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

>Osa02LNT0176200.1

TAATTATACAGAGAGATTACATAGGAGGAACAGATAAAAAACTAAGGAACGTGGGGGTGAAACATTGCGACCCTTTTATGATTTTGACGCATATTAACTACAATGGAAAGAACAAAAGAATAATTGTGGAGACTAAAGTAGAATTTTCCATATGTTTTTTTTCTCCCCAGAGCAGCTCACTCGACTCTTAACCTAGCTAAGCTTGTTTGACTGATATTGACCTGTGCGCATCACATTTTTTAGCATTAAGCTGAACACTATATCTCTTGATTGCGACCATGGCATTTAAGCAGCAGGCTGCGGGGAAGAGAAGATTAGGCTCATCAGAAGCCCAACCAAGAGACCTATGAGCCCAACAAAAGCAGCAAACGTTAAGGAGAAACCCGTATCGCTTTTGCGGCTTCTACGCCTCCTAATCACATCCAATTCACGTTGCATTTGCTGATTTTGCTGCAGCATGTTATCTCTTTCATCTTTCAAGCGTTGTATTGTCTGTATCTCTTCAATGCTTGCATTCTTCAGCATCGTGAAATCGTCAGACAACGATTTGAAGCTCCTGCTTCCTAAAGATGTAATACCAGAGTCGTCGGAACTTCCACTAGGCACTGTATAAACAACCTTAAGCTTTATTTCCTCAATCACCTTATCAACTTCCTTGTTGAACGTATCAGGAGGAATCTCGTCCATGTCAGTACTGGCAGCTACCCTAGTGCTCTGAATCAAGAACTTATCCTTGCATTGCATATCTTGTGGGTACTCTTTCTGCGCCTGGAGCGTAATTGTTATTGTGCAAGAATCCCATGGCTGGACGATGTTCGCGTTCGGCCGGACGAAATACTTCCTTGGTGATGTTGTTTTGACCTTGAATGCAACATGATGCTCGCTGTTGTTCACCACCTTGAGATTGCAATAGCACGGTTTGTCCAGCTCAAATAGGAAAGTGAGGTCCTCGGGGTAGATGGAGATCAGCGTTCCGCCGCCACCCATTGCCACACCTTTCCCTTCGTTGTCTTCGTTCAGAGTAAAATCCGGCCTTTCTTTCCAGGAACTGAATTGAACTGAAAGAAATTTGCATGAGGAATTGGAAGAGCAGGAGCTAGGAGCGAAGGAAGAGAAAGAGAGAGAAACGAATGGGTTTGGGTTTGCCTTTTCTTGGCTTCTCGGCGACAATGACGGGGC

Coding Potentia
Explanation CPC Score
noncoding -1.20144
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0176200.1 2 26308710 A G
Osa02LNT0176200.1 2 26309532 A G
Osa02LNT0176200.1 2 26309940 A C
Osa02LNT0176200.1 2 26310523 A G
Osa02LNT0176200.1 2 26311350 T A
Osa02LNT0176200.1 2 26311440 T C
Osa02LNT0176200.1 2 26311566 T C
Osa02LNT0176200.1 2 26311618 T A
Osa02LNT0176200.1 2 26312172 G A
Osa02LNT0176200.1 2 26312300 T C
Osa02LNT0176200.1 2 26312531 G A
Osa02LNT0176200.1 2 26312627 T C
Osa02LNT0176200.1 2 26312752 A T
Osa02LNT0176200.1 2 26313284 A G
Osa02LNT0176200.1 2 26313416 T C
Osa02LNT0176200.1 2 26314415 A G
Osa02LNT0176200.1 2 26314435 G A
Osa02LNT0176200.1 2 26315439 A G
Osa02LNT0176200.1 2 26313260 A G
Osa02LNT0176200.1 2 26311471 T C
Osa02LNT0176200.1 2 26312569 A T
Osa02LNT0176200.1 2 26312769 A G
Osa02LNT0176200.1 2 26314647 T G
Osa02LNT0176200.1 2 26314675 A G
Osa02LNT0176200.1 2 26314713 A G
Osa02LNT0176200.1 2 26314482 G A
Osa02LNT0176200.1 2 26314560 A G
Osa02LNT0176200.1 2 26314836 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa02LNT0176200.1 DTM_#DNAt_MULE_japo_Os0115 Chr2 - 26314439 26315049 610
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0176200.1 osa-miR397a Cleavage 5.0 15.103 1 21
Osa02LNT0176200.1 osa-miR156k Cleavage 5.0 16.185 1 21
Osa02LNT0176200.1 osa-miR815a Cleavage 3.5 10.494 1 21
Osa02LNT0176200.1 osa-miR815b Cleavage 3.5 10.494 1 21
Osa02LNT0176200.1 osa-miR815c Cleavage 3.5 10.494 1 21
Osa02LNT0176200.1 osa-miR2095-5p Cleavage 4.5 20.14 1 22
Osa02LNT0176200.1 osa-miR2118i Translation 5.0 18.336 1 22
Osa02LNT0176200.1 osa-miR2871a-3p Cleavage 4.0 14.272 1 21
Osa02LNT0176200.1 osa-miR2871b Cleavage 4.0 14.272 1 21
Osa02LNT0176200.1 osa-miR2930 Translation 4.0 16.834 1 22
Osa02LNT0176200.1 osa-miR3979-3p Cleavage 5.0 16.518 1 20
Osa02LNT0176200.1 osa-miR5078 Translation 5.0 22.247 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0176200.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0176200.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0176200.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0176200.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0176200.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0176200.1 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0176200.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0176200.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0176200.1 2 nan Others Others C424 G45
Osa02LNT0176200.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0176200.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0176200.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0176200.1 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