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

>Osa04LNT0245700.2

CCCTGATTAAAATAGTGCCATGAGTATACAAAAGATGCTTACAAGGCCAGTATGCACAGTAAAATATCATACGAGGAACACAAAACAGCAACATTTTGCAGGCAACGCAGTGTGAAAATAAAACTGTCACACCAGGCCATGGAACTGACTGATTCTGAAACAATTTCAAATTATATATGCATCTTTAGCACTAGTATCTCAAAACTAGAAAACCTTTTCCCTAACTTGAAAATTAAAATGGCAGGACATAGTATATAACAAACTGCTCTCTTCTGAAGTTTGAGTGGCACACCAGATCACCATGGTAGGCGAACTTGCCATAGTTGAATGGCATCAGCGATGGCATGCGGTCTTTGCCAACCAACCGTAATTTTTGCTGTCTTCATTGCCCCAGTTGACTTTCTCACACCTTGGACCTTTGCTTCTGTTCTGCCACTCATCTCCCATCTCTGGAGCACTTATCACCCATAGAATCTAGGTGCTGTCCTGTCCTGCTGCATCCAAACTTTCCATGGCTTTATTTTGGTTACAGCGAAATCTCGATAGTTTAATAGCAAACCTTAATCTCGATAGTTTCCCTGCCAATTAAATCTGGTCAATTGAACAAAGATAGGTACATTTGTTGGAACTATATATAGAGAGGGAGGAGAAATAGAGTTCATCCTTCAAACAAGCCTTGCACAGAACGTCGTAATATCTCTGGGGTATACATGCTGCATGTTAAATTTCTCGGAAAACATGAGCAAAATAATCCTGAATTGGAATTTCTCTGCAGTTCCTCAAAGGATATTTCATATGCTGGAAAAATTAAATTTTCTATATCATCTCGCAATTTCTGCTTTAGCTCACTATCAGGAACTTTCAAAACCTTCTGGCAATCAAAAGTACCTTCAAACTTTGAAATGAATGCATTCATAGATTGACGTATGCTTCCGCCTGTATGATTGTTCAAACAAGATATGGCTGGACCCCAAGATGCAGTCATATATCTACTAGTATAATTTTCCATGTCACTCTGGAACTCATTCTTGCACTCTTCAATGAGCTCCCTATGGACCAATAACCCATCCAGCAGACCATTTGTATCCCTATTAAAATGCTTTATGTTATTCAATAAGAATATGAACAAGTTTGGATTGTTTCCGTCTGAATCATTTTTGTCTGGATCATCTAACATGGAAAGCTCTTTGATCTTTAATTTCCAGCAAGCAATGACGCCATTAATAAGATAACCAAATGAGTCTTGGCCATCACCAGGGACCAGAGTGGAATGCAATAAATTCTTGTGAACGTTGAAAATCTTTATTGCATTTATGAGGAAACATGTCGTTGGATGAATAGCAATGTTGTCCCAGGTTTGCACCTTATGTTGTATGAATCGCTTCATATTGTCAATTATTCCCCTGGAAGCATTCCTCATGTTATGTAAGATGCTGGTAAAAAACTCGTCAGGTTCATCAGGAGACAACTCCCTTATGGTAGGAAGGACATCTTGTAGTGTATCATAGGCAAGTAGCATTGGACGGATATGCTCCTCAGACCAGTTTGACTCACTGAAAGAAAGTGCAATCTCCAACATCTTCTTAATAGGTGACTTTGCAAACTGTTGAAAGTAGTCTTTTTTTGTTTGGAAAAATGGTTGATTTTGTCCACAAAACTGACAGAACATCGACTGGAGAACTTTGGTGCTAATTTTCAGCATAATAAGATAATCTTTTCCAAGATCTTCACACTTCGAAAAATCCATGGATGTCTTTGTGTTTTTACCAAGAATCCATGGTGTATCATATTCATAGAAGAGACTGCTCAACATATCTGAATTGTTAGTGAAGACCATGAGCAGTTCTTCTCTGTGATCACCTATGATCTCTCCGCAACGGCCCATAGCGGTATCAAGCTGTGCCACAGACTCAGTTGAGATGAGGTTGACATTCTCGTCGAGAAGATGGACATTTGAAGAATAACGAAGCGGATGCCCGTTCCTTGCTCCAATGCCACCACCATTTGAGTCACTTGCTACACTAGATGCATAATTGTCAGGACTGCTCCTTTCTGATGAGTCGCATGGGCAGGAGCAGAAGTGGGTTAGATTTGTCCGGATCGAAAGGGGGGGTCGGTTGATGCATTCGTAGTGACTGTTGGCAGCTGTTGACAGTCCATCCCGGTTCCACATGTGCAGGCGGCATATCACCTCTCCGGTCTGTCGCATGGAAACGGCAGAGCAGCAGCAGCAGCAGCAGGAATGGCCATAGCCATAGGAGGACGCAGGAAACGAGTAGCAGCCAAGCAGCAATCCTCTGCTCCTCTCTCGTCGATGAAGAATCCGGGCTACCTTTCATCCACCCTAACGATCCTCGGTAAGCAGAAGCGAGGCGCCCCCTCTAGGGTCGCGGCGGCGGCCGCCGGTGGAGTGAGGCGGCGCCTATAAGGGAT

