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

>Osa04LNT0273800.2

GAACAGTTTGCCAGATTTTATTGATGTCATAAATTTTGCTGCAATGAGCAATCTTTTTTGCATCCAATAAATCTTTACAGGACACTTCTTGTACAGGTGTACAAGTGTAAACTTGCTGTCCCAGACTTGAACTCCGGACTGTAGAGACGGCAGATGTGACACAAAGGTAACCTCTTTGTCATGCCTCGATGAGCAACTCGTGCTCTTCGTCTCCCACCATCAGAACATGTGTTCCCAGGAACAGCACCCTTGTGCCTTCGGTGTTGGCAAAGCTCATAAGCTTGCAGGGGTCGACGGTGATCTCCACATCGGTTGATCTGCCAGCGGCAGTGTGCACACGCTCAAAGCCAACTAGCTGTTTTATAGGGGATCCTGGAAAGCTTGGTTTCGAACTCGCGAACAATAGAACGGCATGGCTCCCGTCCATGGCACCATCGTTGGAAACCGAGATGTGAACAGGAAATTGCAGCGCCTCGCATGAGGCAATGTCTTCAACTTGGACATAATCTACTCCATCCCTCCTTGTGTATGCAGGCTTTCTGCTGATAAGATCTGGAACTGACGAACGGGACAAGCTGATTTTCTTTGGGGCCTGCAAGATGCTGTACGAATATTTTGAGTAGCTCAAACCATACCCAAACCCATATACTACATCTCCAGTGTAAAATCTGTATGTTCTTCCTGGGTAACCACGTGACGCATCAGCTCTCATGTTCATATCATCCATCGGAACAGCAGTGAAGGATTCAGGGTACCAAGTTATGGGCAGCTTTCCTCCTGGGTTGTATTTCCCGAAAAGGATTTCTGGAAGAACATTTCCACCAACCTCGCCAGGATAACCAATCCAAAGAATGCTCGCAATACGTGGATCATGCTTTGCAAATGAAACATCAACAGGACCACCACCCATGAGTACCAACACAACGGGTTTCTTTGTTACACTGGCAACAGTATGTATGAGATCCATCTGCCTGCCTGGAAGGAGAAGGCTCACTCTATCATGATCTTCCGTTTCTTCAGTCAGGTTCAACCCAGCAATTAGAACAACAACATCAGCTCTCTTAGCTGCTTCAATCGCTTCACCAAATCCATCCGTTGAGTTACATGGAACATCCTTACATCCAGCAGCAAAGGTTGTTTTGGGAACATATGCTTGCATGCCTTTAACAAAGGTGGTAGAATGACAAGGGACACCTGGAGAAATTAAAATTACCATTAATGTATGTAAAACAGTAAAGTAAGACAGATTTTTTATTGATGTCAGTGGTAAAAACCTGTGTAGTCACCGCCTAATATATATGGATCATTTGCAGCTGGTCCAATAAGAGCAATATGACCAACTTCACTTCTCTTTAGAGGCAAAAAACCGTTATCATTTTTCAAAAGGACAGTACCCTGCCTTACAGCTTCTGCTGCAAGTTCCCTATGCTCTGTAGTGCACACATTGTTGGGTCCTAATTGTGTAAACCACTGATTCTCATTGGTCTTATCAAAAAAACCAAGACGGAGCTGAACAGAGAATAGATTAAAAAGGGCATGGTTGATATCTTCTTCTTGGACCTTTCCCTTCTCAATTGCCGACTTTGTATGACGAATTAGGAAAGAACCACAGTTGATATCCATTCCTGCCTTAAGAACAACGGCAATTGAATCTTCATCTGATGCTGTGTATGTCTGGTTTTCGTGAATTATTGCCACAGCATCACAATCAGATGTAATATACCTTCAAATAATCAAATGGGCACACATAAACAGTAGTGCAGGTTTGGGTTGATATTAGGATTTTTTTTTCTGCCAATATCAGTATTCAAGGATCAAGTAATGTTCTGGGCAAGAGAAAGTAGTATACCCCTGGAAACCCCATTCATCTCTAGCCCTTTGCAGGATATCTTTGCGGGCACATGCTGGCACACCATTTACCTGGTTGTATGAACACATCAAGCAACTTGCACGACCTTCCTGGATGCAGCTCTTGAAAGGAGGCTGGTATGTGTCTTCCATATCTTGCGCATTAACCTTGGCATTGAAGGTGTATCTTGTAAAGCCCCTCCATTTCTCCAAATCATAAGCGATGTAGTGCTTGCAGCAGGCGGAGAGCATCATCCTGCCTTCCTCTCCGTAGTCCCGCTGGAACCCTTTCACATACTCGACGGAGTAGGCGGAGACGACGGCGGGGTCCTCTCCCGGCGTCTCCTGGCCGCGGCCCCACCGTGGGTCGCGGAAGACGTTGATGTTGGGCGCCCAGAACGTGAGCCCGGCCTGGCCGGCGTTGTGCATGGCGCGCGCCTCCACCGCGATGGCCCGCGCCGCCGCGCGCCACAGCGAGCGGTTGAACGCGGCGGCGGAGAGGATGACCTGGGGGAAGATGGTCGCGGAGCGGACGGGGCCCGAGGAGAAGTTGACCCCGGGCCCGTTGTCGCAGACGCCGTGGAGGGACTCCGACCACCACTCGAAGGGCGGGACGCCGAGGCGGGGGGCGCCCGCGGCGGTGTTGGAGAGCTGCGCTATCTTCTCGTCGAGGGTGAGGAGGGAGACGAGGGCGCGCGCGCGGGCAGGGAACGGGAGGGTGGCGTTGCAGAAGGGGTAGGCGCTGGCCGCCGGCGAGGCGCACGGGCGCGCATTCGACGCCGGCGCGGCTCCATCGCCCGCGCCGGCGCTAGCGACGACAAGGAGGAGGAGCAAGGGGACGTTGGACATGGCGGGTTTGGGGCCGAATTTGGCTGAGCACACT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.69207
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0273800.2 4 26544688 C T
Osa04LNT0273800.2 4 26545422 A C
Osa04LNT0273800.2 4 26545849 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0273800.2 osa-miR5541 Cleavage 5.0 20.751 1 21
Osa04LNT0273800.2 osa-miR5079b Translation 3.0 14.119 1 22
Osa04LNT0273800.2 osa-miR398a Cleavage 5.0 15.787 1 21
Osa04LNT0273800.2 osa-miR1861b Cleavage 5.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861d Cleavage 4.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861f Cleavage 5.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861h Cleavage 5.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861i Cleavage 5.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861j Cleavage 5.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861l Cleavage 5.0 18.408 1 22
Osa04LNT0273800.2 osa-miR1861n Cleavage 4.0 18.687 1 22
Osa04LNT0273800.2 osa-miR2866 Translation 4.5 17.485 1 20
Osa04LNT0273800.2 osa-miR2931 Cleavage 5.0 17.355 1 20
Osa04LNT0273800.2 osa-miR395x Translation 2.5 11.727 1 21
Osa04LNT0273800.2 osa-miR2873b Cleavage 4.5 11.612 1 21
Osa04LNT0273800.2 osa-miR5079a Translation 3.0 14.119 1 22
Osa04LNT0273800.2 osa-miR5338 Cleavage 5.0 18.036 1 21
Osa04LNT0273800.2 osa-miR5491 Cleavage 5.0 14.624 1 21
Osa04LNT0273800.2 osa-miR5491 Cleavage 5.0 12.665 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0273800.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0273800.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0273800.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0273800.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0273800.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0273800.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0273800.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
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