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

>Osa02LNT0171600.1

CAGAAGACTCGGTCAGGACTTGGCTGCACCAACAATTCAAAATGCAAGAACTACCAACAACCACACTGTTACTTCAGAGAAGAACCAAAGGTAAGTGCCCCTAGTATTTACATCGATGCTAACATTTGAGTTCCTCCTATGAAATTCAGGAGGGCATGCTAACCACAGATCACAGAATATGTCATTGCAAATGGTCACCAGAATGCTGGTTGAAATTAGCAGAGATCGATCGGGACTCGCTCTGGGTTCTGAGCTCTTTCTTGACCCTCAGAGAGCTTGACACCAAGCTGGCCTTTGATCCCTCCCCCAAAGGCATACAGTTTACCGGATTCCATGAGCGCGAACGTATGCGGGTATCCCATTTCTGAGTTGAGCCAATATGAAGAATTTGTTGTGCTAATCTGTACAGCCTTATCATTCAACACCTTCAGTGATTCTACCAAGCTTGGGGTAGAAAAATCTGCATCATCTGCTGCTTCCTCATCCTCCTGGAAACCTATATTCAGGGATTCAGCGGATCCAAAGGAGTATGTATCGCCGTTATCGGAGACAACAAAGGTGGTGTATTCACCGGTGGAGACATGCACAGCCTTCACATTGCTCAATCCTTGAACCACAGTGGGGAGAACCCTGTACTCCTCATCGCCATGTCCCAAACAACCAGTATGGCCCCAACCCCAGGTGCAGACACGCCCATCGTCACCTAGAGCTGCAGCATGCCAAGTGCCAGCCGCAACTGAAACCGGATTAAAGCTCAATGTCAGGAAATGTTCAATCAACTTGGGGGTGCCCTTATTGTTTTTGCATCCGTGACCAAGCTTGCCTCCTAAACCACAGCCTACAGAATACACTGACATTCCAGTTGGCTGGTAGGCCAACATAAGGAGATAGCAATTCCCAGCAGAAATCTGTGCAACAAGAACACCCTCAAGTGGTCCAGAGAGAAGACGAGGCTCAACATCTGAAGGATCCGAACTATGGCCAAGCCTCTCGGTTCGCCCCCACGAGATCGTGTAAACCTGACCCTCTCTAGATAGAAACGCAGAGAAGTAACCACCAATGGCTGCTTGAACTACAAACACACCCTTTAGCGACTCCACTATCTTAGGAGTGGTAATGTGATCAGCTGCATCAGAAAGCTCTTCCCACACAAAGCTACCCTTCCCAAATGCATAGACACTTCCTGTGTCACTCACAAGCATTGTCTGCCTTGATCCAACTGCAGCCTGTGTGATTTTGATGCTTTGCAAAGACCTAATAAGGCATGGCTTGAACCGATCTTCAGTATCCCCAAGGCCAAGCTGGCCCCAGCAATTAGCCCCAAATGAGTATGCATCTCCCTTTGTGGTGACAACAATACTATGGCCCGGCCCGGCGACAATCCGAGAGTAATTCCTTTCTCTAGCCACAATATACTTGAAAACAAGCTTCCAAGATCCACCACACCTCTGCTTCAGTTGCTCCCGTTCCTGCTGTGCCATTAGCTTAACCATGGGTCTTTTATGGCACATATCAAATGCCGCAACCTCTGGAAGCGATAGAGCAAAGTTTGGCTCGAAATTTGCAGGTTTACTGAAGAATGTACATGTAGCCTCCAGTGCAGCGAGATCTTTAGGATCTAGCTCGCAGGTGGAGAGCACATGTAGCACAATGGAGGGGCTCACAGCAAGGGGGAATTCTCCTGGGGTTTCATGACCATAGCAATGGCGCTGCGAACGTTCCAGCGCCGTGTGCAGCGGAGATGAATGGGAGGGTGGCTCATCAACAATGCCATGGAACTGCATCACAGGCGAAGTTCCACTTGCAGCTGCGTCCATTGGGCACTGCATGCTTCTTGCAGTGCCCCTCGCTGTGTGGATAAATAGGATTATGGGAGCAGAGTACTCAGTCTGACAAGAATAAAAGAAGAGAGGCAAATTACTACTACTTCACATTATAGTGCAAACCCCGGCATCACTAATAAGCAAATCATTTGCAATGGAGGTTAAATTAAAGGAAGCATTGAATTATTCGATCATGTTGGCAGTTCAGTATTTCTAAGCTGTGTTCTGCAGTAGACAGAGTGACATATTCGTCAGATAGCGCATGGACAGGAGAAAGCCTGAACCTCAATCCAAAAACAACAACACACATGAACCCTTGTTAGATCAGGAACCATCTTACAGTGGAACTCAATACTACTAAAAACAGTTAATAGCAGAAACAACACAAACAACACATAAAAAATAAAAATTTTCATTCAGTAGTAAATTAGCAAAGCCTTTGCCCCCACAAAAAGAATGCCATCAGAATGAACTGCAGATGAGACTAGCACGCACAAGACAAATCCATGGATTGACCCCGGATCATGCCACCAAAGCAAGATCAACGCACAGATCAGTCTCCACCACAATGATCTTTCTCTCCGCTCATCTCCGACACGATCAACAGATGAGAAGAAGAGCGAAGCGGAAACAAGAGGATCGATCCATGATCCGATGATCGTGGCCACACAGTCTACAGTTCCACCATCCCCGATCCCCGCGCGCATCACAAAATCTCCCAAATCCGCCGCCTCAAATTCCCCCATTACAGCATCCGAATCCCCCCAACTCCTATCAAACCAAGAACCCAAGAACAACAACAAAAAGCAACCTTTCCTATCCCACACAGATCGGCTCAACAAGATCAGAAAAACCGATCCAATTCCACCAGATTCCCCCTCACCCCTGAACTCCTTATCCCCACAAAAAAGAAAAAAAAATCCCCCAAAAATCCTCCGGGAAAATCCAGATTGAGGGCCGGCTCAGCTGCCAGTAAAGGAATCAAAACAGCACGGAATTGAGCAAAGATTCAGTGTCCGATCGTTCGTACTGGAGAATTCGTCTGGTGACGATGGGTTCATCTGATCCTCGCAAGGCTGCAGAGGCTGCAACCTCGGGGAACCGGATGTGGGGGGCGGTGGGGAGGAGGTGGTCACCTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.960945
