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

>Osa05LNT0310300.2

CATGGTATGATTTATTATGAAATTCTTGATCATAATTGCATCCTCTACAACTTCAGAAATCCAATGGCTATCTTTGAAGGCAACATCTCCAGTATTGTTAGGAGAAAAAACATCCTTCAAGGCAAGACTTAAAGTATGAGCAATACAAGGCATCCATTGGATGTGATCGTATTTTTCTTCAATCAGCAGCCCAGCAGCTCTGCAAACAGGATCATTATCTGTGATCACTTGGACAACATTTTCTGGACCAACCTCTTCAATAACAGCAATGAGCTTCTCTGCAATGTACTCCTTTGTATTCACCTCATCTTCATTGTTAATTGCTTGCAGAAAAATGGGTCCACATTCATTGACAGCCAGAATGTTGACAAGTGAGCGCTGTCGAATATCTGACCAACCATCAGAAACTATCGTCACACCTGCCTTCCTCCACATGCTTTTGATGGGTTTTAGTAAGTCTTCAATGCGAGCCCTTTCTTTTTGCAGAAGAGTTGTCTTCAACCTTTTGCAATCAGGAGGAACATAACCAGGAATAATATTCTTCAAAATAAAAGAAAATGAACTCCGGAAGTATGGGTCCCTTGCAGAGTTGAAGGACAAGCCTGCTGAAGAATAGAACATTCTTGCAAACTGAGCATCGAAGTTATCTCGACATTCAGCTCTGCTCTTCTTTCTTTTCGCTTGTACAATAACTTTGCCCATACACGGTGCGTCACCAGAATAGTCACTACTACAAGATTCTGGTTCGTCACCAGAATAGTCACTGCTACAAGATTCTGTTACATTCCTTTTTTTACGCACCTGGATTAGAATTGAATCTTCTGCTGCATCAACTTCACTGGATAGTTTCATTAAGATATTGAAGGTCACTCCTGGGCAAGCTGGAACACCTTGTTTAGAAATTTTAAGCAAATGTGCCTTCACTGTGGAATAGCTTCCACGAAAGACACAACTGCAATAGTCGCATAGGAACCTCATGTTTGTTCCACAGCGAGGAGCGAACCCATCCAATATCTTAACATGCCCCCACAAAGGCAACTCATTCTCTCCAGGAGAAGGAGACTCATCCTCGCCTTCCATCTATCTCTCAAGCTTTCGAACTGGCGGGCGGCGGCGGCGGTGGGTGGCGGCGGACCCAAAACCCTCGTCGCGGGACGCGGGAAAAGCTTGGCTGCTTCCCCTTCTGAGACCCGCGAAAAAACCTCGCTTTGGTTCGCAACACTGTTGGGGGAGGCTCACCGCCGAACCCAACACTCACAGATGCTTTATGTTCCTGCTTTAACCATTTTTTATCAGTTTTAAAAATGTTTTTCCATAACTAGCATTGCAATGCTATATGTATGTGTCTAAATTCATTAACATAAATATAAATATAAGCAATGTTAGAAAGCCTTACAATATGGAACGGATGGGTAATAAAAACTGTGATGGAAATGATCCGAAACAATGCCATTTTTACAGAAGTGATTTGCAGGTCACTTAGGAATTTCCATATTTATAGATTTTAACTATTTAGTGGCAATCATAATATAGGCAAGGAACGGAATTAGAAAAATTAAATTTTATATATAAATAAATTAATTAAAATGGTAAAAAGAAAAAAAAAGATGCCACTTATATGAAAACGATGTTCGTTCGATCTAGAATTTTGTTAACCATTTATTATCCTGCCTTTTAATTTGGAAAACTTCTGCTGCAGGTTATTGTAAAAAAAATTTAAAAGGGGATTGTAAGGCCCTTCACAGTGGGCGTTACTTCGTCTACATGGAGCGTTCCTTCGTCCTCGCTGGCAAAAAAAGTTTGTGTGTCCCATAGCTTCAATAGCTTCTTCGGTTACCAGCGAAGGAACGAGAACCTCGCTTAAAAAGTAGAGCGCGGGGCCCACTGATGAGAGATGCGAGGACGAGAACGCGCGACTCCGAGGCCAGCTCCAATCCACGCCACCGTCGCCGGTGAAGAGGGTGGGGCGAGGACACGCCACCGCCGCCGTCGGTGAGGAGGGCGGGGCGAGGACGCGCCACCGCCGCCACGTCTTCAGATCCGCGGCGCCGCCGCCGTCGTTGAGGACGGCGAGGACGCTCCAAATCTGCGCAGCCGCCGCCGCTTCTTCGCCAGGTCCCGAGGATGTCGCCGCCGCTCGACGTTGGGGTAGGCGGCGCGCCGGGAAGAGGGAGAGTCGGGCTGGCGGGGATGGCGTGCGCCACCGCGGGCAACGACGACGCGGCGTCGGCGGCGACGACGACGGCGCGTCGGTGGCGACGACGACGACCACCACCACCACCACCGCGTGCGCCGCTCCAGATCTGCGGAGGACGACGAGGCAACCGCCGAGGTTGCCGTCGTCGACCGAGCCGCCGCCGCCGCCACGTGTGCCGCCGCGTCGCCGTCCGTCCAGATCTGAGCCGCCGCCTCGAGGACCTCCGCCAGCGAGGCCACCGCGCCGCCTCCGCCATCGAGGACGCCGCCACCGCCGTCGGTGAGGTGGAGAGGGGAGAGGAAAGAGGCGGTCTGGCGAGAATCAGCGTGTGGGGATGAAAAGCCGAGAAAAGCGGCGTGGGGATTAGGATGAGGAGGAAGACGTGGGTACAGCACTGTGGGGTGGGTGACCTAGAGATGAATTTTGGTCCAAAATCCTTGTTGGAATAGGCTGAAGGCACGCCAAGCCAAGCGTGGCTTGCACTG

