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

>Osa02LNT0187500.2

TCAGGTCTCCACTCTCTCCGCCAGCTTGATACCCGATGACTCCAAGATCTCCAACGCTGGAATGTAAATTTCAGGTTCCAGAGGCCTGATCACTCCTTTCTTTTGGATCTTGTTCTGGAGCAACAGCAGAGCTCCTATTGCTGCTGGTATTCCGACCGTGAGAGCCATGGCAGTGGTAGGCCTGCCATTTTCAACCTTTCCAAACTCAAGTAGGGTTGCTTGGTGCTTTTCGGTTGGTCGGCCATCAGGGTATTCCACCTCCACCTCATGGTGCAGCAGTACCATATCCTGCTCATTGTGGATATAAGCCATTCTCTGCTCCATTCGCTGGCAAATCACATCAAATGCACTTGAACAGTTCTCTGGAATCTGTGTCTCCTCATATAATCCCAAGAACTTGATTGTTTTGACTGTCTTAGCAGCTATTTCCTTATCTTTGCAATGCCCAAAACTCAAGAGTCTGGAAATCAGTTCACCATCTTGTCCTCCAGAGACTTCACTATATTCCTTTCTGGCGGTTGTGGAGATGTTACAAGCATTGAAGAGTTCAACAAGAAAATCCCTGTATGTAGGGCGAGTAGTTTGTTGCAACAGTGGATGACTTGCAGCATCAAAAAACCCAATTTTCGCGAAGGTTGCCATTATCTCACTAAATCGAAGAGTAGCCCTGTACACAGTAGATGCTTCTTTGGAGATCCCATACAGGTCTCCATACATCAAGGAATTCCGGTTTGGCAAGTGTTCCAGTGCAAAAGCTGGAAGTTCTGGTAATCTGAGCCTCTTTGCGGATTCATACAATTTATCACCATCTACATGGATGATTTCTCCATGAAATTTGTAGACAGCAGGGTTTCTCCCTGCACGGATGGCACCAGCTGGACTCCAACTGAACTTATAAGCAAGTGGATTGTTTGCAGAAGCTGGAGATGGAAGTCCTCCACAAAAGGATGTAAATGACTTTATTTTCCCCTTCCGTGAATGTGCTTCGTCAATCATCTTCATTGACATCATATGATCTATGCCAGGATCCAGGCCCATTTCACAGAGAATAGTTACACCAGCACCTTCTGCAGATTGTTCCAACTTTGACATGGACTCATCAACATAGCTTGCAGTGACCAAGTGCTTCTTCATCTCTATGCATACTCTTGCTATGGCAGCATGAAAACTGGCAGGCAGCAAGCTAACTACTACTTCAACCTGAGAAACAAGATTGGAAAGATTTTTAATATCTGCAACATCGAGTTGAGCAGCTGTTGCATTTCTTATGCCATCAATTGTCTCTTCTGCATCTTTTTGGTACAGGGACGCCACAATAACATGAATTTGGTCAATGTCATGATCGTAGGCACTGCTGCTGAAGATGTTTGAATAAGAAGCCAGAAACTCAGCAGCTGGTCGACAGACTCTTCCAGCTCCAAGAATTAAAACCTTTGACCCTTCTTTAGCCATGCTGTCATCAGTTCCACACTCATTGACTTTTCCTATCTTTAGAGATAATTCAATTTCTCTTCTGGCATTAGGATCTCCATGTGCATTAGCTAGAGAAGTCAAGGAATCAATAATCTTATCCAATGTAGCTGTATCATCTGCTCCTACTTCAAGCTCTGAGTATGACATATCATCAATGCTTTGCCCAACATCGCATCTAATCAAGTGAAAAGAACCTCCGGCTGTTTCAATAATATCCAGAGCTTCATTAATAAGGAACTTATCAAAGAGGTGGCCACTGAGAGACACCAGGCTGTTGTACTTCTTATCAGGTAATAGATTTGTTGGAGCTGGTGGCAACTCTATTATAGTCTTTCTCATCCGAGGAATATACTCATACAGAGAAGTGAGTCTGCCAGCATGCGCAATGCAAGCTTTTCTCAAGTGTGAAGGAAGCTCCAACAGTTCCTTAGCTGAGGCCAATCTAGCAACGAATTTGGATAATATGTCTCCAAAATGTTGGGAGGCCTACAGCATAGAAGTTCAGTAGGACAACAGTCAATGGAAAAGGTTTGTGCTTAAAACAAAGATACCCTTACTTATTCTATAAAAGAGCCCACCTCTTTGGAAAATTCTGTAGGGAGAATGTCAACGGCTAAGCAGATCACACCATTTCCTTCCATATCATCATGGCATGAATTAGTACAAGGATCATACCTGAAGAAAGGTCTCTCAATTGAAGTACTCTTGTTCACAAATTCTATGGAACCTCCAATGTCACAAGTTATATCAGAAATACCAACCAAAGGGCAACCATTCTTCATCAGTTGTTGTAACTGGTCAATGCTCAGTAATCGTGGAAACCTCCTCTCCCAGTACATGCAGTTAACAATGGCAGATGCATATGGAGCAATCCTTTCATGAAAAACAGGCTTGTAGTGTTCTGGATGAGCATAATAGTCAGCTTTGTTGAAGCATCTGGTGGGATCCTTGGGAGTGACCATGTCTCTAGAAGAGACAACACAACCATACAGCTGGAATACTCTCTTGCTTGATTGTGGATGTTGAGACAGACTTCTAGCCGCAGAAAGCTCTGGAAGCTTCCCAGCATCAACAAAGCTATGGGGCAGTAACTTGAATATCTCTTGCGCACCCTGAGAAACATTTCCAGTTCCAGTGAATACAAATACTATTGGGCAAATTCCAGATGGAAGTCCAAATGTTGCTATCTCTTCACCAATGGCAATGACTGCAGCCTTGGCTGCAGCGAGTGAAGGATACATATGTGATTGCCCTAGAGAGAGAAATGGGGTCGAGTATCCAAGGCTCAAGTACCGTTGTCCGAGACCGTGTAAGAAGTCTATCAGTCCAGCTCTCCCAGCAAATTTCCCAAATGCAAGCAATCTTTTCCCATCATCTCCAGCAATTAGCTCATAATCAAACAGGGATACTCTTTTTTCAAGGATCTCATCTAATAGTGGCATATTTTCTTTCTGGGCCTTATGGGTGTGAGAAAAGAATCCATATGCTCTATGTGGAAGAATCATCTCCAGCTTTGGTTGTTTGATTCCTATAATAAGACCACACTCTGACAGGTCTTTTGAAATCTCACACCCAACATCCTCGTATTGAGCATCATGATGGATCCTCTTTGTACTTGGTTGCACGATAATCCGATTTACCCCAGTTCCCCTCTTGCCTCCTCCAAGCAGAAGGCGAGCACAATGGGATGGGGTTAATGGTGCTCTCCTTTCCCACATATTAGCAGTCTCGGCAAGAATCCCAACAACTCCATTGCCTAGTAATGTGTCACTGTTTTCATTTCCCGCAGAACCCATAGAGAAGCCCTGTTAAGGTGCCACAGTGAAGAACCTGCTATTTACAATTCCTCGGATTGCCGCGGAACGGAGACGACGACGGAATCGTAGCAGGCGGCGGAGTGGAGGCGCAGCCGGAGGGATTCGAGGAACGGATGCGCTCCAGCTTCCAGTTTCCAAGGAGGTACTAGTAAAATAGGAAGGCGGAAGAAGAAGAACTGCGCGATTTGGACACGTCGGCTGCGGCGGCGCCACTGGCCGTGGGATGGCGACGCCGGGCCGACGACGCCACGGGAGAGGAAGGCGGCGTCGCTGGACCTGGACCTGGACAGGAGTTGGTTCTGGGCGGAGTGGAGGCGACGGCGACGAGGACGGGGACGGCAATATGAAGCTGCAGCGTGGCCGTGTACGGGGGCGTGGCAACAGTTGGCAAATTTGTC

Coding Potentia
Explanation CPC Score
noncoding -1.04541
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0187500.2 2 33256216 C T
Osa02LNT0187500.2 2 33254824 T C
Osa02LNT0187500.2 2 33255442 G T
Osa02LNT0187500.2 2 33256565 C A
Osa02LNT0187500.2 2 33257006 C G
Osa02LNT0187500.2 2 33257071 A G
Osa02LNT0187500.2 2 33258876 T G
Osa02LNT0187500.2 2 33259175 T C
Osa02LNT0187500.2 2 33259270 T C
Osa02LNT0187500.2 2 33259515 T C
Osa02LNT0187500.2 2 33260845 A C
Osa02LNT0187500.2 2 33254450 G T
Osa02LNT0187500.2 2 33260883 C T
Osa02LNT0187500.2 2 33262379 T G
Osa02LNT0187500.2 2 33263273 A T
Osa02LNT0187500.2 2 33263804 T C
Osa02LNT0187500.2 2 33263810 C T
Osa02LNT0187500.2 2 33265919 T 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
Osa02LNT0187500.2 osa-miR5824 Cleavage 4.5 15.356 1 24
Osa02LNT0187500.2 osa-miR1440b Cleavage 4.5 14.542 1 21
Osa02LNT0187500.2 osa-miR6247 Cleavage 4.5 24.682 1 21
