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

>Osa02LNT0190600.1

CAGCAAAGTCATAGAATTGCTATATAAACATTGGTTAATTTGCATATACAAGTGATACTCCGTTCTGACGAAAACGCTAACAAAAAAAGGGTTAAATTAGCAACTTGATCCATGTACGCACAATGAAACTGCAGGCTCTGTAGTCTCCATTAACACTGGAAAATTGCTAGTTAAAAATTGGTTAAATCTGCGTATATGTGTATAATTTCTATACAACGTTTAGCTGTACAATCTTCTATGAGTTCTATCATCATTTGTGATGTATTGTTTGCAAAAAAGGGAGAAATAACTGTTTGCAATCTCCCGTCGGAAGTAAGAAAAATCACTTCACAAAAATGCCTCCCGGATCAACCGTGCAAATACTCGCGATGACAACCGGCTCATGACCTCTGGTAGGATCTTCGACGAAATGCTCGGCAACACAGGTAGAAGCTCTTGTACAAGATACACAACATTTACATCCCCATCAATTGTTGTTGGATTGTTCCCAGCTGTCAAAAACTTCACAACCTTCTCAACATTGTTCAAGATGACCCTGTCTTCCTCTGTGATTGTAGGAAGCAGTGCTCTAGCTCTGACAGGAACCATGCTGAAAACTGGGGTAGCATTTCCTAGCCCAAAAGATGCAGCAATTTGTATCAGTTGCTCCCTTGAAACTGCATCTATGGCTTTGACAATCTCATCAAGAATGAACTCCCTAAAAAAGTCGCCCCTCTCAGAGAGTAGAAAAGAAAGAGCAGCCCGAGCTTTGACTGGTTGCTCAGGCTGTGATATGGCCATTGGAAATGCAGGAACTAAACTTGTGCTTGGTAGAGTTCCTATCTCAGCCAGCTCAGCCATGCTGCCTTTCAAGTTCTCCCCACCACCACTCTTTGCTGCACGAATAAAATTCTCGAAAGCTTGCATGACATCAATGAATCTTTCTGCGTCGAATACACCTGTTTTGCCATATATTGTGTATCGCAAGGCGCTCCTTAGACGAGGTGACTCATCTGTTAGTAGTCTCTGCGCAATATATGGGTATGCTTCATCCACAATGGCAAATTCAGGGTCACCCACCAAAGCTATACCCTCCAATACTCCAATGGCTCTGATAATCAAAGCAAAGTACGGAGGTATCCTGAATGGGTAATCAAATGTTATCTGTGCTAGATCTGCTGCTAACTCTTGAAAGTTTATATTCTTTGCGCCACCTCCTTCAAGTGCTTGATCAAAAACTTTGGCCAATACAGGCAAGATTGGGTCCAAGTTAACTCCCTCAGGGATGAAACCAAGCTTCACAAAGTCCTTGACTATCGCATCATAATCACGATGAATGAGGTGGGCTATTGCTTCAATCATTCCGTACTTTTGGTCATCTGTCAATTTAGTTACAAGCCCAAAATCAAGAATAGCTAGTTTTCCATCTGGTGTCCTAATCATATTGCCAGGATGTGGATCAGCATGGAAAAATCCAGTATCAAGCAACTGTTTTAGGTAGCATATGACTCCTACACTGACCAATGACCCAACATCATCCTCTGTACTTTGTGACAGCTTCTCCCCATCTATCCATTGTGTAGTAAGAACTTTTCTAGATGTGTATTTCTGGTATGTCTTTGGTACAACGACCTGCGGAAGATCCTTTTTCATCATTTCAGCAAAGCGATTGCCATTTTCTCCTTCATTCACATAATCAAGTTCTTCGAAAAATCGAGCAGCCCACTCATCTACTAGGCCAACAACATCAATGGAGACCTGCGGAAATCTCCTTAGTACCAGGCCCAAGTTTCTAATGATGAATAAATCAATTGTGACAGTTTCAAGTACAAACGGCCTCTGTACTTTCACAGCTACAAGTTCTCCGGTTTCTTTCAAGCGGCCCTTGTAAACCTGCCCCAGAGATGCGGCAGCAATTGGGGAAGGAGATAATTCAGAGTATATTTCGTGCCACGGCCGCCCAAGCTCTTCTTCAAGAAGAGTCATTGCAAGATCATCGGAGAACGAAGGAACCTTATCACAAAGTTTCTGCAATTCAGTCATTGCTGCAGGGGACAGAATATCTGGTCGAATACTTAGTGCTTGGCCAAGCTTAATATAAGCAGGACCCAAAGATGTCACAATTTCCCTCAGCTCAATCGCACGCGCTACTTCATTCTCCTTGAGCTTGTTGTTTATGAGGTCTGATATGAGATGAGAGATGAAACCACCAGCAACAGACAGCAATTGCACGATCCGTGTGGCGACGGCCCTCGGGCGCTTCCCCCAGTATGCAGAAATGATCTCAGGACTGTACACGAGAGGCAGCGCCTCATTGTTGTTCATGGATGAAACCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.482328
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0190600.1 2 35005008 T A
Osa02LNT0190600.1 2 35005071 A G
Osa02LNT0190600.1 2 35005235 T A
Osa02LNT0190600.1 2 35005361 T C
Osa02LNT0190600.1 2 35006159 G A
Osa02LNT0190600.1 2 35008022 A G
Osa02LNT0190600.1 2 35008195 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0190600.1 osa-miR395v Cleavage 5.0 12.334 1 21
Osa02LNT0190600.1 osa-miR444b.2 Cleavage 4.0 15.954 1 21
Osa02LNT0190600.1 osa-miR444c.2 Cleavage 4.0 15.954 1 21
Osa02LNT0190600.1 osa-miR1861h Cleavage 5.0 19.325 1 22
Osa02LNT0190600.1 osa-miR1861j Cleavage 5.0 19.325 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0190600.1 2 nan Morphological trait Panicle/flower RG256 RG151
Osa02LNT0190600.1 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0190600.1 2 ss2 Physiological trait Source activity RM240 RM213
Osa02LNT0190600.1 2 nan Morphological trait Root RG256 RG151
Osa02LNT0190600.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0190600.1 2 gn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190600.1 2 gw2.1 Morphological trait Seed RM250 RM208
Osa02LNT0190600.1 2 pl2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190600.1 2 sn2.1 Morphological trait Panicle/flower RM250 RM208
Osa02LNT0190600.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0190600.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0190600.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
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