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

>Osa12LNT0130100.2

TTTATGAAAATTCTAAAATTTCAAATAAGAAAAGAAGTACTCCCTCTGTATTTTAATGTATGACGCCGTTGACTGTTTGATCAATATTTGACCATTCGTCTTATTTAAAAAATTTAAACTTATCAGTCAGCAAGACCAGTGTATTTTAATCTGCTAGATTACTATTAAACTACCAGTCATGAGATTACTGTTAAACTGCCAGTCATGATTAGTCTGCTGCCTAGCCTACTGCAGGTGGATATGAAGATGAAAAAATGTGTCTTTCCCTTCTTCTTGGATAATCCCTGACAAATTGCCACTTATGGTTATCCTGGACCAATTGTTCATCTTCTTCAGCATTTGGATCCATATCCACTACGAACAGAAACACGCCCTTATCTAGAAGCAGCCCATGATGTCGGCACCGCTGTACGGTGGACCTCCACCTCCTCCTCCACCCCCACCACCACCTTACATCATAACCATAAGCACACCCAAAAATTAGTTATCAGCAATGGGAACTCCACCAAAAAGTAACATATCAATATCAATCAAACAATCCTACCCCTTCATCAAACCATTGATGGAAAAAACCATCACAAAGATTCCCAGCCATATGCAAAAAAAAAGGTTGTGTATGAATTTTATAGACTCCACGCATACGGGCCATGCATACACAAACTCTGAAATAAAAAGACAGCAGCAGCTGTACTACCGGTAGCTAGCACACTGGATTTTATATTATATAGTATATTCTTGAACAAGCAGCCTTACAGTTATTTATCCTTCTTCTGAGAAGCTCTATATTTTGACCAATCGTCTAAGGTTTTCCGGTGAACAGCATTCATTTTTATCTTTCTTTTTTCTCGGATGATGTTTTCTGCATCCTTCCAGTTTTCAGCAATGCCCAATGCTACTAGAACTGCACACACAACACAAGCGCTTCTTCCATGACCAAACGCACAATGTACATAAACTGGTTTTCCTTTAGCTCTCTTTTCACATGCCCAGCGTGCCGCAAATTCAATTTGGGATATCGTCGGGGCTCTTGTATCCCAAGTAGGAACACAAAGATACTCATTTGTTGGGACAAAATCACTTCTTGGCAACTCACAAGTGCAATCAATAACAGAGGGGTCTCCTGGGGGCAAATGCTTCAACATAAACGGCCATCCTCCTAGATAAACGCCTTCAGTGATCATGTTATACACAGCCTCCTTCTTCCTCATATGTCTCTTCATAGTTGCATATACCCGGGCAAGTATCAAGAAAGGACCAAAAAGTACACTTGACCAAATTGGAAACCTCCCCTTTGAATTCTTTCCCAACATCCAAGGTATGTTGATGGAATTGTGGGATGCAACAGCGATGATATAGGCAATTGTACTGGTGGCTAGGAAAGGAACCGCGACAATTCTTAAGCCAATCTTCCACAGACCAACAGACGTGACCAGAAGAGATGTTCCAGCGATGCCAATCACCTTGGATATCCCCATTATCGCCCGCTTGAACTAAAACCTCTTCTTTTGGATTATGAAGGTCAGATCTAACACGGGGAGCAGGGGATTCAGCGCGAGGAGGTGAGGCCGCACAGGGGAGGAGCCGTGCGTCTTCTCGACGGCCGCGTGCGCGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGACAACGCCAACCTCCCTGGCTCGCACTGCAGATCGGAGACGCAGAGAAACTTTTTCCCTTTTTCTGATGGAGGAAACCAACAGAGGGGCGAGAAGAGTGGCGTGCCATTCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.912328
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0130100.2 12 18893693 T C
Osa12LNT0130100.2 12 18893783 C T
Osa12LNT0130100.2 12 18894435 T C
Osa12LNT0130100.2 12 18893897 G A
Osa12LNT0130100.2 12 18893201 T A
Osa12LNT0130100.2 12 18893225 A C
Osa12LNT0130100.2 12 18893239 A T
Osa12LNT0130100.2 12 18893242 A G
Osa12LNT0130100.2 12 18893376 A G
Osa12LNT0130100.2 12 18893488 C T
Osa12LNT0130100.2 12 18893922 A G
Osa12LNT0130100.2 12 18894363 C T
Osa12LNT0130100.2 12 18894370 C T
Osa12LNT0130100.2 12 18894832 C T
Osa12LNT0130100.2 12 18895249 A G
Osa12LNT0130100.2 12 18895434 A G
Osa12LNT0130100.2 12 18895618 T C
Osa12LNT0130100.2 12 18895703 C A
Osa12LNT0130100.2 12 18895774 C T
Osa12LNT0130100.2 12 18895804 G T
Osa12LNT0130100.2 12 18894536 A G
Osa12LNT0130100.2 12 18896029 T C
Osa12LNT0130100.2 12 18894122 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
Osa12LNT0130100.2 osa-miR5799 Translation 3.5 12.739 1 24
Osa12LNT0130100.2 osa-miR5143b Cleavage 4.0 14.271 1 24
Osa12LNT0130100.2 osa-miR6253 Cleavage 4.0 17.69 1 22
Osa12LNT0130100.2 osa-miR394 Translation 4.5 23.8 1 20
Osa12LNT0130100.2 osa-miR398a Cleavage 5.0 19.556 1 21
Osa12LNT0130100.2 osa-miR812a Cleavage 4.0 14.227 1 22
Osa12LNT0130100.2 osa-miR812b Cleavage 4.0 14.227 1 22
Osa12LNT0130100.2 osa-miR812c Cleavage 4.0 14.227 1 22
Osa12LNT0130100.2 osa-miR812d Cleavage 4.0 14.227 1 22
Osa12LNT0130100.2 osa-miR812e Cleavage 4.0 14.227 1 22
Osa12LNT0130100.2 osa-miR1436 Translation 4.0 13.079 1 21
Osa12LNT0130100.2 osa-miR1852 Cleavage 3.5 17.901 1 21
Osa12LNT0130100.2 osa-miR812g Translation 4.5 12.739 1 24
Osa12LNT0130100.2 osa-miR812h Translation 4.5 12.739 1 24
Osa12LNT0130100.2 osa-miR812i Translation 4.5 12.739 1 24
Osa12LNT0130100.2 osa-miR812j Translation 4.5 12.739 1 24
Osa12LNT0130100.2 osa-miR2275a Cleavage 4.5 18.28 1 22
Osa12LNT0130100.2 osa-miR2275b Cleavage 4.5 18.28 1 22
Osa12LNT0130100.2 osa-miR812o-3p Cleavage 4.5 15.231 1 24
Osa12LNT0130100.2 osa-miR5143a Cleavage 4.0 14.271 1 24
Osa12LNT0130100.2 osa-miR2122 Cleavage 5.0 12.023 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0130100.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0130100.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130100.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130100.2 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0130100.2 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