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

>Osa04LNT0269800.3

ACTCCAATTTTATCCCGATTTTATGTTGAGTCATGCTATTAATATTACATGACATTACATTACAAGCAATATAAATGATAGAAGCAGACAAGGCTCTTCCTCTAAGACATCAAGCCACCTTTCTATCAGGCAATAAAAAGATCGCAGTCCATTAGTCCGGTAGGAGCTTTTCTTTCCCTTTTCTTTCCGTTCAGGAGTTCGGTCGCTTTTCTTTTCCTTTTCTATCCGTCCAGCAGTCTGATTGTCCCGCCTTTTTTTCCACTATTTTTAGCACTCCCACTAACATGATTTTACATATTTCTCTCGCAAGCCAGCAAGACATACAATATTATTATTAGAAGGGATAGAAATAATAGAAGCACACAAGAAAATACAGATCGCAAGTCTCTTCCTGTAGGGCATCAAATCACCTCCAATCATTATCTCCAGGTTATCATTGAAGTCAACCCTGTTGATCATTGCAGGCACATTCTCAGAAGAAATGATCACAACTGGTATGTCCTTCAATGAAGATGACACTTGTACCCCCAAAATGAGGAGCAAAAGGAGCAAATTTTACTCCACTTCACCCTCTTCAGTAGATCATACTGTCATGCCAGGCATGTAGTAGTCAGTGATTATCACGTTGACATCAATCTCCAGTACAACAGTTCAAAAAACCACAGGATTGATTTCCTGATGGTCAGGTGAGGAGGAAGAAGGGGAAGAAGAGGAGACGTTGCTCTCATCCCTCGATCCATGCAGCTCCAAGGCCCTCTCGTCGTCGCTGGCGACGGATCCGCGCGAGAGGCGGGCGGAGAGAAGACGGGACACGTGCGGGAGGGGAAGAGGTCGCCGGATCTGCCCCTACCGTCGCCGCCGACGGTGGATCCACGTGAGAGGGGGCCGAAGAGTGGACGGTATCCGTGCGGGAGGGGAAGAGTCGCCGGATCCGCCCCTCCCGTTGCCGTCGACGGCGGATCACGCGAGCAGAAACGATGGCTTGAAGGCTCGGCCCATCCCGTCATCGCCGGCAGCGGATCCGCGCGAGCAGGGGCAGAGAGACGACGAGAGGTGGAGAGAGAACGGCATCCGGTTGAGGAGGGAGAGAGAAAGAGAGACTGGGAGAGAGGAGAGAGTGGGGGAGAGTAAACGAGAGAGAGAGCCTGGAAGACATAGGAGAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.385251
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0269800.3 4 24720734 T C
Osa04LNT0269800.3 4 24719789 A C
Osa04LNT0269800.3 4 24719647 C T
Osa04LNT0269800.3 4 24719654 G A
Osa04LNT0269800.3 4 24720679 C G
Osa04LNT0269800.3 4 24722215 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0269800.3 osa-miR6245 Cleavage 5.0 18.182 1 21
Osa04LNT0269800.3 osa-miR529b Cleavage 4.5 13.931 1 21
Osa04LNT0269800.3 osa-miR1432-3p Cleavage 3.5 16.212 1 21
Osa04LNT0269800.3 osa-miR827 Cleavage 4.5 23.282 1 21
Osa04LNT0269800.3 osa-miR529b Cleavage 4.0 14.155 1 21
Osa04LNT0269800.3 osa-miR2275b Cleavage 5.0 7.663 1 22
Osa04LNT0269800.3 osa-miR2275a Cleavage 5.0 7.663 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0269800.3 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0269800.3 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0269800.3 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0269800.3 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0269800.3 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0269800.3 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0269800.3 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0269800.3 4 nan Morphological trait Culm/leaf RM3785 RM1388
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