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

>Osa02LNT0190900.1

GATCCTTTCAGATGACCTTCGTTTTCCACCTATAGGCTGTAGCATACAGAAAGCGTCGCCTGCATCGATGACCACTCCGTTCCCGGCGGCCCACCTCCACCTCCAGCAACCTAAGGCCCTTTTGCCCCCCCCCCCCCCCCAACACCAACACACACACACACAAAGGAATAAGTCCACTATCCCTCCCTCAACATGGCCGTGTATGAATACCATCCCTCAACCACAAAACCAGGTATAACCCGTCCCCCAACTCCGAAAACCGTTGCAAATCAACTCCCCGGGTGGTTTTGGAGGCGGTTTTGTCCTACGTGGCATCTTTGACCCTGTTGACTTGCTGAGTCAGCAGGTGGGACCCACCTGTCAGTGGCAAGGATAAAAGAAAAATGGTGGGGCCCACTATCAACCACACTTCTCTTCTTCTCTCGCTCCTCCGGCCGATCCCGACGGCTAGGAGCTCGCCGCCATCACGGTGCCTAGCCACCGCGACGATGCTGCGGGGAGAGGCTTGCCGGGGACAACTGTGGATGGGCAGAAGCGCGGCGAGACCGAGGCCGGCATGGCGGTCGTCCCGAGACCCCGCGGCGAGCAGCGAGAGTGTGCTGAGCGCCACGAGGAGGAGCAGCGCCGCCCGTACCACCATCATATACGACAACTTCTCCCCGCCGCGCTTTCCCCTCCTCCTGCACCTCTGTCTGCACATCAGCGCACATGGATTGCCGGCGGCAGCCCGTGGCAATGCGGCATAGCGTGATTCGTGCGGCCGGCCTCGGGGGAGACTTGGTGGGGGCAGCGCGTGCGACGGCGGTGGCAAGACCAATTGCTTCTGTGGCCTATGACTATGAGAGGGTGGTCGCAGAGCCCGCAAGCTTGAGGTGAGTGACGGCGGATGCGTGACGCCAAGGCACCGTTGCCCGCAGCTGCTCGCCGACGAACCACGCCTGCTCCCTGACCGCCGTTGCCTCTCACACTCGGTGCCTCGGTAGTCAGTGCTCAGGAAGGGATAAACATAGCCCATGTGTTAAAGAAACAATCATCATTATTGTAGGGTCCAAGGACAAAGCGCACCAACCCATTGTACTCACTCCTCCCAAAAGAATCAATTATTGAGGATGAATTTAGATATGCATTTATCCAGATTCGTCTGTAAAAGTTAGATGTTTTTTTATGAAGTACAATGCATTTAAACGTGCTCACTTTGCACTATTAGTGTAAAAAATATATATATGAAAATTATATATGTTTGCTAATTTTTTAATAAGTATAATCAAACTTAAATAAAGTTGTATGTGAAAAAAATCAAAACGTCTTATAATATAAAATGAAGGGAATACTGAGCTAGTAATAGTCATTTATTTTTAGATAATGAAAGTTTTTATTAAACTTAATTAATTAGTACATAAAAATGATACAGTACCTCAGAACACTTCTACCTTGCATAACTAGTAATGGCCAATAATTGCAAACTGTTTCAGTGTGTTCATTTGACAGTGGTAAAGTTGTTTCAGAGAATTGGCATAGTGAAAATCAGGGGATGACCTGAACAGAAACTCACAGTTGGAGTTGGAACGGAATCAACAAGTTCAGAAGCTCTCAATGGCTAATGAACAGATTTTTTTTTCTAAGATGCAAAAGCACTACTACTATAATGGAGTAGTATAGTACCTTGAAATGGGGGATGCCGATCCATGGTTGAAGCCCTAGGATCCGCTTCCCTTCGTCCTCCTCCGCCTCCTCGCTCGATATGTCTTCTGGGACAGGACATCCAATCGACTTACAAGTGCATGGGGGCGCCTGCCTCGGGGGTGGAGATAGGGTTTGGGGTTTGGAGAGGACGGGAGATAGGGTTTGGGGTTTGGAGAGGACGGGGGAGGAGGAGGAGATGTGCGGACAGTGCGAATTCGGCGCCGTCACGGTGTTCGACGAAATGCGCGAACGAGGCGTAGGGGACGACGGGGACGACGGGGACGACGGGAGCGGAGCAGAGGGGATGGCGAGCCCCTCCAGGTTGAGACTATGGTCACTACCATTGGTCGCGAACGAGCAGAATTTGCAGAGAAAAATAGTCCTACAATCCACCGACGAGGAGTCAATGAGCTCGCCGGTGATGGCACGGCGGCGGCTCACTCCTCTTGCAAGCCGCCGGCGATCATATGCACTCAACATCTCAAAAAATGTACTAGCACTCTGTGTATATCTTCACCTTCACATGAACAATGACAGTGAAGCATAGTACAAATTAGCTTGTACAGTACTCCCCCTGTCCCAAAAAAGTCCAATTCTAAGGATGAATGTGGAGGGAATACTACTCATAAGAAGAAAAGGTGGAGTACAACATCAACTGGGCAATACTAGTATGGATCAAATTTCATGCAAGTTTGACATCCTTAAGAAGTCTTGCAGCCATAGCCCCGCATCTTCTGATTTCCCAGTCGTCGTCCAAGTAGCCTGCAGTTTTGGCTTCTGCTGAATCCACTGAGCCAGTACAAGGTCCACCACTCTCAGCTCCAGGATCTTCATCATCTCCTGGATTGGAGACAACCTCCTCCTCCTCGTTGTTGCCGTTATCGCTGACCTCAGGGATCAATGTCGCTTTGGGGTCCATTATGTAAAGATGAATACTAGGATGTTGGTATTTCACATCCATCTTCGATTTCGAGACGGTTTTCACATTAAAATTGCTTTTCCACATTTGCATCATCTGTTCATGGACAGTGGTAGAACGGATCTCGTATCCTAGCATTATTTTTGTTTTAGGACCAGATAATGCAATGATTGTCTCCATTAGAGGTTGCAACAGATGTTCTGAATAAACAACATCAGTTCCAATGATGTAATCGAATGGAGGATCAACAGCTCTTATATGATCTTTGTTACCCCAGTCCAATTCTGCAACGGTGACAGAGCCGATGGAGCCTGAGTCAGAGTTTGACTGTGAAATCCAAGATTTGTTGCGTTCAACATTCCTCAAAAGCAGCGGGAGCACCTCAACTTGGTCTGTTGTAACCACGTCACAACCCAGCAAAGCCATTCCAAGCCCAGCTAGACCACAACCAGCTCCTAGCTCAATCACCCTTTTTCCTTTCAGTTTAGATGGAGAAAATCTACCTTTTCTGCTATTCTTTTCCAAGAACTTGACGAACACCATGGATGCATCCCAGACCGTGGTTCCGAGGTGCTTCGAGTTAGGATCCTGAGAAATGTGCAGCCGATGGCCCAGCAACTCCAGCGAAATCGCGGACGTGCTCGGGGAGTTCAACCTTTCGTGGTCCATGGCCTCCCCGGAACTGCTTCGCCTGAGCTCCGTCGAACGGCGGCGGCGGCGGCGGCGGCGTCGGCGGCGGCGAGGAGGAGTGGTGTGTAGTGTCCGGAGGGAGAGAGATCTCTCTAGGTGTAGGTGAACTGGGC

Coding Potentia
Explanation CPC Score
noncoding -1.11534
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0190900.1 2 35117882 T A
Osa02LNT0190900.1 2 35117893 A G
Osa02LNT0190900.1 2 35117907 T C
Osa02LNT0190900.1 2 35117910 C T
Osa02LNT0190900.1 2 35118586 C G
Osa02LNT0190900.1 2 35118939 A G
Osa02LNT0190900.1 2 35118976 A G
Osa02LNT0190900.1 2 35119164 A G
Osa02LNT0190900.1 2 35119380 A T
Osa02LNT0190900.1 2 35119480 A G
Osa02LNT0190900.1 2 35119816 A G
Osa02LNT0190900.1 2 35119084 C A
Osa02LNT0190900.1 2 35120595 C T
Osa02LNT0190900.1 2 35121230 T C
Osa02LNT0190900.1 2 35121458 G A
Osa02LNT0190900.1 2 35121668 T C
Osa02LNT0190900.1 2 35121736 A G
Osa02LNT0190900.1 2 35121757 A C
Osa02LNT0190900.1 2 35122271 C A
Osa02LNT0190900.1 2 35122720 C G
Osa02LNT0190900.1 2 35121783 C T
Osa02LNT0190900.1 2 35117798 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa02LNT0190900.1 DTM_#DNAt_MULE_japo_Os2537 Chr2 - 35116159 35117733 1574
