14.341 1 21
Osa12LNT0118100.2 osa-miR419 Cleavage 4.0 14.962 1 21
Osa12LNT0118100.2 osa-miR1428e-5p Cleavage 4.5 21.042 1 22
Osa12LNT0118100.2 osa-miR1428f-5p Cleavage 4.5 21.042 1 22
Osa12LNT0118100.2 osa-miR1428g-5p Cleavage 4.5 21.042 1 22
Osa12LNT0118100.2 osa-miR2874 Translation 5.0 18.036 1 24
Osa12LNT0118100.2 osa-miR5524 Cleavage 4.5 11.447 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0118100.2 12 nan Physiological trait Eating quality RM20 RM101
Osa12LNT0118100.2 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0118100.2 12 Pi-4(t) Resistance or Tolerance Blast resistance nan nan
Osa12LNT0118100.2 12 gy12 Morphological trait Seed RG869 RG98
Osa12LNT0118100.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0118100.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0118100.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0118100.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
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