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

>Osa02LNT0190400.1

GCAGCATTTACATGTAAATGAGTGGTGTCTTTAGTCTGGAACTTCTAAAAAGGTACTCGTGCTATGTTACAAGTGTACACCATCGAGAGATGGATAAGCTAACCATGCCTGGCACTGACTTATTGTGAGTTTGTTCCTGAACTACAACTACAATCTGACACTGGTTACACTACAGCATAGTCATACTTTTTCACAAAAAAGCAGCAGCTTTGGATCTCCCTGAACGAAAACTTGTGTACCGAAGGAACAGCAACGCAGTTTCAGATCAAGTGGACAGCTCATACTCCCAGTATTTGGGATATGAATATGATTCTCATCTTCTACAGCCAATGAGCAAATCATGTCTGAATAAAATTGGCCCTGATTCTCACTTCCTGCAGCCAATGATTCAGCATAAGGCGTCTCTTCTGAAATTTCCAGATTATGCATTCATTTCTCAGGTTTTTGCTCTGCTGAATCAGCATCTCCTGTTTGTCCCTCGCACGTTTCCCTGTTATCCAAAACCTGAGTGGGTGCATCTAGAGATCTTGGTAATGCTCCCAGTTGTCTTAGGCTCTCGCTCTGCTTCTCGATTATCATGGCGAGGTACTTGCTGTGTTCTTCTACTTGCAGCTGCAGCTTTCTTTGGATCTCAAGTTGTTCGTGAAGTTGTTTCTGCAAGCCAATCTGGACCCTTAATCCTTCACAGGTGGTTTCCATGCCTTTCAAGGGCTGAGAAGAAACTTCATCCGTTTGGCCACTTTTCGCAGATTCACCATCAGATAGTTGAGGTCGATGATGAACTGTGCGATACTTCTGTAGATGGCTTTTTACATGGTATATAGTTAAGCCGTCAACCTTCATAACTTTCTGGACAGCTTTTGGAGTTGCTTTTTCACTTCCACCAAGCTTGTTAACAGCATCAACAAACCGCTCATGGAGCTCAGGTGTCCATCGCATCCTTGGTTTGGTTGGAGCAATGTTTGAAGAAGCGATATTACCAGAACAAATTTCATTGAAGTTGGGAGGATTTGATGTATTTCTCTGTGCATGACAATGCAAATAATTTGAAGGTGTTGTACTTGTCGCATCAACAGCCTTCAGCACAGAACCAGCAGACACCGAACTTTCCAAATACTGCAAGGAAGTGCCAGATGAGAACCACTCATTTTGCTTTGCAAGGTTGGTGCTAGGACTTGCTGCAATGTTATCTTGTATTTGTTGGTCAAAAATAGTCATATCTTGTTGATCGAAGAAATCAACACTAGTTGGACAAACAAATGGTCCAGGCAGTGGTTCTTGACTCCAACTATTCTGTTCAGATACTTTAGGATAAACCATCCTTAAAGAACTTGGATTACCCTTGTATAATGAACATTGGAGTAGAAGCATCAAATGAGTTGATAGAACTACCACACTGCTCCCTTTCGATATAGGATGGTCTATGCTCTGAAAAACTAGGAAATGTAACTTCAGAGAGTTCTGGTACTACAGTTATAGCTGGCGAAAGATATTGGGGAACTTTTCCATTGCGAAGCTGATTCATAGTTGATGTAGGCCTGTTTCATGTACCCCTAAGATGATTCACTTCAATTCTGAAATATCAGTGCATACTGCAAATCTCCTGCACTGTCTTGAACTGTGGCCCATGGCTACTGCCACTACTGAATTGTCAGTTGAGTTCTTTGAACATGGAATGTGTAGAGACATTGAATCCTTTCAGAAATCTCACAGTTTTGATGCTGGTCTATTCCATCTCCTCCGCAATTGCATTTTCGGTCTTTGGAAGCAGCTTCACCGAGTTGCTTATCTATTTCAACAAGGTATATCTTAAACAAGCTTGACCGTGGCGGCATTGCTGCAGCAGTAAGAACTGGAGGTAGAAGCCATAATATGTACGGTTCGCTCTCTAATGATTGCCTTGCATACTCACAAATATCCATCTCCTTGAAACCAAGAAGCTTGTCTTGGCATTCATCCTGAGTTGTTCCTTGAAGCAACTGGTGCAGATCAGCATATTGTTTTGATATAGGAAAGGAACTAAAAGTATGTGACATGATGCTCTCTATTAATGAGTTCCATTGCCTTGCAACCAATCCCAACAAGCATAGCTCCATGACTTCAATGATGCCACTTTGACTAGAATCTGCAGAAACTTTTAATGGTTCAAACAATCCCATCCACTGCTCCTTGGGAGCATTAAAGATCATATTAGTTCCTGACATGATCCGAATGGTACGCTCATCAAGCAAGTACGACAAACACTTTGCTTTCCATTGCTTCCACAGGATAAACTTGTCGATGATTTGTGTTTTCTGAGCAGTTGCTGAGGTGCACAATGTACTTCCTGCACTATCAAAGCTGTCCTTTTTCATGCTTTTTAGAAGTGTGTTCAGTTCTCTCTCAGCCAAAGAAATACACGATCCTGAATCCAGCTTCTTCTGTAGTTCTTTAAGTAGAATTCTTGGCACACATTGCATTCACCACTAGCAGAAATGCCATCCATATCCATCTCAACAACTGCTTGAAGTACAGCACCTAAATTCTCCGCATTCGTTGTTTTCAGAAAATGCTTCACAACCAACTCTCTTGCCATCGCAAGTGTTTTTGATCGGATATCCTCAATACCCTTGGGGAAATTCGGGCTTGAAGCGAGTTGAACGAGTGCAGCATCGAGCTCACTTGCAGACTCATCGTACTGACCATCGTCACGCAGGTTCTTGAAAACCTCCTCGAAGAAGAGGGCCCATTGGAGGGCCTTCTTGACGTCACCGGAGCGCCAGGTGGCGGCGGCGCCAGACGAGGTGCGGCCGCCGGCGAGGACGAGGACGTCGACGAAGCCCCGCACCAAGCCGAGCAACTCCTCCATGGCCACCGTCTCGTGCGCCCACCCCATTTGCGATCCCCTTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.627428
