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

>Osa01LNT0012900.2

GCTTCATAAACATTGCAGATCCTTTTATTCCCAAATATAACATCAATTACAATCGTTCGCGGTACGCGTCGAACAACAACAATTTCTCCGCTGAACTCTCAAGCATACAAGAGCAAGCAGATCGCCAGACACTCTGACAGAGAGAGATGCTACGCCAAGAGAGTCCCGGCCATCACAGTGACAGCTTCTCCCTGGATCCGGACTCTCCTGTTCTCGCCGTCCAGCTCCAAGTACAATGTTCCACTCCTTGGCGAAGCCTGAAACGCCGTAAGTTTTTGTTTCCCCAGCTTTCCACCCCAGTAAGGTGCCAGAACACAATGTGCGCTTCCACACACAGGATCCTGTAAGAGTATATCCGAGTTGTTAGTGTTTTAAAAGCCTGTGCTAAAAAATATACTACGAGAAGTTTCAAATTTTGGTCGATAAGGGGCATAGAGATTAACTTGCCAAGTTATACCAAAAGTTTCTGAACACTCAAGGAACGATACAGCCATACAGGGAATCGTCATAAAACTATCAAATGCATGATAACAAGTTTATGGAACTGTCACAAGAAATCATGACCAAAATAAATTTCAGTACTCAGTCAAATTCACACTTTGGTCACTTCACAAGTCTATCTAAAATGATGTTTTTTTAATTACTAGTTGTCGATAACCCCTTGACTCACCTTGAGGTATTAAGAGGTTCTGATTCTTTGGAGAGATTATATCAGTCATCTCTGCATCAATGCCAATGTTTTTCACCTAGTGTGGTAGGAACTAGGAAGATTAAAACTACGCATAAACCAGAACTGTAGAGACTTCAAATAAAAAACACCATATTATATAGAGTTAAGTATTGTTTTCTTTTATGAAAGGAGTTAAGTATTGTAGTAATCATGCAAGGTGTAATCAATTTATGTCTCTGATTGATGAAAAATAGCTTGTGATGATTTAACAATTTTGAATTTAGACAAGCAACATTGGTAACATCGTGACAGCAGAGAATCCTTCTGTACCCATGCAATGACTAAAAAGTGTACCACATATGAGATTATATCTACATATTCTGGAACTAAAATGGCCATTTTTAACTTAACAAGCCACATTGTCTGCATAAAAAACTTGGTTGTTGGGTGGAAAGAATCGGCATACCTCATCTATCCCAAATTTTGGGCAGAAGAATCGTGAAAAGAAGTCATAATCAGATCCAGCAGGTGCTGGTCCCGTAACAATAACTCCTCTACCATCACATTTTTTAATTTCATTAATGTTAGGGATAATATCAGCAACCTCTTTTCCGGAAGAAAGTTCCACGATGAGGTCACCGGCGGTTGATGATTTCCAAACACTGACGACTCGGGCGCCATTCAGAGTCTCCGGAATCGACAGCGTCTCCGCGGAATCGTACTCCACGAGATCGATCATGGGGAAATCCAGCTCGATGAACAGCTTCTCCTCACCCGGGACGCCGCCATCGTTCGCCGGAGGCGGCGGAGCAGGAACCTTCTTGGCGGTCAGGATGCCGGACCTCGTCACGAACTCGACCATGGCGGCGGCGGCGTGCTGCTGCTTCGCGAGGACGGTGGTGAAGAGGAAGTGGGCGGATGCCAGCGTCGCGTGGCCGCAGAGATTCACCTCGGCGACGGGGGTGAACCAGCGGAGGCGGAACCGCGGGGCGGCGTCGGCGGCGGCGGCGGAGGAGGAGGGGTCGCGGATGAGGAAGGCGGTCTCGGAGAGGTTGAACTCGGCTGCGACGGACTGCATCCACCGCTCGTCCGCCGCCGCCGCGGCATCCTCCCCTTCCAGGAGGCATACGGCGGCGGGGTTGCCCTTGAACGGCTCGGCCGCGAACGCGTCCACCACGGCGTACTGGATGGCGTTCTTGACCATTTCCGGCGAGGCGGCGGCGACGACGACGACTGCGGCGGGCGGCGGCGGCTGCTCCGAATTCGCGCGCGTGCTGAGGTGGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.531386
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0012900.2 1 9114796 T C
Osa01LNT0012900.2 1 9115623 G T
Osa01LNT0012900.2 1 9116152 T G
Osa01LNT0012900.2 1 9116913 G A
Osa01LNT0012900.2 1 9117390 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
Osa01LNT0012900.2 osa-miR5543 Cleavage 4.5 17.316 1 21
Osa01LNT0012900.2 osa-miR5795 Translation 5.0 18.375 1 22
Osa01LNT0012900.2 osa-miR1437b-5p Cleavage 4.5 11.26 1 21
Osa01LNT0012900.2 osa-miR2095-5p Cleavage 5.0 11.045 1 22
Osa01LNT0012900.2 osa-miR2118i Translation 3.5 16.552 1 22
Osa01LNT0012900.2 osa-miR2928 Translation 5.0 10.012 1 20
Osa01LNT0012900.2 osa-miR2928 Translation 4.5 12.648 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0012900.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0012900.2 1 An9 Morphological trait Panicle/flower nan nan
Osa01LNT0012900.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0012900.2 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0012900.2 1 nan Resistance or Tolerance Insect resistance RM576 RM3412
Osa01LNT0012900.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0012900.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0012900.2 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
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