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

>Osa03LNT0204800.2

GCATTTGCCATTGATCAATCTGTATAGCTTGAAAGCCTTATTCCAAACTTATACATCAATCAGGCTAGCAAGACTGACGGAAGTGTTCTTTACATCTCGTCAGGTTGTAGCCAGTCTATACATGCCCCCGCAGTGCTTGATCAGACAAAAAAGCAACATCACAGGCACTGCTTACAGATAGACCACTGTCAAGCACATTAACATTCATATATGGTTTAATTTATTCACTCGGCGATGATTTCACTGGAGGCGAGGATAAAATTGCGGATGAACTGAACAATGGCTCGTGAACTACGGTGCTGTTCGAGACGAAAATCGGCTGTCTGTTCAGCTGCATCATCACTGCCCTAAGGATATCTGTCAGTAGTTTCTTGAACCCGGCCTCGTCTACCGCTGTTCTTTCATCAGCATTAACTGTCTTGAGCGCCTCATTCACCACGGCATCCACCTGATTAACGGCACCGTAAGGTGGTAAGCCTGCTGCATCTGCCATCTTATCGAGTGCGGCTATCAGGCACTCCCTGGATCCTTTGTTCTTATGCTCTATGAGTACATCTTTCCAGACAGAATCCAACAACTTGTCCAGCTCGAATTTGTTGTCCAGCAGCCTCTTGACACAACTACCGTCGAATGTGTTCTCGGTGTGTGCGACAATCACAGGCTGCTCCTGAAGCCTTTCAGCGATGTTGCTCAGGAGCTTCTTGAGCTGTTCTAAGAAGATATCTTGCGAGGCCGGTTGCTCAAGCTGGCCGGCAGGGAGTTTCTGCAATGCCGGCTCTATGATGTTCTCTGCAACCCAAGGGTCAGAAGCTGGTGGCATTCCGTTGTCGACATTCAGCAGCTGAAGAGCAGCTAGCAGGCACTGACGCAGAGACATGTCTTCAGAACCTATCTTTGAGAAGATGGCAGCAGCTTCTGGCTCATACCTGGGGCTGTCAACAAAGTCCCTCAGGTCCTCGCCGTCGATGCGCAGTATAACGATCGGGTCCCTCTTGAGGCCAGCCGCCATGCCGAGGAGGATATCGGACAGGACCTCCTGGAACTCTGTCCTGCTCACCTCCTCTTTCTTCCCATGAGTGAGCTCGCTGATTGCAAATCTGGACTTTTATCTCCGTAGAACCAGTGGTTGCCATCGGCAGAAGATGCTGCTAGTGGATTATTCAAGAAATATCAGACATGGCAAAAAGAAAAGAACATGATTTGCCAGAATGCTATTTGCATAGTTGCATTGGTGTTCCTGTCTGAAGTAGGACTCAGCAACTACGATGTGAAAGCCGGCATAAGAAAGTTTTAACAAATTGGCTGGGAGCCTGGGACACAAGAATTTCTGTCATTGCTTCAGAAAGATATTGGAAGTTTGGACTGTGACGTTTTAGGTTCTCCAATGGCAAGCTTAACTCTGGTTCAGGGCATCTTGACATGGACCTGTGGGCAAGCCCTCATCCTGCATTGCATGGTAAAGTCTCTTTTCTGCCAATCTGGAATTCAGGCTGACAAACGCTTTAGTACTGAGGCAGATTAGATATCAATAAAAATCTAGGCTGTTACCATATGATCGATCTGCTAAATACACCAGCCACAGTTTTTCTATCCTCATTTTCTTTTGCGATAAGACCATGTCTCTTTCAGGTTGTCTGATAAATACTAGTACTCCTTGCAATAATTGAGCAATTATTTCTAGGAAAGCAATAATACTATGATTCAATAATTGACACGTCTACTTGTCAAAAACAGTTTCTACTCGACAAATTACAAAGATTTGCTCAAGAACCGCATTACATGCCAACTATACAAGGTGCATATGTATTCACATATGTACGATTCATTAATACCAAACTCAGGAGAACAGACTTACATAAAGGTACTTGCTTCGTTTTAAATTACTTGCCGTTTTAGCTTTGTCCTAAATCAAAGGTGAATACCTTTGACCATTAATTTATAAAAATTCATGTTAATATAGTTTAACGTAATAAGATTACGTTTTTAAGATGCACCATGAGAAATGCTTTCATAACATACAATTTACGTGTTGTTAAATGGGAGTACCTATACATCTTTCAAAAGATTTTTATGATCGTATCACACAGATTTTTAATCTTTGGATTAAAATCCGATAGATTTAATAAAAAGCAAAAAACAATTAAGAAACACCATAATGGACACTAAATTACCATATCCTCAAGAAAAAGACCAAATCCAATACAAAATTTAAAATTTACATGCGAAGATTCAAAAATTACAGTGTAACTTACAAAAGTTACAGTGTAAGTTTCATAAATTACACTGTAACTTACAAGAAAATGCACTGTAAATTTGAGTGAGAAAATCAAGTGAGAGATAAGAAAAAAACTTTCAAGTGAGATATAGCAAAATCGTTGTTAAATTGCACAAATTACTAGAAATTGATGTCAACGATTTACTAAGTGTTTGACTTAGAAGGACAGGAGCAAGATGGTAATAACTTCCCTACTAGTTGTGCAACTGTTAGCATTCTTCATTGAGGTTCTAAGTTTGAACTGATTACTGAGAACTTTGATACTAGAAGCAGCACCCAAAAAATGTCTAGTGTTGTTTTTCTCAACGCGCAAGGCTTAATTAAGTTGTTAACGAGATAGTAAAACCAATCTGTTTTTCTCGAAAGAAGTGTCTGGCGGCTGGCCGGCGCAGCATTCTGAACGATTTTTTTTTTCGCCGGGCAGCACTACGAAGAATTTTCCAGCGTTCTGTACCTCGGAGTAGATGTGGTCGGCGTTGGGCGAAGACCCGCGCGCCGGCAGCCCGAGCGCGGCGCCGATGCCCTCCACCGCCGGCTGCAGCTCACGCACGGACAGCCTGCCGTCGCCGTCGGCGTCGAGCTCCCGGAACTTGCTCTCCGCGAACATCCCGAACGCCTCCCTGTCCTCCACCAGCTCCCGTATCTCCGACCCGTCCACCACCACCTTCTGCCCCTCCCCCTCCTCCCCTCCGCCGCCGCCGCCTTCTCCCCGCGCCTTCCTCCTCCTCCTCCTCCCGAACCAGCTCCTCGTCCTCTCCATCCGCCGCACCTATATATACACACACCCTCCTCCTCCTCGACGGAGAAAAAGTTGCGTCGCACTTGCACCGGTCTCGTGACGCCTCCGCCTTTCTCTTCCACTAGCCAGCTAGTACGTAGGTCGCTTTGCGTCTTGGCGTTTGGTTGCGTTGCCGCCGTTGCGAAGACGGGGAGGAGGAGGAATACT

