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

>Osa12LNT0124600.2

CCTCATCAATAAACAAGCGACTTAATTCTAGTCTATAGTAATCCAAATACAATCCTTTGTTATATCTAGCGATCTCTACAATCTACATTGTCTATGTATCCAACATAATTCGCACCTCACCATTACTTTTAGGATAAGTGATTTTGCTCTGATCTGCCTCTGTATTCGTGGGAACTTGCTGCTGCTGCTCTTTTATCTCCTTCCCTTTTCCCCAGAGGAAGGAATAGAGGCCAATGATTATCATAAATGCCCCTAGCAAGCTCCCGACAGAGATGTCGCTTCCAAGCAGCATCGAGTCAAGGACGACGGTGATGATCAGCGCAAGCGAGTTGAACATGGAGGGGTAGGTTGGCCCTCGCCGTGACACCGCCCACGTGATCAAGCAGAAGGTGGCAGCCGTGTTGAAAACCCCCGAATAGATGATGGTGATCAGCTGCAGATCCCAGTGGAGTGCCCATGCCGACCGGTCCCGGTCGACGGCGATCCCGATCACCACCGCCTGGATTGTCCCCATCAAGCATGCGAGCATCGTCGAGAAGTACTTAGATGGGAACTCCTTGTTCACTTTGGCCTGAACGATGAACCAGAAGGCGTAGCTGAGGCAACTGCCGCAAAGGAAGAGCGTCCCGATGAGCATGTTGTGGTGGGTAGGGAAGGTGGAGTCGTCGCTGCCGCCGATCGCCCGCAGCTGCGCCGGCTTCAGCAGGTGGGTAGGCCACAAATGCAGCAGCTTGCCCCTGTACAGGCTCACCACCATGGTGCCCACAACACAGATCACCGTGCCAATCACCTTTATCATGCCAGACCGCGTCTTCAGCTTCAGCTTCTCCAATCGGAAGATCGCTGCAATGATGAAGGTAACGACGGGGACCAAATTTAGGAAATTGACGGTGTATCCAGCATTGGTAGCGCGTAGGCCGTAGTAGTGTAGCCCCATAGCCAAAACAATTCTCCAGTAATAAAAAAAGAAACCAATTAAATCAGATTTTTCTGGGGGTGGGAGGGGAGAGGATTTCTTGTTTTGAGGGGTGTAGTACTGACCCGAACAAAGCGTTGAAAAATATCCAGCCCAGTACCTTGTAGTTAACCTTTTTCATCATTTGCCTCTCGAACCAGAAGGCGAAGGGTAACATGGTGACGGTGCCAATGAGGTTGCGGTATGCGAGGAGGACGAAAGGTGCCATCCCACTATTGAATGATAGCTTCGCGAGGAGGAGGGCACCTATGGTGAATAGCTGGACCAGTACCATGCTCAATGGGAGCAGTAACCGCTCCGCCATCCCTGGCTTCGTCTTCGTGGTCATCGTCTCTGCCATCATGTTGGTACCCTTAGAGCTTTTTCAAGAGAGAAGATAAGTGTTCATTCCATTGTAGCCACCCCTTCTGATCACTCTCGCATGGTCTGCAACAACGTCAGCATCAGTTGGGAATAAAACTAATTGAGCGATTTGCAACAAGGTCATCAGCATCAGTGGGGAAAACCAATTGAGCAATTTTTCAGGATTAAGAACTGTAATCACTCGGGCCATATCCACACCAAAGATGATGAGGAGATGTCCACAGCGACAACTTCAGTTGAGCTTAAATCTACATGCCACCAATTCCTCAAATACTACTACTTCTAAGCCAGGGGCCTGAATTCAACTCCCTATGGAAATGGTGATGGCAAAGTGAGAACCAAGTTTGATATGATCAAAACAGAAAGAGGGCGATGGTAGGGATTGATAGATGATGGAAGCAAATATGAGTAGAGAATATAGCTCGCACTAGCCGCGCCGAATTGATGGAGAGTAGTTTGGCTAAGAGAGATTGAGGTTGGAGAAGAGAGGGGGTAATTGAAGCCTGGAGTGCAGAGTGTCGAGGAAAGGGATGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.860936
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0124600.2 12 10999506 C T
Osa12LNT0124600.2 12 10999509 C T
Osa12LNT0124600.2 12 10999761 G A
Osa12LNT0124600.2 12 11000086 T C
Osa12LNT0124600.2 12 11002222 T C
Osa12LNT0124600.2 12 11002458 G C
Osa12LNT0124600.2 12 11002941 A C
Osa12LNT0124600.2 12 11003771 G A
Osa12LNT0124600.2 12 11003962 C T
Osa12LNT0124600.2 12 11002057 T C
Osa12LNT0124600.2 12 10999518 T A
Osa12LNT0124600.2 12 11000880 C T
Osa12LNT0124600.2 12 10999410 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
Osa12LNT0124600.2 osa-miR5536 Cleavage 4.5 14.076 1 22
Osa12LNT0124600.2 osa-miR5832 Cleavage 2.0 19.951 1 21
Osa12LNT0124600.2 osa-miR1440b Cleavage 3.5 14.04 1 21
Osa12LNT0124600.2 osa-miR168b Cleavage 5.0 20.402 1 21
Osa12LNT0124600.2 osa-miR529a Cleavage 5.0 12.27 1 20
Osa12LNT0124600.2 osa-miR1424 Cleavage 5.0 20.843 1 21
Osa12LNT0124600.2 osa-miR444d.3 Translation 4.5 16.373 1 21
Osa12LNT0124600.2 osa-miR1850.3 Translation 4.5 16.079 1 22
Osa12LNT0124600.2 osa-miR1871 Translation 5.0 24.479 1 24
Osa12LNT0124600.2 osa-miR2919 Cleavage 3.5 22.556 1 19
Osa12LNT0124600.2 osa-miR3979-3p Cleavage 4.0 21.926 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0124600.2 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0124600.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0124600.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0124600.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0124600.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0124600.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0124600.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0124600.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0124600.2 12 nan Morphological trait Seed RG543 RG81
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