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

>Osa12LNT0130500.2

GACATTCGCATGTGGTAAGTCAATCTGTGCCCTCCAAACAATATTACAAGCATATATAGTAGTTGCCAATGTACCCCACGCATTTAAATTCTAGTGATTAGCAAGTGACATTAACACCTAGAACACTGAGTACAACCACAAACTAGGTTCCCAGGTTCCAAAATCGATTTGTCCACAAATTTAAGAAATGAAGATGGTAACTGCATGCACTGTTGTCCTATCTTTGACACCATTTGATCTTCACCTAATAATATTAGCTCCATGACCTCACAAAAGCACCCAATCTCATGTAAATCAACCCATCTGAAGTTTCAGCCACAAAATTCTAGCGGTTGGATTAGCACTGATAAAGATTTCTCTGTTCTGAGCATCCTTAAAAACACTAAATGACCGGGCATTTTCCTCAGGGGATAGTTCATTCATTGTGCTCAAGACATCGATACATTTCTTGATTGAAAATTCATCAACTTGCTTTGTAGCCTCTTTTTCCCGTACCATTTCCTCCTCAGCTTGTTTATGTCACAGCTCTATGTATTTCTCCATTGCATCAGCCACATTCCCATTTTGCTTATGTCTTTTTGGGTTCTTCTCTCTTTTATCCTCAGGAGGTTTCCTTGATGTACTGACAGTTTGTCTTCTTTGATTTAACTGATTTGACACTTCAACTTTTGATTGTTCACTTGCTGTGATTGGATCATCATTGTTTAGGTCATCTTGATTGTTCTCCATCAGCAAATCATCAGCACCTACTTGTGTAACAATATCATCTTCTGTGTTTCTTGACTGATCTAGTGTATTTGTTGGCTGAAGGGATGTAAAGTTCAAGAGGCCCTCGGCAGTTTGACCATCATATAGTTCTCCTAAAGCTTCAAAGATTGGAAATGGTTTGTTGCGGAACTTCTTAGCTCGAGGGAAAGAATGAATAATATTATCCCAAACTGCAGGATCATCAGCAATAATCATCCCGAGTTTTTCGTCCCAAGATGCCCCACTTTGTGTTCTTGCATCTTTCAAGCACCTGTAGTCTCTCTTAAGCTCCTTTTCTTTATCTTGAATTTGTCCTAGACAAGCTGGTAGAAGATGACGACGAGGTCCTGGAGGTTCTTGTTGGGGACGAGGTCCTGGATGGTGGAGACCGAACGGAGAAGGCCACACCGTTGTTGAACTCCGGCAGATCTGACGAGAGGCGGCGTCGTTTCCGGCGAGAGGAGGAGGCCAAAGTGACGGCAGGCGCCGGCGCGAGTAGATGCGCGGCCCACCGCCGGCACGCGATGGGATGAGCAGCGGCGGCGCGGGCGTGGCCCACCGCGGCGCGCGTCTGGACGAGCAGCGGCGGCGCGGGCGCCGCTCCAGTCGAGAAGAGGCAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.99739
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0130500.2 12 19068421 G C
Osa12LNT0130500.2 12 19068415 A T
Osa12LNT0130500.2 12 19068195 G A
Osa12LNT0130500.2 12 19068264 C A
Osa12LNT0130500.2 12 19068448 C T
Osa12LNT0130500.2 12 19068712 G A
Osa12LNT0130500.2 12 19068845 G A
Osa12LNT0130500.2 12 19068908 C T
Osa12LNT0130500.2 12 19069027 T A
Osa12LNT0130500.2 12 19069182 T C
Osa12LNT0130500.2 12 19069258 A G
Osa12LNT0130500.2 12 19069553 T C
Osa12LNT0130500.2 12 19069589 T A
Osa12LNT0130500.2 12 19069739 A G
Osa12LNT0130500.2 12 19070200 T C
Osa12LNT0130500.2 12 19070351 A G
Osa12LNT0130500.2 12 19070518 A G
Osa12LNT0130500.2 12 19070976 T C
Osa12LNT0130500.2 12 19071318 G A
Osa12LNT0130500.2 12 19071893 T A
Osa12LNT0130500.2 12 19072396 T C
Osa12LNT0130500.2 12 19072433 T C
Osa12LNT0130500.2 12 19072437 T C
Osa12LNT0130500.2 12 19072265 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0130500.2 osa-miR5801 Cleavage 4.5 13.578 1 24
Osa12LNT0130500.2 osa-miR5808 Cleavage 5.0 13.578 1 24
Osa12LNT0130500.2 osa-miR395b Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395d Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395e Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395g Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395h Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395i Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395j Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395k Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395l Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395s Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR396a-3p Translation 4.5 21.987 1 20
Osa12LNT0130500.2 osa-miR396b-3p Translation 4.5 21.987 1 20
Osa12LNT0130500.2 osa-miR395m Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395n Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395p Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395q Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR395r Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR1855 Translation 4.5 15.719 1 21
Osa12LNT0130500.2 osa-miR1870-3p Translation 3.5 14.245 1 24
Osa12LNT0130500.2 osa-miR1320-5p Cleavage 4.5 18.042 1 21
Osa12LNT0130500.2 osa-miR395y Cleavage 4.5 15.254 1 21
Osa12LNT0130500.2 osa-miR5501 Translation 5.0 15.798 1 21
Osa12LNT0130500.2 osa-miR2094-3p Cleavage 4.0 9.439 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0130500.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0130500.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130500.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130500.2 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0130500.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
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