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0171600.1 2 23183163 T C
Osa02LNT0171600.1 2 23183457 A G
Osa02LNT0171600.1 2 23183953 T C
Osa02LNT0171600.1 2 23184307 A G
Osa02LNT0171600.1 2 23184336 A G
Osa02LNT0171600.1 2 23184348 T C
Osa02LNT0171600.1 2 23184360 C A
Osa02LNT0171600.1 2 23184780 T C
Osa02LNT0171600.1 2 23184833 G A
Osa02LNT0171600.1 2 23185018 T C
Osa02LNT0171600.1 2 23186221 C T
Osa02LNT0171600.1 2 23186386 C T
Osa02LNT0171600.1 2 23186095 G 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
Osa02LNT0171600.1 osa-miR5544 Translation 4.0 17.387 1 22
Osa02LNT0171600.1 osa-miR5179 Translation 4.5 18.092 1 21
Osa02LNT0171600.1 osa-miR5079b Translation 4.0 9.506 1 22
Osa02LNT0171600.1 osa-miR167a-5p Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167b Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167c-5p Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167d-5p Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167e-5p Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167f Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167g Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167h-5p Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR167i-5p Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR171c-5p Translation 5.0 18.147 1 21
Osa02LNT0171600.1 osa-miR167j Cleavage 5.0 15.472 1 21
Osa02LNT0171600.1 osa-miR426 Cleavage 3.5 10.924 1 21
Osa02LNT0171600.1 osa-miR444a-3p.1 Cleavage 3.5 16.778 1 21
Osa02LNT0171600.1 osa-miR444d.1 Cleavage 3.5 16.778 1 21
Osa02LNT0171600.1 osa-miR1866-3p Translation 4.0 22.211 1 22
Osa02LNT0171600.1 osa-miR5079a Translation 4.0 9.506 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0171600.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0171600.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0171600.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0171600.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0171600.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0171600.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0171600.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0171600.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0171600.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
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