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

>Osa02LNT0172300.1

ACTAACGAAATGAAAGGAGTAGCTTTGATAGTATCTTTTGGTTTTGTCATACAAACCATCAGTTCAAACTTCAAAAACTATCAAAATTTCGAGCCGTTCTTGTATCAAGAAACAACAGATCTAAGAAGCAGGGTGCATTAATCGCGCGGAATCAAGGACAGTTTCCCAGGCAGTGTTACTTTGACAGCATATTCGCGTGATTACATTTCAAATGGCAAAATGCCATTTTTCTGGATTGAGACACCATTTCACTGAGTAGAAGTGGATTTAATTGTCATCAGCAGAGGCTCCGGATCCTTCAGCAGCCTTCTTCTCCTTCTGTTTCTCTCTGCGCTTCTTATTTCTCAGTGCATTTTTGCTCATCTCTCCTCCCGTAGAAGCAAGCCCACCAAAAAGCTTATCCTGAACATCTGCAGAATTCTTTGAATGAGGTGGTCGATATGCTGTAGGTTTCGCTGCTATATTTGCAGGGGCCTTGCTTGATGGTTGTGCTGATTTAGAACCCTGTGCTGAAACTTGTTTTTTCGTTTCTTCAATTTTTATGCTACCCAACGATATCGTGAGGTCGGCAATGTCACTAAATTTTTCAGGCGCTTCTGGCTTCCAGTCAGCCTGATACAGCTTTTCAAACATCTTCTTGAACTGCAGAGATCCATTGTGGTCAAATATTTTAATCCCGTTGTCTATTTGGAGTCTCGGAGCTGTTGTAGCAGTCATAAAATGGCGACCATCAGGGGACCATTCACTCGTAACAGAACATTCAGCCTTTGTTTTTCCTACCAATTTCTTTTCTGAATAATCCCAGAATGCCATGTCACCAGGCAAATTACCAAACCCTGCTAAAACGATAAATCGCCCTTTTGGGTTCCATCTTATTGTATTGTAGGGGCCTTCACCGAGCTCCAGAAGAGGGTTGCATTTTTTGTTGAATATTGTTGCTCTGGCCGGCATAAATCCATAGACCACAGCAAATTCTGAACCTGAGTAAGACCACTGCACATCATGCACCGGACCATCCTTTTTGAGAGGAACAATTCCTTCAAAGGCCCTATCAGTTGTTAAATAGTTCAACTTGGTTTCACCATAGTAACTCTGGTTAGTTTTATCCACATCAGCTTGAGCAACAACTAGAAGCCCAGTGGACCCCTTATTCCAGTGAAATTGAACAGTAGAACAGCGAAAAAAACTCCTACGCGCAACAGCTTGGCCCTGTGCATCCTTGTCACAAGAAAAGATCTGAACACTAGCTGGAACACCCTTTGCCTCAGGAACAAATCCAGCAACATGAGATCCCGGTGCACTTGCTAGCTGCATAGCAGCTATACCAGGCATTCTTAGCTTGTACACAAAACCTTTTGTGAAATCTTTTGGATCAAAGAATTGTATCTCATTAGTCATCATGCGGCAAGCAACTGACTCATCCGCAGAAAATTGAACCATTGGCCACGTGGCCTTAGACATATTCTTCTGGTAGTGCTGGTAGAGCGCGGTGGCGGTGTCGACATGCCAAACGGTGACATTCTTCTCCTGCGGCGAGGACGACTTCTGGAAGGTCTGCAGGAACGTCCCCGCGGGCGACAGCGCGGCGGCGAGGAGGCCCGGGAGCTCGAACGACCTGACGACGGAGAGCGTCCGGCAGTCGTAGACCGTGGCCGAGGCCGAGGCCACCGTGGCGAGGAGGCGGGACCCGTCGCTCGAGAAGTAGGTGGCGCTGCACGCCGTCTTCGGGAGCCTCACCGGCGGGGCGGAGCCCGTCGGGTAAGGCGGGCCCGACCACACGCTGAATCCATCCGGCTCGCGCACTAGGATATCGAGGGCGGGCGGCTGAGACGCCATATCCGGTGAGCTGCGACGATCGATCTCCCGGCGCGCGGCGGGCGGGAGGAAGACCACGGGCGGCGCCGGCGTCGGCGGAGGCGGATGCGGCGGCGCGGTGGGGGATTGGACGGAGAGGTTGGGGACGGGTGGGTTTTACCGGATGCGGGTTGTGCTCCC

Coding Potentia
Explanation CPC Score
noncoding -1.20404
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0172300.1 2 23749543 A C
Osa02LNT0172300.1 2 23749764 T C
Osa02LNT0172300.1 2 23749856 A G
Osa02LNT0172300.1 2 23750044 A G
Osa02LNT0172300.1 2 23750125 A G
Osa02LNT0172300.1 2 23750265 C T
Osa02LNT0172300.1 2 23750345 T C
Osa02LNT0172300.1 2 23753104 T C
Osa02LNT0172300.1 2 23750392 G A
Osa02LNT0172300.1 2 23752377 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
Osa02LNT0172300.1 osa-miR1440b Cleavage 4.0 22.61 1 21
Osa02LNT0172300.1 osa-miR5079b Translation 4.5 18.409 1 22
Osa02LNT0172300.1 osa-miR160c-3p Translation 4.5 15.02 1 21
Osa02LNT0172300.1 osa-miR816 Cleavage 4.5 16.269 1 20
Osa02LNT0172300.1 osa-miR1320-3p Cleavage 3.5 18.745 1 21
Osa02LNT0172300.1 osa-miR2097-5p Translation 4.0 13.548 1 22
Osa02LNT0172300.1 osa-miR396f-3p Cleavage 5.0 23.307 1 24
Osa02LNT0172300.1 osa-miR3980a-5p Cleavage 4.0 16.606 1 21
Osa02LNT0172300.1 osa-miR3980b-5p Cleavage 4.0 16.606 1 21
Osa02LNT0172300.1 osa-miR5079a Translation 4.5 18.409 1 22
Osa02LNT0172300.1 osa-miR5157a-3p Translation 5.0 15.914 1 24
Osa02LNT0172300.1 osa-miR5157b-3p Translation 5.0 15.914 1 24
Osa02LNT0172300.1 osa-miR2866 Cleavage 4.0 17.589 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0172300.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172300.1 2 nan Others Others C424 G45
Osa02LNT0172300.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172300.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0172300.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0172300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0172300.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0172300.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0172300.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0172300.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0172300.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0172300.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0172300.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0172300.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0172300.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0172300.1 2 Sn2a Morphological trait Dwarf C424 G45
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