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

>Osa06LNT0359700.1

GAATAAACGACGAAATATATACACATTTTCAGGGATGAATATAGTAAAACACAAGGTTTATTCATATACAACTTCATGAAAATGGGAGAAAAAAGTGGCCATTTGGTAGAACTCATGGGCCGATACGTCATTAGCTTTGTGGTATACAACAAAAATCGAACATCATACAATATCACCAAATGTGAAACATGTGCATGGCAAAATCAGTTGCCAATAATCAATCTACTCGCCTACAAGAATGAAGGGGTTGTACTACATGCAGAATGTTACAACATGTTGTGTTCACAGATGCACATACATTATACATAGTGGTCATAATCATATGCTGCTGTGTCTCCAAAGAACCTGCTCATCAATTTTAGTTAGTTTTTCATCATCTAACAGCTTCCAGGTGTGGATCGACTCGACTTCCACCAATGATTTCTGCCCTTTCTTGAGTTCAGTATGAATTACCCGAGCTCTTCTTGGCCAATGAGGTCTTCCATAGGCATGATAACCAAAGCCACCACCATAACAGAACCATATCCCATTAAGGTCGCCACAAAAATCATTAAGATGGTCATGGCCAAGAAAGACAGCTTTCACATCTCCCATGGAGGTTAGGGTGCCAAGAACACCGGAGTTTACAGTTGAGCAAGCCACCCCTTCCTGATACTGGCCCTTGAAACCTGTATACCACAGCCCTCTGACTTCTGGAATTGGGATGTGAAAGAATGCAAATGCAGGAGCATGCAAGTTTTGCTGAAGCTCCTGTGAGGTAGCACGAAGCCAAGCAAGTTGAGATTCTTTGATCCATCCATAGGTTTTTACTCCATTGACCACTTCACGATCACCACTATCCAGGAAGTAAAGGTTAAGTAAACTAGTATTGACAAACTCAGAACCAAACGGCCCATGTATGCTGACATGATAGTTGCCAAACCCATGTACCAAAGAACCAGGAGGGTTTACTTGAGATACCGAGTAATCCATCAGGGACATGAACACCATCAGTTCCTCTCTGGTCATAGTGGACTCCTGGTCATGATTTCCTAAAATGGCAGCCCATGGTACTTTATACTCGATTGCAGGGCTAATTGCTTTGAGTAGTGACTCAGCTGCATCAGATGCACTGCCCCCAAATATATTGTCTCCGGTGAAGGCGATGAGGTCGGGCCTCTCGGCCTCGATGACCCGCCGCAGGAACCGCGTGGTGTTGAGGTCGGAGCAGCGCGCGCCGCCCACCTCCGGCGCCACGTCCCGGCACCGCGTGGCGGCGCCGTTGCCGAAGTGCATGTCCGCCACCTGGAGGATCTTGAAGGCGCCGTCATGGCGGAAGCGGAGGGGGAAGGGAGGGGTCCTCTTGAAGCGGGGCGCGGCGGCGGTCGGGTCAGGGTTGAGGTGGGTGGAGAGGCGGATGAGGAGCAAGGAGAGGAGGCAGGGGAGGAGGAGGGAGACGAGGGAGGTGGAAGACGAAGAACCCATCGATCTCGCCGGTCGCCGCCTGCCACCTCCCACCGCATCGCATCGCACTACTCAACAACTCCCCTACTGTTGCTCATAGTTTTTTTTTTTTTTCAGAAACTTTCGGCTGTGTCCTTTCCTCCGCCTTTCCAACTTCCACAAATTTTTGACAATTTAACCCTTTTCGAAAACTAATTTTACAAATAAATCGTGCCCAAACTTATTTAAAAAATGACGCTTTTGTTCAGCGTCAAATCGTATGGCGCTGAAATTAGACACCTCAACGCCAAATAGAACGACGCTGAATGCACGTTGGCACGCCGACTCAGTCTCTCGTCCGCGGTGACACGATATTCTGCGCCAATTGACGTAGCACTGAGGTGTCTAAGTTTAGCGACATACGATTTGACGCTAAACAAAAAGTGTCATTTTTAAAATAAGTTTTGGCCACGATTCATTTGTAAAATTAGTTTTTGGAAAGAGTCAAATTGTCAAAATTTGTGTTCCAACTCTTGTGTCCACATTTTTAAAACAAAATTATAGTAAAGTTTATTTTTAAAATACATATTAATCTATTTTTTAAAATTGCTACAGCTGACATTTAATTAATCATATGTTCCTTTTAGTCCGCAGAGATTTAGTTTTCGACCTGATTTGCCGTACACTGCCAGAAATTTCGTGAGAGAGCTTGATTTCGAAAATAATCATTGCTTTCCGAATAGTCTTGTCTTAAAAGAAAGAGCTTTTTTTTTACTTGGTTGAATTAGCTACAGCCTTATAGTTGGTCCATTGGGCCCTGCAGAGATGGAAATTGTGCCTAGTTGATGTGGGACTTGGGCCCATCGTGCTTAGTGCCAAAACGGGCCAGGATTTTTATACCGTGTGGGCCGACGTGACTTGGGCCGGCCCGATAAAGTACAGCCCAAGTCCCAGGTCTACCTAGTGTTCTACTAGATGAATAGGAAATACAGTAGTGCAGTGCACCAACCTCTGAGGCCTCACTGAGTTGGCGCGTAACCTCGTCGCGCCAGCTCAGCTTTTGGTCTACGTGGAGCATGCGCCTGGGACCTCACTTGGCGACTTGTCCCTAAGCTAAGGAGCGCGAAACTTCGTCGAAGCGAGGAAGCGCGCGGCGCCGAAAAAGCAAGGCGCGTGCACTGTGGGCATCGTTCCTGGCCGAGCTCTGCCCTCACATCGATTTCGCCTGGTGAAATCCCCGAACCGCCCTCCTGGGGGCGGCGGGCTTGGCGCGGGAGGCTGGGTCGGGGTGCCGACGACGAGCCGGTGGCTGCCGGGGAGGGGCCTAGAACACTTCCAGTTGATTCAGCTGTGGCAAAGCGTCTCTCCGATGGCGTTGAGTGTGACGCGGGCGGCGGCCGCGCCATGACGCCGGTGCCAGTGCCGCTGTGGTGGTGGCGATGAAGACCATGACGGCGCAAGGGAGTGAATGGATGGATTTGCAACGCAACCAAACCATGGCCCTTCACCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.160263
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0359700.1 6 29384983 A G
Osa06LNT0359700.1 6 29384235 T G
Osa06LNT0359700.1 6 29384887 G A
Osa06LNT0359700.1 6 29383517 A G
Osa06LNT0359700.1 6 29383961 A G
Osa06LNT0359700.1 6 29385798 G A
Osa06LNT0359700.1 6 29385879 A G
Osa06LNT0359700.1 6 29386889 T C
Osa06LNT0359700.1 6 29386955 A G
Osa06LNT0359700.1 6 29386979 T C
Osa06LNT0359700.1 6 29386901 C G
Osa06LNT0359700.1 6 29386210 A T
Osa06LNT0359700.1 6 29386236 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa06LNT0359700.1 DTM_#DNAt_MULE_japo_Os0085 Chr6 - 29385944 29386289 345
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0359700.1 osa-miR7692-3p Translation 4.5 17.039 1 24
Osa06LNT0359700.1 osa-miR1430 Cleavage 5.0 22.368 1 21
Osa06LNT0359700.1 osa-miR1879 Cleavage 5.0 23.292 1 24
Osa06LNT0359700.1 osa-miR2122 Cleavage 4.5 6.235 1 22
Osa06LNT0359700.1 osa-miR5159 Translation 5.0 15.257 1 24
Osa06LNT0359700.1 osa-miR5487 Translation 4.0 9.963 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0359700.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0359700.1 6 nan Morphological trait Culm/leaf RG653 RZ140
Osa06LNT0359700.1 6 qLVG6 Resistance or Tolerance Cold tolerance RM340 RM30
Osa06LNT0359700.1 6 qREP-6 Resistance or Tolerance Other soil stress tolerance nan nan
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