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

>Osa04LNT0274300.2

CAAAAAAAACGGGTTAAAAGGAGACAAAATTCCCCACGGCAAAGAAAGAAAAGAAACAAAAACAAGACACCTTCTGACCTCTGCTCCAAATTGCTGGAAATGTATGTAATTGTTGTATACCCGTATACAAACTTGTATACCGCCGTCGCCGGAGGGGAAGGAGAAAAAGAGAGAGAGAAAAAAAAAACAGAGACATCAGGGACTGTTACATCGATGTACAATTCTTCCTTTACCACGACGAGGTGACCTATAGAGATAAAGTTACCCGGACTCATTTTCTCTACCACCCCCTCTGCTTCCTCGGGTTAAGGTGAGATCAGGGAGGGCTCTTATTACACAGAGAAATCAATAAATAATGGAATGGCACGGGAGAATTACAAGGTGAAGGAGAGGGATGCAAATCCACTGCTGTACTGGTGTCACTGGCATGTGGGTCCCACCTATTCCGGGCCCACATGTCATTGGCACTTACCGCACATGCATTACAGGAGAGATCCCAACTCGAAGGAGAGTGGTTGCTGATTGCTGATGCATGCATGGTGTTTGTGTTGGTGGTGGTGTAGTGAGAGGATGCGATGGTGATGGCGATGCTTTGATTTTTTTTCTTTGAACAAGTACGTACTTGGTGATGCATCGTTCGCGCGCCTATTGAACCATGGCGAGGAAGGTGCTCGTCGGAGTCGAGGTTGGCACCGCGGACGCCGGGGTTGTCGCCGGCGGAGGTGCGGTGTTGGCGCCGCCCGGGTTCGGCCTCTGGAACTGTATCCTGTACTGCATTTTGCCGTCGTCCTCGCCTTCCTCGCCGTCGTCGGTGTAGTCATCGCCCATGTCGTCACTGTCGGTCTCGTCCGTTGTGAACTCCCGGGGCGGCTGCTCGCTCAGCTCCCTCACAATGTCTTCTTCTTCATGCCGCTATCGACGTCGAACGTGGCCGTGGTCGGTGCCGTGTCGCCATTGCTGGTGGGCACCTGCGCGCCGCCGCCTCCGCCGTTCTTCCTCTTGTCGTTGTCGTTTATGTTCTTCCCCTCTATCTCGTGCCGGTTCGGGTTCTGGTGCTCGATTGCCGTGGCGGCGACATTGGCCGCGGAAGCGCCGCCGCCGCCACCGCCGGTGAGGTGCTTCCTGCGGTAGATGACGTCGAGCTGGTGGAAGTACGGGCATGTCTTGGAGTCCTCGGGCCGCTTCTTGTTGCTCTCCTTCACCTTCTTGAAGTACTTGTTGATGTTCTCCCACTTCTCCTTGCACCGCTTCGAGCTCCGGTTGTACCCCAGCCGCCGCATCCCCGACGAGATCTCCTCCCAGAGCGGGCCCTTCGGCCCGGTCTCCTGGTAGCGCATATCGAGCTCCATGCGCAGCTGTATGAGTGCCTGCACCTCCGTCTTGGGCCACCGCGACGACGACGCCGACCCGCCCTCCCCTCCTCCTAGCCCGCTCTCGACGTGCTGCTCCGCCGCGGGCACCAGCTCGAGTGATGAGCCGGACGTCGGTGGCGCCCTGCGCGGCGTCACTGCCTCGTGGTGAATCGTCTCCTTGTGCTGCGGCTGCGGCGGTTGCTGCTGGAGGGGCGCGGCCGGGATTGGCGCCGCCTGCGGCGGCGGCGGCGTTGGCTGTGGCTGGTGCTGCCTGGCAGGTTGCTTGACCGGCGGAGGGGTCTGGAGCTGCACCGGTGTGGGCATCTGGATGACGGTGGCGGCGGGTGGGACCTGTACGGACTGACCGCCGATGCGTTGGAGGAAGGAGATGATGGCGGCGTCGCGGGAGGCCGCCGCGGCGCGCTCCTGGGCGAGCTGCTCCTGCTCGCGGTTGAGGCGGGCCACCTCCTGCCTGCGCCACGCCTCCTCCCGCGCCGTGCGCTCCGCCTCTCGCTTCTCCATAGTCTCCAGAAACCGCCGCTGCATCTCCTCCTGCCTGTCGACGACTTGCTTGATGAGCCCCTCGAAGAAAGTCGCCAGCCTTTTGCCGCCGGCGCCTCGCTTGCGCTTGCCGAGGCGGTCCTGGCTGCCGCCGGTCTCCGCCGTCATCTCGTCGTCTTCAGACTCATCGTCCGACTCGGACCCCGACATGGACGAGAAGCTTAAGCCTTGCAGGTTGATGGGCGGCTGCGGCGGCAGCTCCAGGGGCACCGCGGGAGCCGCAGAAGATATCGGGGCCGGCTGGATCGGCCCCGGCGGCGGTGGCATTGCGCTCATCGGCGGTGGCGCGGGAACCGGCGGCGCGAAGGCGTGCATCGCGGGTGCGCTGCTTGTAACCGGCGGCAACTGCTGCTGCTGCTGCTGCTGCGGCTGGGGCGTCTGCGGCGCAGCGGCATGCAACGCCTCCAGCTCAGTGAAGAAGCGGTAGCTCTTGCCGTCCTGCCTCCCGGCGCGCCCTTCCTTGGTGCGCTTGTAGTACTTGTGGACGTTCTCAAACTTCTCCTTGCACTTCTTGGCGCTTCTCTTGTAGCCCAACTCCGCGAGCTTCTACGGGCAGGAGAAGCATCTAACGCAGAGGCATAGTAAGCATCAAGTGCTTGGCCGACTGCGTATGAGTGGTTTTTCTCCCGGGGAGAAAGGGACAAGGAGATGGGAATTAGGACAATGGCGAAGAGGAGGCAAGGAGGAGGGTGCTGTATATGCAGAAGGGAGATTAGTTAATCACAGGCCGTCTCGTCTTTTTAGGGATCAGGAGGAGATCGATGTGATGAAGTTGATGGCAGTGAAAAAAAATGAGAGTGAAGAGGGGGAGTGAAATGCTTAAATTAAGATGATGCCGCATTGGGATGGGAGCAAAAGGCTGCCTTCCTTCTTTTCCCAAAAACTGGAAACCATGAAAGCAAAAAAACGACAGTGTGGCAGACTGAAGCGGCAGCAGCTGCTGCCTGCCTGCGCTAGCACTCACACCGTGGTACGATCCCCAGGCGCGCAGATTCTTATCATCATCCTACCTACACCTACTCCCTGCCTCCCCCGTCTCGCAGAAACCGAGAAGTATTTGATT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.436837
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0274300.2 4 27077520 A C
Osa04LNT0274300.2 4 27077918 G A
Osa04LNT0274300.2 4 27080114 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
Osa04LNT0274300.2 osa-miR5534a Translation 4.5 13.152 1 21
Osa04LNT0274300.2 osa-miR5534b Translation 4.5 13.152 1 21
Osa04LNT0274300.2 osa-miR5789 Cleavage 5.0 16.687 1 21
Osa04LNT0274300.2 osa-miR5819 Cleavage 4.5 13.367 1 21
Osa04LNT0274300.2 osa-miR5819 Cleavage 4.5 14.579 1 21
Osa04LNT0274300.2 osa-miR414 Cleavage 4.0 17.051 1 21
Osa04LNT0274300.2 osa-miR1865-3p Cleavage 4.0 16.902 1 24
Osa04LNT0274300.2 osa-miR2097-5p Translation 4.0 7.524 1 22
Osa04LNT0274300.2 osa-miR2097-5p Cleavage 4.5 19.736 1 22
Osa04LNT0274300.2 osa-miR2928 Cleavage 4.0 15.504 1 20
Osa04LNT0274300.2 osa-miR5487 Cleavage 5.0 19.035 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0274300.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0274300.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0274300.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0274300.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0274300.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0274300.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0274300.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
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