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

>Osa01LNT0054500.2

ATCAAAATTTTGGTAGGATTTCTTATGTATTTATCAAAGTTTGGCAACAAACTAAATGCAACACTTCTTTTTGGTAATTTTAAAAAAAATAGTTCGGTTGAAAATGACATCAATCCGAACAGCCCCTGTGTAAACGCTGTAGTGTAGTGTAGTGTACCAGTGCAGTGCTAGAGCTTCCAGTAGAGGCGAGCACGGTGGAGGAGGCCGGCGACAAGGGCCCAGAACAAGATCTGCGCGAAGAGGACGTAGAGGAGGATGCCCACACGGGTGGAATGCCACACCTTCACGAACACATGCTTCCTCACCCAGTAAACCAGTGTGTTGTTGGTGCCCTCGTAGTACCACCCGTTCAAGAACCCTTCGAAGATGCCTGCCGCCGCCATCACGTACACCAGCATCGCGTTCATGCCGGTCCATTTCAGGGGTGCGAATGGGTAGTGCAGATTCAGGATGTCAACCAGGAAGTAGAACATGCAGAACACGATTCCAGCCGCACCGGCAGTAACACAGATATAACTGAAGGTGTACAGTTGCTTGTTCAAAGGAATTGCATGTGAAAAGTGCAGAGTAAGCCCAAGAATGAGGAGAGTTATGCCCATGATAGACCACTGCTTTAGTCTGTCCGTGTGGCTCTTCATATGAACAAGCACATGCCCATAATGCACCCCGATGATCGTACTCAACACCGCGGACAGTGAGCTTAGTAACCCTTCAGGTTCAAATGGTGCATAACACCACGCCGGGGAATCAGTTTTAAAAGGTCCCTCATGTGGGGAATCATCAGTACAGTCCTTGTGCCTCCTCCATGCTGGCCTGTGGTACATATGATTGATACCAAGAACTTTACGGTCAATATAACCTACAGCATTGCAAGGAGGACTTAATTTTCCCCGTGTACCACATGTCACCGTCAAGATTTTGCCGAAGTTTGGATTTTTAACATCTGACACTCTGAAATCCCAGTCAGGAACATAAATCCCATATACAAGGGACAGGTAGATCACAAGGATGCAACATGCAACAATCCACTGGGAGAAGTACATCCTGAAAATCGAGAAGCCCGAACTTGACTGGTCCTGAACCTTTGCATTCTTCGTTACGATCTCTAGAACTGCAACCACCAAGTATGCAAGAGCAATCCTTTGGAGAATACCACACCATCTCACGTGCTTCATGTCAACTCCATAAGACAAATCATCAGGGGCATGGGAGTAACCGCCTTGCAACAGAATTCCCCAAAAAAGCAGCTTCAGTGTCCTGAGCACTACTCTCCTCACAGCTCGACCGCGGTCTGGAATCCTCTGCATGTTTGCTTGAGGGAGAGGGGAATAGCCATGCCAACGATGAAGAGGAAGAAGGGCATGACGAAGTCGGCGAGGTTGCATCCGTTCCACGGCGCGTGGCCTATCACCGGCCACTCGCCGCCGGCGCCGTCCACCAGTATCATCAGAGCGACGGTGAGGCCACGGAAGACGTCGAGCGACGCGACCCGCCTGCTGGTCCGGCGAGGCGGAGGCGCCTTCTCGTCGACGTCGACGCCGTCGTCGTCACCTTCTTTCCCCGAGCGGTCGCCGCGGCGGCGGTCGGGATCCTCCTCCGCCACCGCGCCGTGCCGCCGCGCGACGCCCTGGCCACCGCCGTCCATCCCCAGCGAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.98849
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0054500.2 1 40858617 A G
Osa01LNT0054500.2 1 40858633 T C
Osa01LNT0054500.2 1 40858636 T C
Osa01LNT0054500.2 1 40858669 T C
Osa01LNT0054500.2 1 40858805 T C
Osa01LNT0054500.2 1 40858909 G T
Osa01LNT0054500.2 1 40859680 A T
Osa01LNT0054500.2 1 40860427 C G
Osa01LNT0054500.2 1 40861459 A G
Osa01LNT0054500.2 1 40861594 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0054500.2 osa-miR393b-3p Translation 5.0 16.326 1 21
Osa01LNT0054500.2 osa-miR1426 Cleavage 4.5 18.636 1 21
Osa01LNT0054500.2 osa-miR2925 Cleavage 3.5 21.112 1 19
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0054500.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0054500.2 1 FSM Morphological trait Shoot/Seedling nan nan
Osa01LNT0054500.2 1 rrw1b Resistance or Tolerance Other soil stress tolerance C86 RG236
Osa01LNT0054500.2 1 nan Morphological trait Root RG109 RM104
Osa01LNT0054500.2 1 grl1-1 Morphological trait Seed RM431 RM104
Osa01LNT0054500.2 1 nan Physiological trait Eating quality RM8084 RM6827
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 qRNd1 Resistance or Tolerance Other soil stress tolerance RG236 C86
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Morphological trait Root RZ730 RZ801
Osa01LNT0054500.2 1 nan Morphological trait Seed RZ730 RZ801
Osa01LNT0054500.2 1 tn1-4 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0054500.2 1 ph1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Other disease resistance RG109 RG236
Osa01LNT0054500.2 1 fll1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0054500.2 1 sd1 Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0054500.2 1 qPHT-1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Drought tolerance RG810 RZ730
Osa01LNT0054500.2 1 qNOP-1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0054500.2 1 Fh1-2 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0054500.2 1 nan Resistance or Tolerance Drought tolerance RZ730 RG810
Osa01LNT0054500.2 1 nan Resistance or Tolerance Drought tolerance RG690 RG810
Osa01LNT0054500.2 1 qPL-1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0054500.2 1 qPH1-1 Morphological trait Shoot/Seedling C86 RG236
Osa01LNT0054500.2 1 yd1b Morphological trait Seed C547 C2340
Osa01LNT0054500.2 1 nan Resistance or Tolerance Drought tolerance C86 RZ14
Osa01LNT0054500.2 1 qPHT1-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0054500.2 1 sd-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0054500.2 1 pl1.1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0054500.2 1 qRIE 1 Resistance or Tolerance Submergency tolerance C86 G54
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