Osa02LNT0187500.2 osa-miR5512b Cleavage 3.5 21.018 1 21
Osa02LNT0187500.2 osa-miR395b Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395d Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395e Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395g Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395h Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395i Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395j Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395k Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395l Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395s Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395c Cleavage 3.5 13.458 1 21
Osa02LNT0187500.2 osa-miR167e-3p Cleavage 4.0 19.741 1 21
Osa02LNT0187500.2 osa-miR167h-3p Cleavage 3.0 19.741 1 21
Osa02LNT0187500.2 osa-miR167i-3p Cleavage 4.0 19.741 1 21
Osa02LNT0187500.2 osa-miR395m Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395n Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395o Cleavage 4.5 13.458 1 21
Osa02LNT0187500.2 osa-miR395p Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395q Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR395w Cleavage 3.5 13.458 1 22
Osa02LNT0187500.2 osa-miR395r Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR1846a-3p Cleavage 3.5 20.542 1 21
Osa02LNT0187500.2 osa-miR1846b-3p Cleavage 3.5 20.542 1 21
Osa02LNT0187500.2 osa-miR395y Cleavage 4.0 13.458 1 21
Osa02LNT0187500.2 osa-miR812k Cleavage 4.0 21.967 1 24
Osa02LNT0187500.2 osa-miR5490 Cleavage 4.5 14.302 1 21
Osa02LNT0187500.2 osa-miR5512a Cleavage 3.5 21.018 1 21
Osa02LNT0187500.2 osa-miR5521 Translation 4.5 15.301 1 21
Osa02LNT0187500.2 osa-miR812m Cleavage 4.0 21.967 1 24
Osa02LNT0187500.2 osa-miR812f Cleavage 4.5 21.967 1 24
Osa02LNT0187500.2 osa-miR812l Cleavage 4.0 21.967 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0187500.2 2 sk1(t) Morphological trait Seed nan nan
Osa02LNT0187500.2 2 nan Morphological trait Seed C747 C1445
Osa02LNT0187500.2 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0187500.2 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0187500.2 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0187500.2 2 ss2 Physiological trait Source activity RM240 RM213
Osa02LNT0187500.2 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
Osa02LNT0187500.2 2 33261820 Lemma-and-palea-pubescence 14.42553711 -