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

>Osa12LNT0120500.1

TTTAGAAACAAACATCAATGAAGAAATAAAATCAGCAGGATCATCACAACTGATTTCTGTCACGACAGGCACCAAAAGAATCTTTAGTCACTCATCAGGAACAAAATCCACAATCTTTCTTCTGTCAAAAAACGAGGGATTAAACTTACATTCATACCTTTTGTATAGGCCACCGATACACCCTAGATACAGCTTACAATGCTCATTGAACCCTACATGCAGTAACAGTGTTTCTACGCGCTACAAAACTCTTCGTAAACTGGTGAATACTCACCTTGATGAGCCCACAGCCCAGTAAACAAAGAAGCAGATCACCTAGTGTGAAAAGGTAATCTATGTATGTATACGTCAAATCATGAAAACAGGAAATCTTCTATTTCCTCTGTGTAACATCCTACCGTATGCCTTTCTCACCTGTGCAAGGGGAACTTCTCAACACAAAAGGGAGTGGATTCGGTATCAGCATTAGTACGGCGAGTAAGAGATGGAGGGGACGGGCTGGACTGTCAGGAGGACAAACGTAGTGCGATCTCATGAAGGAGCAATCTCTTCTGAGCAGCATCAATCACACCATTGCACTCTGCATTCATGAGGACCTCGCTCATGATAGCAGCGGCATGCCCGGTGGGTTCTTCGGATGTCCTCCTCAACATGAACATCTGCCCACGATGAGATATCTCAAGGCACCCGGGTGGCTGGATCCATGGCTCACCATCAACCTGAACAGGGAATGAACTGTGGAGATGCAACCTTATAACTTTCCCTTGGGCTAGCCTGTGTGCTCTAGAGAGTCCCACCTGCAGTTTTCCTAGATGCCACGTCCCAGATATACAGACAACCTCAAGCATTTTGTCATGCATGGATTGCAAACCAAAATCATCATCATGTTCATTGTCGTTTTGCCAAAGATCAACACCGCCCATGTAGCTAGGAATGTTCAGAACAATCACACCTTCTGCGTCCTCTGGAATTTCGACGTTCTTTCCATCAACTTCAAGACTAACATGCCATGGTAAATCAGAACATGACCTATCCATGATATCCTTAGCGCCTTCTCTAGCATATATCAGCTTGTTGACAAACTGGCTGCAAAATTTATCTGGTTTTTCCTCTCTCGTAGTGTGGAAGTCATATGCAACCTTGGCATCACATCCAACACCTATATAATTAGTCATAAATTTAACTTGCTTGGTACATTGATCTTCTGCTCCATTCTTCTCTTTGATGGCAACATTCCAGCGATCAAGCACGGTAACTGCTGCGTGGTCAACATCATTTAGAAGTGCACATATTCCCCCTTGTCCTTCAACAGAAGACAGACCTCCACCCCAGCGCATAACACGAGATAGGTCATTTCCTGTTCCTAATGGAAGAATGGAAACAGGAGGAGGAGATTCATAGTTCTGCTTTTCAATAGCATCAAGAACCCATGCAACAGTCCCATCCCCACCACAAACAAGGATTCTGAAGTGTTTTACATTGTGGAAAAATTGCAATCCAACTTCAGGTCCCTGAGAAGCACTAAGCTCAAATATCTGGATAGGATTTAGCAACATGTTAAGCCTTCTTCTAAGAGAAGGTCCATTTCGTCCTCCACTCTTGCCGTTAATGAAAACAAGCAGTGGCCTTGAATCTTGTGGCAAATCAATGATTTCATACTTTTTCTTCCCTCCATTAGGGCTGTCATATCCATGTGTTTGCTTGACAGAATCCCCACTAGACTTATGGTTTGCCAGCGCATACTTTCCATTCAAGTTCTGCAGTCTAGCAAACCCTTCAAGCACAGAATCAAGGATAGAGCTGTTTGTGGGGACTGGACTTGTCTTACCACCAGGATGGTTGTTCATGCGTTTCTTGTTGCCTCGCCTCTTAATCCTGCCCCTAACTGATGAAGTGACAAGACCTTCCTTGATCGAGTTGAGCATTCCAGTAATTGCTGGTCCTTGGGCAACTTCTTTCACAGACAGAGGAGGAACAATGAGCCTCCTGAGAAGGCCTAGATCACAAGTATTCCCCGTCTCCTTTAACAGCTTTGCATGACAATCAACATGGATCTGCCGCTGGCACCACAGGCAGCGCCATATTGGAGAGACGCCGAGAAATGGCACACCACATGGCTCATCGCAGTAGTAACAGAAAGAGGACATCTCTGGGTTGTCATCCAGCTCCACCCACCTCTCCGACCAGTGATGAAGCAAGGTGGAAGCACCATGCTGTGAAACACACTTGCAGTCCTTCTCGGCGCCACGAGAGCAGCCAGAATGGGCCGCCACCCCACACACCGAGCAGCGGTGGACCACAACGGCATCGGCACCCCGAGAGCCCACACCCTGAGCTGTGGTCAGGGACGACAGGCACACGCAGCACGTCGAAGGCTGGCCGCCGCGGAAGTAGTCCTCGGTCCAGGTGTGGCCGGAGCTGGGGCACCGCAACGACTTCCACGCCGCCTTCTTCTCCCTGGCAGCCGCCTTGATCCAGTACAGCGACGCCGCCCTCTGCAGCCTGAGGAGGGCGTAGATGAGCGCGGCGAGGCCGAAGGAGCCGGCGGTGATGAGCCAGCCGAAGAACTGGAGCCCCGAGGTGTCAACCAAGTGAGTCATGTTCACCAGCAGCGATCCCACAAGGTCCATCCCAATTAGCCGCCAGGCTTGACAGCCTCAGAAGCAGAACCCTCGATCGGCCTCGTGGCGGCGGGGGCGCGGGCGGGTTCAAGGGGTGGAGCAAACCCTAGCTCTCGCTTCAGCTTCGGCTGGCGGCCCCTCGCTGGCTGGACTGCGGCTTCGCGGGTTTCTCCGCCGCGTCGGTCGCGTCGTGGTGGAAGGGAGGAGAGGAGACGGAGAGGATGGGGAGAGGCCGGGTTGGCCGGGAGTGGCGTTTTAAAAAGGAAGGGTGCGAAAGCGCGTGCACCCGTGTTTCTC

