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

>Osa04LNT0276600.1

GTCGGTGATAAGAGGTGCCATTGTGCATCCACAGATCCACTTGTAAGCGCAGAGGATTAAGGGGGGAAAGGACAAAACTAAAAACTAGTTGGAACATGACGAGATACAGAGATAGAGATGCTCCAGTCCAACATCCTTATTGATATGCTACAATGTGAATATGGATTTTCCTGATAAGCAATTGCTACGTACTAACAATTGCCCAATCATTGAAGTCCAGAAACACAGCACCATACGGATGGGCAATATTCTGTTGCCATCTCCTCTGTTTTGCCATTAACTGACCCACCCTTATTAACGCATTCATCAGTTCCGTAACAGGCTTCTTGTTGGGTCGCGAACAGGGTTCATAATTTCAGAGGAACAACATGGTTCAAATTGGATGCCCACCCAATCACACAGCTTCCACTTCATTGTGAACTTTGGATCCATGATAAGAGAACAGCTTGGTCGCATTCTTGTATGTCACTTCAGCAAGTTCTATTTCTGATATTTCAAGCAGTGAGGCGACATACTTCATAACAATGTGGATATTAGATGGATGGTTCAAAGACTCATTTGAAGTGGTAGATGCCCGTGAATTAGAATCTTTTTTACTTTCTCCATTATCTGCACTTGAGCTATCCACAGGTACTGCTAATAGAGAAATATCATCCAATTTCGGTAATGCATCCGGTGCGTCGGTCTCTAGCAGAATTCTGTCTAAGGGCATTGATTTTAGCATTTTCTTTGCCTTCGTGGATTTCATGCCTGTAAGGAAGCCGGACAACGAAAAGTAACAGCCTAAAATTTCAAGGCTGGACACCATTTCTGCAGATCCTAGATACGAATGCAGCAACACACCAGCTGGGAAAGGTCCAGTTCTCTTTAGTATCTCCAGAAGATCACCAAAGGCGCGCACACAATGAACAGAAACAGGCTTGTTCAACTCCTTAGCAAGTTCAAGTTGCTGCTGGAAAACTTCAACCTGTTCTCCAAAGTCAATGGTTTTTCCATGTGAACCTTTGTCCAGACCAATCTCCCCAACAGCCGCCTCTGGTGTTTCAGCGAAGAACCGCCGGAGCGAATCCATCCAATCCGGCGATCTCTCCGGTACCCACCATGGGTGGAGGCCGAAGCAGGGGACGACGGACGGGTACTCCTCGGCCATCTGCTTCACCAGGTGCCAGTCTTTCTCGGAAGTGCCGTTGACGGCGAAGCGCGCGACGCCGGCGGCGGTGGCGGCGCGTATGAGGGAAGGGGCGACGGACAGCACACGCGGGTCCTGCAGGTGGCAGTGCGCGTCGAAGAGCCGCACGACGGAAGCGGCGCGCGCTGGTGCCTGGGCCATATCCGGCGACCCCGCGGTGGCCGGAAGCGGAAGTGCTCAACGGCGCTTCTAGCGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.859807
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0276600.1 4 29115289 T A
Osa04LNT0276600.1 4 29118064 T G
Osa04LNT0276600.1 4 29118123 G A
Osa04LNT0276600.1 4 29118143 C T
Osa04LNT0276600.1 4 29118246 C A
Osa04LNT0276600.1 4 29118284 T A
Osa04LNT0276600.1 4 29118780 C T
Osa04LNT0276600.1 4 29119254 A G
Osa04LNT0276600.1 4 29117901 A G
Osa04LNT0276600.1 4 29115478 C 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
Osa04LNT0276600.1 osa-miR5525 Translation 4.5 24.484 1 22
Osa04LNT0276600.1 osa-miR5179 Translation 4.5 22.857 1 21
Osa04LNT0276600.1 osa-miR1876 Cleavage 4.0 15.977 1 24
Osa04LNT0276600.1 osa-miR5144-5p Translation 5.0 15.396 1 21
Osa04LNT0276600.1 osa-miR5837.1 Translation 4.0 17.581 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0276600.1 4 qCTS4-3 Resistance or Tolerance Cold tolerance RM241 RM317
Osa04LNT0276600.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0276600.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0276600.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0276600.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0276600.1 4 nan Morphological trait Root RM3288 RM5503
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