Coding Potentia
Explanation CPC Score
noncoding -1.05317
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0245700.2 4 665437 T C
Osa04LNT0245700.2 4 661253 G A
Osa04LNT0245700.2 4 662579 A G
Osa04LNT0245700.2 4 662639 C T
Osa04LNT0245700.2 4 662743 C T
Osa04LNT0245700.2 4 662754 A C
Osa04LNT0245700.2 4 662953 T A
Osa04LNT0245700.2 4 663446 C T
Osa04LNT0245700.2 4 664266 A T
Osa04LNT0245700.2 4 664447 C T
Osa04LNT0245700.2 4 664565 C T
Osa04LNT0245700.2 4 664805 T A
Osa04LNT0245700.2 4 665302 T C
Osa04LNT0245700.2 4 665325 A G
Osa04LNT0245700.2 4 665627 G A
Osa04LNT0245700.2 4 666426 A G
Osa04LNT0245700.2 4 666545 A G
Osa04LNT0245700.2 4 666782 C G
Osa04LNT0245700.2 4 661220 C A
Osa04LNT0245700.2 4 666942 A G
Osa04LNT0245700.2 4 666608 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0245700.2 osa-miR5791 Translation 4.5 10.651 1 21
Osa04LNT0245700.2 osa-miR156f-3p Translation 3.5 24.264 1 22
Osa04LNT0245700.2 osa-miR156h-3p Translation 3.5 24.264 1 22
Osa04LNT0245700.2 osa-miR393a Translation 3.5 11.96 1 21
Osa04LNT0245700.2 osa-miR156l-3p Translation 3.5 24.264 1 22
Osa04LNT0245700.2 osa-miR159c Translation 4.0 12.146 1 21
Osa04LNT0245700.2 osa-miR159d Translation 4.0 12.146 1 21
Osa04LNT0245700.2 osa-miR159e Translation 4.0 12.146 1 21
Osa04LNT0245700.2 osa-miR393b-5p Translation 3.5 11.96 1 22
Osa04LNT0245700.2 osa-miR415 Cleavage 4.0 8.201 1 21
Osa04LNT0245700.2 osa-miR395o Translation 5.0 13.946 1 21
Osa04LNT0245700.2 osa-miR1857-5p Cleavage 4.5 18.829 1 21
Osa04LNT0245700.2 osa-miR1857-5p Cleavage 4.5 14.834 1 21
Osa04LNT0245700.2 osa-miR1857-5p Cleavage 5.0 12.264 1 21
Osa04LNT0245700.2 osa-miR1866-5p Translation 5.0 14.037 1 24
Osa04LNT0245700.2 osa-miR812n-5p Translation 4.0 11.484 1 24
Osa04LNT0245700.2 osa-miR812n-5p Translation 5.0 15.753 1 24
Osa04LNT0245700.2 osa-miR5487 Translation 4.0 11.606 1 21
Osa04LNT0245700.2 osa-miR5487 Translation 5.0 19.51 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0245700.2 4 qOVA-4 Resistance or Tolerance Insect resistance R1854 C946
Osa04LNT0245700.2 4 nan Resistance or Tolerance Other soil stress tolerance C946 R1854
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