Coding Potentia
Explanation CPC Score
noncoding -1.0338
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0204800.2 3 7916064 A G
Osa03LNT0204800.2 3 7916838 A G
Osa03LNT0204800.2 3 7917079 G A
Osa03LNT0204800.2 3 7917135 A G
Osa03LNT0204800.2 3 7915082 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0204800.2 DTM_#DNAt_MULE_japo_Os0377nt Chr3 - 7917073 7917409 336
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0204800.2 osa-miR5337b Cleavage 1.5 11.031 1 21
Osa03LNT0204800.2 osa-miR6255 Translation 5.0 24.861 1 22
Osa03LNT0204800.2 osa-miR810b.2 Cleavage 5.0 14.894 1 21
Osa03LNT0204800.2 osa-miR1439 Cleavage 3.5 9.284 1 21
Osa03LNT0204800.2 osa-miR1428e-5p Cleavage 4.5 20.428 1 22
Osa03LNT0204800.2 osa-miR1428f-5p Cleavage 4.5 20.428 1 22
Osa03LNT0204800.2 osa-miR1428g-5p Cleavage 4.5 20.428 1 22
Osa03LNT0204800.2 osa-miR2096-5p Translation 5.0 22.039 1 21
Osa03LNT0204800.2 osa-miR396f-3p Cleavage 4.0 22.575 1 24
Osa03LNT0204800.2 osa-miR5081 Translation 4.0 14.964 1 22
Osa03LNT0204800.2 osa-miR5487 Translation 4.0 17.715 1 21
Osa03LNT0204800.2 osa-miR5490 Translation 5.0 13.779 1 21
Osa03LNT0204800.2 osa-miR5499 Cleavage 5.0 24.502 1 21
Osa03LNT0204800.2 osa-miR5499 Translation 5.0 9.376 1 21
Osa03LNT0204800.2 osa-miR5521 Translation 5.0 15.785 1 21
Osa03LNT0204800.2 osa-miR1435 Cleavage 4.5 17.424 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0204800.2 3 Gy3a Others Others RG266 C63
Osa03LNT0204800.2 3 qTAA3-1 Morphological trait Shoot/Seedling C316 C63
Osa03LNT0204800.2 3 S34(t) Physiological trait Sterility nan nan
Osa03LNT0204800.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0204800.2 3 qOE3-1 Physiological trait Eating quality 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