Coding Potentia
Explanation CPC Score
noncoding -1.01429
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0120500.1 12 6732045 A T
Osa12LNT0120500.1 12 6729699 G A
Osa12LNT0120500.1 12 6729724 T C
Osa12LNT0120500.1 12 6729895 A G
Osa12LNT0120500.1 12 6729949 C A
Osa12LNT0120500.1 12 6730019 T C
Osa12LNT0120500.1 12 6730130 C T
Osa12LNT0120500.1 12 6730363 C T
Osa12LNT0120500.1 12 6730364 A G
Osa12LNT0120500.1 12 6730472 A C
Osa12LNT0120500.1 12 6731674 C T
Osa12LNT0120500.1 12 6732226 A G
Osa12LNT0120500.1 12 6732434 A G
Osa12LNT0120500.1 12 6732543 C T
Osa12LNT0120500.1 12 6733299 A T
Osa12LNT0120500.1 12 6733311 T C
Osa12LNT0120500.1 12 6733405 A G
Osa12LNT0120500.1 12 6733540 A G
Osa12LNT0120500.1 12 6733855 C A
Osa12LNT0120500.1 12 6734057 C A
Osa12LNT0120500.1 12 6734076 G C
Osa12LNT0120500.1 12 6734217 A G
Osa12LNT0120500.1 12 6733347 A G
Osa12LNT0120500.1 12 6732646 C T
Osa12LNT0120500.1 12 6733344 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
Osa12LNT0120500.1 osa-miR5528 Translation 4.0 19.555 1 21
Osa12LNT0120500.1 osa-miR5788 Cleavage 4.5 14.28 1 21
Osa12LNT0120500.1 osa-miR818f Cleavage 4.5 16.89 1 21
Osa12LNT0120500.1 osa-miR1858a Cleavage 3.0 17.456 1 21
Osa12LNT0120500.1 osa-miR1858a Translation 4.0 15.711 1 21
Osa12LNT0120500.1 osa-miR1858a Translation 3.5 24.296 1 21
Osa12LNT0120500.1 osa-miR1858b Cleavage 3.0 17.456 1 21
Osa12LNT0120500.1 osa-miR1858b Translation 4.0 15.711 1 21
Osa12LNT0120500.1 osa-miR5147 Translation 5.0 14.142 1 21
Osa12LNT0120500.1 osa-miR1858b Translation 3.5 24.296 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0120500.1 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0120500.1 12 gy12 Morphological trait Seed RG869 RG98
Osa12LNT0120500.1 12 rv12-2 Resistance or Tolerance Drought tolerance RM491 RM101
Osa12LNT0120500.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0120500.1 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0120500.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0120500.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0120500.1 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0120500.1 12 nan Physiological trait Eating quality RM20 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