Coding Potentia
Explanation CPC Score
noncoding -1.02889
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0310300.2 5 20278917 A C
Osa05LNT0310300.2 5 20281127 G A
Osa05LNT0310300.2 5 20280544 A G
Osa05LNT0310300.2 5 20279468 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa05LNT0310300.2 DTM_#DNAt_MULE_japo_Os0124 Chr5 - 20279951 20280210 259
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0310300.2 osa-miR5788 Cleavage 5.0 14.564 1 21
Osa05LNT0310300.2 osa-miR5830 Cleavage 3.0 19.511 1 24
Osa05LNT0310300.2 osa-miR393a Translation 5.0 23.125 1 21
Osa05LNT0310300.2 osa-miR166g-3p Translation 5.0 22.547 1 21
Osa05LNT0310300.2 osa-miR166h-3p Translation 5.0 22.547 1 21
Osa05LNT0310300.2 osa-miR393b-5p Translation 5.0 23.125 1 22
Osa05LNT0310300.2 osa-miR529b Translation 4.5 17.721 1 21
Osa05LNT0310300.2 osa-miR1428a-5p Cleavage 5.0 14.561 1 21
Osa05LNT0310300.2 osa-miR444d.3 Cleavage 4.0 18.703 1 21
Osa05LNT0310300.2 osa-miR2094-5p Translation 5.0 21.712 1 21
Osa05LNT0310300.2 osa-miR2922 Translation 3.0 13.642 1 20
Osa05LNT0310300.2 osa-miR5076 Translation 4.0 17.674 1 22
Osa05LNT0310300.2 osa-miR5147 Translation 4.0 23.58 1 21
Osa05LNT0310300.2 osa-miR5484 Translation 4.5 17.33 1 21
Osa05LNT0310300.2 osa-miR5495 Cleavage 5.0 10.785 1 21
Osa05LNT0310300.2 osa-miR5505 Cleavage 4.5 12.944 1 22
Osa05LNT0310300.2 osa-miR5505 Cleavage 5.0 8.933 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0310300.2 5 nan Morphological trait Seed RG13 RG573
Osa05LNT0310300.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0310300.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0310300.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0310300.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0310300.2 5 nan Physiological trait Eating quality RM163 RM31
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