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

>Osa06LNT0358000.2

TGATGGTAAAGGACAGGTGATCATTGATAAGGCACAGAATGCCTGATTGCCTGTAGGCTTTTGTTCAATGTTGACATGATTCCACACATGAAAGATCAGTAGTACAAAGTATGCACACTGCTATATAAGCTACTATGACAAAACTGTGTCCAGAACTCCAGACGCCAAGCGTGACCCTGAAACACTGGGATGCAACAATCCTATTCTTTTTTGTCACAAACCCACGATTTTTTTTCTTGTATTCAGACAATTGTGATGCATACAACAACCAAGAGTACACAACTAAGGCTTGCCACTAGCTCTTGCGCAGGTATTTGCTCACTTGGGCTGCAAGCGCTACAGATTTGGCATTGATGTCGTTCATCAGGTACTCCCTTTCGGCGCGACGGCGTTGCTGTCGTTCTCTCTTGGCTCTCTTTGGGGCCAACCTTGCTTCTCTCTCCACATAGGCTAGCCTGAACTTCTCGGCGATTGGTATTTCAGGGGGCGCATTTGGGTTGGTTGGAACGGTGGGTCTTCGAGGGGCGGCAGCAACAGCCCATGTTTTGGGGTCAATATCTGCGATTATGGAGTGATCCAGTGGTACACTTGCCAGAGCTTCAGCTGGGACCTTGTGTCCACGAAGGTCAAAAGGTGATGGCTGTGGGTTGACAGTAATACGAGGGCATTCCATAGATATAATTTCCTTTGAGTTATCATCTATCTTTGGCCAAACTAGCCATCTTAAGGACTCTGCACCCCCGCCAATTTCTACCGTATCAAGTTCTTCCCACGAGTCCTCTTCAAGAGTATTCAATTTGGGTTTCAAGAGATACACAGATCTGCGCGCGGTGGATTCACTTCCTGGACAGCCTCCGCATCTCAATATCTCCAAGGATGGGCAATGGCATATAACCTCAGAAACAGCTGCAGCAGTTATTCTTTCACAGCGACTAATATCGATAGCCCACAGATTATTAGAAATATTTGCCACAGTAGCCAGACCAATATCAGATACATCAGAGCCAGATATATCTAGGATCTCCCATGAACTATCAGCAAGAGAGATCAAAACTTCATCATTTAGAAGCCTTCTTCTCCTTGCAATGGACAAAATTGCCAGCTTTATGTGGGGTGGAAAGAAGGTAGAAAATTCGGAAATATCAGTTATGATATCTTCAAGATGCTGTCCGAGGATGCCAAGGCACAAACTAACCAATTTCCGAGGTCTAGCTTTGTTTGTTGGAGAATAGAACGAAGCTGCCGGTAACGAACTCGCTGGCTTCCGGCGCGGCGTGACCTCGACATCTCTCAGCGACGCCGCGAGCTCTGCGACCACCGACTTCCCCTTCTCCATCAACTCCAGCCCCGCCCCACACGGGGGGTCAGATCGAATCAGAAATCAGATGGAAGCCTCTTCTTGGGGGATGGCGGGTATCGGGGTATGCAACGCGTAGGTAGGAAGCGGGGATGGCCGCCGGCTAGTCGGCCGGGAGGGAGGAGACGCGGGGGCGGCGGCAGCGAGGCGGCGCGGAGGCCGGCGGTGAGGGGGGAGAAGAGGCGGTGCGGCGAGGCCGGCCGGAACGGGAAGGGAAATATCTGTTTTCTTCTTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.893597
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0358000.2 6 28281222 T C
Osa06LNT0358000.2 6 28281230 A C
Osa06LNT0358000.2 6 28282343 T C
Osa06LNT0358000.2 6 28282562 C T
Osa06LNT0358000.2 6 28282812 A G
Osa06LNT0358000.2 6 28283316 T A
Osa06LNT0358000.2 6 28284183 C T
Osa06LNT0358000.2 6 28284599 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
Osa06LNT0358000.2 osa-miR156a Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156b-5p Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156c-5p Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156d Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156e Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156f-5p Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156g-5p Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156h-5p Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156i Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR156j-5p Cleavage 5.0 14.049 1 20
Osa06LNT0358000.2 osa-miR159a.2 Cleavage 4.5 17.331 1 21
Osa06LNT0358000.2 osa-miR408-3p Cleavage 3.5 24.365 1 21
Osa06LNT0358000.2 osa-miR419 Translation 4.5 17.907 1 21
Osa06LNT0358000.2 osa-miR1428e-5p Translation 5.0 22.248 1 22
Osa06LNT0358000.2 osa-miR1861e Cleavage 4.0 13.598 1 22
Osa06LNT0358000.2 osa-miR1861k Cleavage 4.0 13.598 1 22
Osa06LNT0358000.2 osa-miR1861m Cleavage 4.0 13.598 1 22
Osa06LNT0358000.2 osa-miR1428f-5p Translation 5.0 22.248 1 22
Osa06LNT0358000.2 osa-miR1428g-5p Translation 5.0 22.248 1 22
Osa06LNT0358000.2 osa-miR2118a Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR2118b Cleavage 4.0 18.592 1 22
Osa06LNT0358000.2 osa-miR2118c Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR2118d Cleavage 5.0 18.592 1 22
Osa06LNT0358000.2 osa-miR2118f Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR2118h Cleavage 5.0 18.592 1 22
Osa06LNT0358000.2 osa-miR2118j Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR2118k Cleavage 5.0 18.592 1 22
Osa06LNT0358000.2 osa-miR2118m Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR2118n Cleavage 4.0 18.592 1 22
Osa06LNT0358000.2 osa-miR2118p Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR2118q Cleavage 4.5 18.592 1 22
Osa06LNT0358000.2 osa-miR5514 Cleavage 5.0 18.532 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0358000.2 6 nan Morphological trait Culm/leaf RG653 RZ140
Osa06LNT0358000.2 6 qLVG6 Resistance or Tolerance Cold tolerance RM340 RM30
Osa06LNT0358000.2 6 qREP-6 Resistance or Tolerance Other soil stress tolerance nan nan
Osa06LNT0358000.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0358000.2 6 nan Morphological trait Root RM4447 RM5509
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