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0190900.1 osa-miR5802 Cleavage 4.0 12.096 1 24
Osa02LNT0190900.1 osa-miR5819 Cleavage 4.5 17.17 1 21
Osa02LNT0190900.1 osa-miR5821 Translation 5.0 10.748 1 21
Osa02LNT0190900.1 osa-miR5337b Cleavage 4.5 16.567 1 21
Osa02LNT0190900.1 osa-miR7694-5p Cleavage 4.0 15.846 1 24
Osa02LNT0190900.1 osa-miR7694-3p Cleavage 4.5 22.782 1 22
Osa02LNT0190900.1 osa-miR395c Cleavage 5.0 14.478 1 21
Osa02LNT0190900.1 osa-miR395o Cleavage 5.0 14.478 1 21
Osa02LNT0190900.1 osa-miR1429-5p Cleavage 5.0 19.565 1 21
Osa02LNT0190900.1 osa-miR1439 Cleavage 4.0 22.447 1 21
Osa02LNT0190900.1 osa-miR1439 Translation 3.5 9.003 1 21
Osa02LNT0190900.1 osa-miR1428e-5p Cleavage 5.0 12.073 1 22
Osa02LNT0190900.1 osa-miR1858a Translation 4.5 21.966 1 21
Osa02LNT0190900.1 osa-miR1858b Translation 4.5 21.966 1 21
Osa02LNT0190900.1 osa-miR1861d Cleavage 5.0 14.875 1 22
Osa02LNT0190900.1 osa-miR1428f-5p Cleavage 5.0 12.073 1 22
Osa02LNT0190900.1 osa-miR1428g-5p Cleavage 5.0 12.073 1 22
Osa02LNT0190900.1 osa-miR2919 Cleavage 4.0 5.564 1 19
Osa02LNT0190900.1 osa-miR2927 Cleavage 5.0 16.972 1 23
Osa02LNT0190900.1 osa-miR5817 Cleavage 4.5 11.684 1 24
Osa02LNT0190900.1 osa-miR1428e-5p Cleavage 5.0 20.947 1 22
Osa02LNT0190900.1 osa-miR1428f-5p Cleavage 5.0 20.947 1 22
Osa02LNT0190900.1 osa-miR1428g-5p Cleavage 5.0 20.947 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0190900.1 2 ss2 Physiological trait Source activity RM240 RM213
Osa02LNT0190900.1 2 nan Morphological trait Root RG256 RG151
Osa02LNT0190900.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0190900.1 2 gn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190900.1 2 gw2.1 Morphological trait Seed RM250 RM208
Osa02LNT0190900.1 2 pl2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190900.1 2 sn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190900.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0190900.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0190900.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0190900.1 2 nan Morphological trait Panicle/flower RG256 RG151
Osa02LNT0190900.1 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