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

>Osa04LNT0276900.1

CGGGCGAGCTACAATACTGCATTGTTTGGGATTTGGGCACCTGATCAACAATACTGCTTATATATACTCTGACGCCCTGGTGCCAACTCAAGTATAGGGTTTCAGAAACAGAGTGTAGAATCCTCAACGAATTTTAAGATTACTTAAGCATACGGTGATATCCTCTACATTTTCTTCTGTATCCCCGGGGAAACCACCAATGCCAGTTGAAGTTGAAGGGCTTTCATCTTTCATCCCACTTCGGGATGGCACTTGAACCCAAACCCCACTATTTCTGACTTTGAATGGTGTACTCTTTCTATCTTTAACTTTATTGGTCTCAATTTTGTGCTTAGCAAGCACACGGGAGATATCCTTATCACTGTTTGCGTTGAAGAAACACTGTCGATCCTTCGCGTCACGAACTAGATCTGCCCAGATAGAGCCAGACCTAGATAAGGTTGTTGCATTTCCCAAAATCCAAAGGCAATACCTTGCTCGTGTAAGTGACACATTTGTGCGCTGCCGGTTTGAAAAGAAAACCTACAGCCCCATCTGAGTTGGACCTCACAGTTGATAAAATGATTATGTCTTCCTCACCACCTTGAAAGCCATCAACAGAATTAATTTTTACTATGACCGGGTCAAACTTCATTTTCCCGAGTTTTTGTTGAATTGCTAGGACTTGAGCAGTATATGGACATATGACACCAACTGTAACCTTATTTTTGGTTTTAGAATGGGCTCTTTGGAGATTTCGCAATATTTCCTGTATGACAGAAACCTCAACCACATTCTTTCTGCTGCGGCCAAGTTCATCAAGATCCTCCTTACCATCTTCAATATTGAAGAAAGAGTAAGGACCAAACATAAGACCTGGAAGGTACTTCTTTCGGTGTTCTTTCTGCTTGACATTAGGAGCATCTAAGAGTTTCCTATCATAGAAGCTGATGTTTGGAAAGATACTAATGGATGGGTGCATTCTGTATTGCATATTAAGGAGATGTTTTTCATGTCCCAGTGAACTCAACCTCTCGAAGAGGCTTCTCCCGAACGACGCATCCTCACAAACCTTGCTTTTGACAGTTGCTGGCAATTGGCACTCGTCACCAATAAGAATAGCATGCTTTAAAGTAGGCAAACGCAACGGGATCAATCCTTCACATTCTTTTAACTGAGCAGCCTCATCAACAACAAGCAACTGTAGTTTTTTATTACTTATTTTGGAAGAGCTAGATACAGTGCAGAAAACTATGGAGGCGCTTTCCATACAGAACTCCCGAATGGTACGTTTGGAGGAAGTTATAGGAAGTTTCAAGCTACTTAATAACATATTCAGTAGCTCGAGACATCTAATTCTGATTTTCCCGAGGCTGATTGCTGTTTTAGAAAATTTTGTCAGACTGGATACACTGGAATCAGATTGATCATCATTATACAGGAAAATTCCCTTCACTTCATCCTCAATATTTTTGTTCATGAATTTCTTGTTGAAATCTTCAAGCAGCTCTAGAAGTGAAATGATATTGTTGTAATTCACTTCCAAGATAGTGGATTTTGGAACATGGAATAGTACTTCT

Coding Potentia
Explanation CPC Score
noncoding -1.00569
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0276900.1 4 29439330 A G
Osa04LNT0276900.1 4 29439439 T A
Osa04LNT0276900.1 4 29439966 A G
Osa04LNT0276900.1 4 29439482 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
Osa04LNT0276900.1 osa-miR5179 Cleavage 5.0 20.585 1 21
Osa04LNT0276900.1 osa-miR5337b Cleavage 4.0 13.07 1 21
Osa04LNT0276900.1 osa-miR396a-3p Cleavage 4.5 19.356 1 20
Osa04LNT0276900.1 osa-miR396b-3p Cleavage 4.5 19.356 1 20
Osa04LNT0276900.1 osa-miR535-5p Cleavage 5.0 21.914 1 21
Osa04LNT0276900.1 osa-miR2105 Cleavage 4.0 14.365 1 20
Osa04LNT0276900.1 osa-miR396g Translation 4.5 12.518 1 21
Osa04LNT0276900.1 osa-miR396h Translation 4.5 12.518 1 21
Osa04LNT0276900.1 osa-miR396d Translation 4.5 12.518 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0276900.1 4 qCTS4-3 Resistance or Tolerance Cold tolerance RM241 RM317
Osa04LNT0276900.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0276900.1 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0276900.1 4 nan Morphological trait Root RM3288 RM5503
Osa04LNT0276900.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0276900.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0276900.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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