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

>Osa01LNT0039200.2

GGGACAATAAGGAAATTTAGTTGCTTGCACAACTCAGATAACACGAGTTGGTGCTTGGTAGCAATACAGAAAATACGGCACGTACAATACAGAAAATACAACATGTGACCCACATTATGGATTACACTAGATAGATGTTGGAATAATAAATATGATTATTTAGATTTATAATTACTAATCATATAGTGGATTGTGAATATGACCACGCATTTTGCAGTAGTTAAGGTGCCTTTGTACCGCTTGGGTCCTGTGTAACAGGAAGGTGTCCATCGGACGAGCATCTCAAAACATCTGGAAGCCTTCTCAACTTTGGTCCTTGTTTCCCACTCAGGCGTTTTGGTTTTACATCCTGGTCAAATATTGCTGTAGGGATGGCAAGAGTTGCCACTGCATTAGGGGAGTCTACTATTCCAGATATCCTACCCTCACATGGGCAGCATGATAGCAAAAGGTATACCTGCTCCTTGGAGTACCCAAATCTGGAAAGGTACTCAATGGCATTGAGGACAGCACGCTTGTAGGCAACTGATGCATCAAGAAAATGCTGCTTCCCAGACTCGTCTACACTGATGCCCTCAAAGACTAACCAGTCTGAGAAACGTGGTTCCACTGGACCTATATCAAAGATAGGATTCACATGAAGTGGTGTTGGACCTATTGGAGTCAAGTATTCCTTCATCCCACCTCTTATGATCTCACACTTGAGCTCAAGAAATCCACTCATTTCTATTGCTCCACAGAATGAGACTTCGCCGTCACCCTGGGAAAAATGCATGTCACCAGTACTCAGATTTGCTCCATCAACAAATACCGGGAGATAAACCTTGGAACCTCTACTTAGATTCTTGATGTCACAATTCCCTCCATTCTCCCTTCCAGGAATAGTTCTTGCTGCTTCATTTGCGATTTTCTGCCAATCAGCAGTCCCTTCTTGAATCTTTCCAAGTAAACAGTTCTCAGGGGTTGGTAAGTTGGCAAGAGGCCTCTGATGTAGAACTTCACAGATTTTGATTGACTCATGATTTGTCTCAGCCAATATTTTTTCCCTCTCATTCCATATATTGAGAAGCTCAGCAGATGGTGCAGTCCCCACTATACCAGGATGAGTTAATCCTGGAAATCGGACACCTGGTATTTGAGGGGAGTATGCATAAATTCCTTCAAAATACCAAATCGCCTTTCTTGCACTAGGGAAGTGGTCGGTTAAGAATCCACCACCATTCTCCCTTTCAAATATGGCAGTATATCCCCATTCGTCACCGGGAAGTGGACCAAGGTTGCAGATCTCTACAGCAAGAAGATCACCAGGTGCAGCTGGAACCCCTTCAGCATCAACTATTCTTAAGGGCCCACTAAGATAATGAGTAATTGTGAGATCCAGGAATTTGATGTCATCTGCGGAGTTATCATCACTGACTCTTCCTCCAGTCCAATCGACCATCTCAACACGGAACAATTCCCCTTCAGTTACATCTGCAACAGGAGGGATATCTGGATGCCAGCGGTTATGGAGAGGGACTTTTTGCTCCCATGGCTTCTTGCTCACATCTATAGGAACTACCAATCTTGGTGTTGGAAGAGCCATGTTCTTCCAATGTTGTTCCTCACTCAACATACTCCAACAAACATCCATCAGTAGTATACTTCTTTGACTTGTCCTCTAACATTCGAAGGCTCCAGCCTGCATCTTTCCTCAGTCCCTTCTTCTTCATCCAATGCAAGATCCCCTGAGCTTCCTGCCACCTCCCTGTCTCAGCATACAAATTTGATAACAGAACATAATGCGATGCATTCTCAGGTTCCAACTCCACCAGCCTCATTGTCACATGCTCACTCAACCATGAGTCGCCACGGGCCCTGCAGCCTCTTAATAGCAAGCCCCATATCACTGCATTTGGCTGTGATGGCATTGTCTCAACAACCCTAAAGGCATCATCGAGGTGTCCAGAGCGACTAAGAAGGTCAACCATGCACCCAAAGTGCTTGATCCCAGGTTGAAACCCATACTCACCTTGTATGGCCAGGTTAAATATTTTCCTCCCAATGTCAACAAACCCGGCATGTGCACAGGCACAAAGAACACAAATAAGTGTGACTTCATCTGGCTGGACACCATCATTCTGCATCCGAGAGAACCACTGCAATGCCGTCTTGCCATCCTGTGCAAGAGCAAGTGCTCCAATGATAGAGTTCCAAGTATAGACATTCCTCTTGGCCATCTTTGAGAACACATGCATTCCATCTGAGACTTTTCCACACTTCCCATACATGTCTACCAGCGCTGTGCCCAGTACAACATCCATCTCCCATCCCTGCTTCTGCACGTACTCGTGAATCCAGATGCCAGTGTCGACCGCACAATGGGCCGCGCAAGCGCCAAGAGCAGCAACCATGGTAACGCGGTTGGGTGCAACATGAGCAGCAAGCATCCGCCGGAAGGTCGCCAGAGCGTGAAAGGTGCGGCCTCGGTTCCTGTATGAGGTGATCATAGTGGTCCACGCGACAACCTCCGGTCGGGGCATTTCGTCGAACATCTGCTCGGCGTGCGCCAGGTCAGGGTCGCAGTCCGCGTAGCGCGCGAGGAGGGCGTTGCGGACGTGGAGGTCGGGCCCGAACCCGGACTTGACCACCTGGCAATGCACGGCCCTCAGGTCGGCGAGGGAGGACAGGGAGGTGAGCAGGAGAGGGAAGGTGAAGCGGTTGGGGCGGACGCCGCGGCATCGGAGGAAGTGGCGGAAGAGCGGGAGCGGGGAGCGGGCGGGGGCGCGGCCGAGGGAGCGGAGGAGCGAGTTGAAGACGAACACGTGGGGGCGCGGGTGGCAGGCGAAGAGGGAGAGCGCCGGGTCGAGGTGGCGGAGACGGCCGCAGGCGAGGAAGAAGGCGGAGACGACGGCGGTGGAGCGGAGGAGCGCGCGGTCCCCGAGGATGGCGCCGCGGATGGGCGCGAGCGCGGCGGCGGTGGTGCAGGTGTTGATCGCGTGCAGCGCGCGCGTGACGGAGGGCGGCGGCGGCGCGGTGGACGGGCGGAGAGGCGGCGGGAGGCCGCCGGTCATCACGGCTGGCGGTGCGTGGGGCGTGGAAGCGCGGCCGCCTTGAACAACCCTGGATGTCCTGGGTTGAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.614661
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0039200.2 1 32226386 G C
Osa01LNT0039200.2 1 32226916 C G
Osa01LNT0039200.2 1 32227147 C T
Osa01LNT0039200.2 1 32227173 A T
Osa01LNT0039200.2 1 32228560 A G
Osa01LNT0039200.2 1 32229625 G A
Osa01LNT0039200.2 1 32230429 G T
Osa01LNT0039200.2 1 32230468 G A
Osa01LNT0039200.2 1 32230596 A G
Osa01LNT0039200.2 1 32230945 G A
Osa01LNT0039200.2 1 32226395 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
Osa01LNT0039200.2 osa-miR1862d Translation 4.5 15.561 1 21
Osa01LNT0039200.2 osa-miR5522 Cleavage 4.5 15.298 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0039200.2 1 qCC-1 Physiological trait Source activity RG541 RG101
Osa01LNT0039200.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0039200.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0039200.2 1 qLRC-1 Resistance or Tolerance Drought tolerance RM237 RM302
Osa01LNT0039200.2 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0039200.2 1 gpy1 Others Others RG541 RG101
Osa01LNT0039200.2 1 nan Physiological trait Source activity RG532 RM472
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