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0190400.1 2 34904003 C T
Osa02LNT0190400.1 2 34907035 T A
Osa02LNT0190400.1 2 34903448 A G
Osa02LNT0190400.1 2 34904254 G A
Osa02LNT0190400.1 2 34904594 A C
Osa02LNT0190400.1 2 34904802 C G
Osa02LNT0190400.1 2 34905050 C G
Osa02LNT0190400.1 2 34906302 T G
Osa02LNT0190400.1 2 34909053 C T
Osa02LNT0190400.1 2 34909085 G A
Osa02LNT0190400.1 2 34909593 G A
Osa02LNT0190400.1 2 34909632 T C
Osa02LNT0190400.1 2 34907210 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
Osa02LNT0190400.1 osa-miR166i-5p Translation 3.5 18.237 1 21
Osa02LNT0190400.1 osa-miR815a Cleavage 4.0 24.73 1 21
Osa02LNT0190400.1 osa-miR815b Cleavage 4.0 24.73 1 21
Osa02LNT0190400.1 osa-miR815c Cleavage 4.0 24.73 1 21
Osa02LNT0190400.1 osa-miR1853-3p Cleavage 5.0 22.702 1 22
Osa02LNT0190400.1 osa-miR2091-5p Cleavage 4.0 24.05 1 21
Osa02LNT0190400.1 osa-miR2093-3p Translation 4.5 23.672 1 20
Osa02LNT0190400.1 osa-miR2907a Cleavage 4.0 20.309 1 22
Osa02LNT0190400.1 osa-miR2907b Cleavage 4.0 20.309 1 22
Osa02LNT0190400.1 osa-miR2907c Cleavage 4.0 20.309 1 22
Osa02LNT0190400.1 osa-miR2907d Cleavage 4.0 20.309 1 22
Osa02LNT0190400.1 osa-miR1862f Cleavage 4.5 17.982 1 20
Osa02LNT0190400.1 osa-miR1862g Cleavage 4.5 17.982 1 20
Osa02LNT0190400.1 osa-miR5083 Cleavage 4.5 18.332 1 20
Osa02LNT0190400.1 osa-miR5150-3p Cleavage 4.0 19.206 1 24
Osa02LNT0190400.1 osa-miR5515 Cleavage 4.5 16.653 1 21
Osa02LNT0190400.1 osa-miR5807 Cleavage 5.0 18.666 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0190400.1 2 ss2 Physiological trait Source activity RM240 RM213
Osa02LNT0190400.1 2 nan Morphological trait Root RG256 RG151
Osa02LNT0190400.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0190400.1 2 gn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190400.1 2 gw2.1 Morphological trait Seed RM250 RM208
Osa02LNT0190400.1 2 pl2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190400.1 2 sn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190400.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0190400.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0190400.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0190400.1 2 nan Morphological trait Panicle/flower RG256 RG151
Osa02LNT0190400.1 2 Hd7 Physiological trait Flowering R3393 R2511
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