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

>Osa04LNT0277000.1

TGTGCTTATTCTAAGGAGAGTACTAACAGAACCACTAAAATGTGTAGGCCAATTCCAAGAAGGCATAGGGTTAATATGTGCAAAGTATTATACTATGCAAGAAAAAAGAACCATTAGGAAACTTTGAAGTATATGATTACACTGGAACGAAAGGCATCAACATAACTAGGTTAATTAGCATGTCAAGAAATGCCATTTAACCCTGAAAAGCTCGAGGGCCCCCCTGAGTCAACAAATCCGCGAACTGAAATTTCAGGAGTAGACTCATCCCCATCTTGTAGGAGCTCATGATCAATGAAAACAACCACAACCGTGATGTCATCATGGAAGAAGCGGCGTACTCCTTTCTCAAGTTTCTTGATATCATTGTACTTCATTTCCCTCTTCCGGGCAGCTTCTTTCAAAGCTGCTTTTACTAACCTCCTTGCAATACCTTCTCGTGGATTGTTGTGGACAATTTCAACTGCTTGCTGGTTTGTCAAGTGCTCCCATAATCCATCCGATGCGAAGATAAAGAAACTATCTTGTGAATGAAGAACTCTCGTATATATAGACGGCTCTGATGTTAGAACAGGCCGTCGTAGAGGCTCAGAAAGGTGGAAACGGGTCATAGATGGATCAAGAGCGAATTCTTGCTTCTTCAAGTATGCATCACCTATAGACCTTGAAACCTGTATTATGCCTTTGATGCGCCATACACCATTCTTAAGAACAACAATTTGCGAATCGTCGGGATGAAGGGATCGAAGTTCCTGCCTCACTTCTTCCATGCTTGCATTGTGGTCTCTTGTTAGCTGCTCAGCAACAATTTTGTTTGACCCGGTTAAACAACCAACAACTGCCCGAGAATCTCCAAGATTGGCCAGGTAGAGTGTTCCTTTCCATATGATACCTACTAGACAGCAAGACCCAATAGAGGCAATAGAAGGCTTTATTAAATGTGTCCTGCGCACAAGTGACAAGAAGCCTTCCTCTGTAGCAGAAAAGGCATTTCGAACAATATCCTCCGAAATTGTTCCACGCTCTTGAGCCAGACGGACGAGGTGCGCGGCAAGGTGGTTGGAGATGAATCGGGAAGCCTCCGCGCCGCCGTGGCCGTCGTAGACGCCGATGAAGGTGGCGGCGGCGCCAGTCTCGACCTGGCTGTGGTCCTCGAGCACGTCGTTCGCCTGCACCACGGCGAAGGAGAACTCGCCCGCCGCGTGGCGCACGAGGTCCCGCGACCACAGCAGCAGGTCGTCGGCGTCGCCGCCGCTGCCGCTGCCGTCTTCCTCATCCCTCCTCGTAAGCGCGTACCTCCGGACCCGGTCCCAGCACGCGGACGCAATCCTCTCCAGCCACGGCCACATCCCTCATCTCCCTGCTAAGCTTGCCCCCTGTGTCACCGCCACCCCTCCCCAAATCAACTCGGAAACCCCCCCCCCCCCCCCCCCGGCGCAAAGATGCGATGTTTTTGTTGCCTATTGCACAATTCCAAGACCAAGAATCACTCAATTTCACCTTTAGCAAGTGAAATTTGCACCTAACGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.731715
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0277000.1 4 29517031 G A
Osa04LNT0277000.1 4 29515823 T C
Osa04LNT0277000.1 4 29516598 A T
Osa04LNT0277000.1 4 29516808 A C
Osa04LNT0277000.1 4 29517972 T C
Osa04LNT0277000.1 4 29518156 C G
Osa04LNT0277000.1 4 29518212 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
Osa04LNT0277000.1 osa-miR5819 Cleavage 5.0 24.669 1 21
Osa04LNT0277000.1 osa-miR5179 Cleavage 5.0 22.102 1 21
Osa04LNT0277000.1 osa-miR160f-3p Translation 4.5 14.769 1 21
Osa04LNT0277000.1 osa-miR160f-3p Cleavage 4.5 13.764 1 21
Osa04LNT0277000.1 osa-miR1425-3p Translation 5.0 18.766 1 21
Osa04LNT0277000.1 osa-miR5505 Translation 4.0 21.57 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0277000.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0277000.1 4 qCTS4-3 Resistance or Tolerance Cold tolerance RM241 RM317
Osa04LNT0277000.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0277000.1 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0277000.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0277000.1 4 nan Morphological trait Root RM3288 RM5503
Osa04LNT0277000.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
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