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

>Osa09LNT0445400.1

ACCAATACCCCACATCTGACTTGATATAGGTAAGAGTTCATATAATAAGTTCCATCATAAGCCGAAAATGGAGAAGTCGGGTAATTCTGAATGTTTAGAATTTACAAGAGAATATATTTTTCGATCAGACAACAGTTTGGTGTTTCTGAAGTTGCTAAGACACTAAAAGATATACAAATCATCCATTGGAATGGAAGTACCATCCTTCGGTCCAGTTTTGCATTTCAGAAAGTATAGCTGCTACATCTAAAAGGCAATGTGCAGTGCACAACAAGAGCAGCAACTGCTCGTCAGTGGCCAAGCCATGCAGATGGTACTGGCTGAAACCTAGACTTGGCACCCGCTAGTGCATCATGGTAATCCCCTCGGCTGAAGCAGTCACGGAAGTCGGTGAACAGCTTGTCGAACACCCTCCACAAGACTTTATATGATCTGGAGTATGGGAATGGAAGGAAAAATTCTCCTTCTTGAGAAAGGTGTTTTAACAGCAAGAAAGTTTGCTGGTTTTCTTCCAAGTTGTCAATAACTGCAAGCCATATCTTTGAAGCAAGTTCATGTGCCTTTTCTCCTGTCCTACCACAAGCAATGAACTGATCGATGATGGTGCCATGGAGTATGCTGGAAGGAGCAACAACTGGGCGCTCAAGCTGTTCTTTCAAATAGAGATAAGTGTGGCCAACAAGTTCATCAATATCCCCACCAGATGAGACAAGGTTCTGGCTGACGTATAATGCTTGGAATCTCCTTCTAGCAGAACCTCTGGGAATTGGCCCAGGCCAGCGTTTCCGTAAACCAGCTGATGGCCAGTTCCTTGCAATAGCAGTTTGCCACATACATTCTCCTTGAAATATGCTTGCCCAGTGCTTGCTGACACATGATATTTGAACCCATTCGCATGTTGGTAACCGGATAAATATTTCTACAAGGAGATGTTCAGGGAGCCTACCAAATGGTCCATTCCTGTCTGTCATAAGGCTGCGGCCGGCGGCGCGGCTCAGCTCCCTGGACTGTGGAGGACCAGGAACCCCCACCCCACCCCACCCCACCCACCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.990071
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0445400.1 9 19241223 G T
Osa09LNT0445400.1 9 19241625 G A
Osa09LNT0445400.1 9 19242158 T C
Osa09LNT0445400.1 9 19243738 G C
Osa09LNT0445400.1 9 19244170 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
Osa09LNT0445400.1 osa-miR5543 Cleavage 5.0 19.218 1 21
Osa09LNT0445400.1 osa-miR166a-5p Cleavage 4.5 17.871 1 21
Osa09LNT0445400.1 osa-miR166c-5p Cleavage 4.5 17.871 1 20
Osa09LNT0445400.1 osa-miR166e-5p Cleavage 4.5 17.871 1 21
Osa09LNT0445400.1 osa-miR319a-3p.2-3p Cleavage 3.5 19.787 1 20
Osa09LNT0445400.1 osa-miR166l-5p Cleavage 3.5 17.871 1 21
Osa09LNT0445400.1 osa-miR2864.1 Translation 4.5 24.942 1 21
Osa09LNT0445400.1 osa-miR5155 Translation 5.0 13.127 1 24
Osa09LNT0445400.1 osa-miR159e Cleavage 5.0 20.025 1 21
Osa09LNT0445400.1 osa-miR319b Cleavage 3.5 19.787 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0445400.1 9 cisc(t) Resistance or Tolerance Cold tolerance nan nan
Osa09LNT0445400.1 9 qGL9 Morphological trait Seed RM257 RM242
Osa09LNT0445400.1 9 mrl9a Resistance or Tolerance Drought tolerance RM201 RM410
Osa09LNT0445400.1 9 Symptoms Resistance or Tolerance Other disease resistance RZ228 RG667
Osa09LNT0445400.1 9 ta9 Morphological trait Culm/leaf RZ228 RZ12
Osa09LNT0445400.1 9 Ta Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0445400.1 9 Ta Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0445400.1 9 Ta1 Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0445400.1 9 qCCAI-9 Physiological trait Source activity RM257 RM201
Osa09LNT0445400.1 9 nan Resistance or Tolerance Other soil stress tolerance R2638 C1263
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