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

>Osa03LNT0228500.2

CACAACTTTATCCAAAACAAGAAGAATTACAGAACCGGAGAGAGTATTAATCAAGTCGATTACATCATAAATACAAGAGGGGCAAACAAAAAATGTTCAGCAACATAGAGCCTTTCTCATGGCAAAACTGTTGTATAAGTGCACGCAATGCTTTATTTCCGAGGTATACAAGCATCGTGAGAGATGTGGCACATTGCATCTCCCTATCTATACGGCTATATATGGTGCCACCAGATTCTACAAACATGCAGGTTAGTAGTGGCACCCAGCACCAATGACCAAACACATCGGTGTGTTGGATTTGGATACCATGCAACGGATATGGGGCAAATTTACAATTTACAGGTTGCCCCAAAAATGCCGCCAGCTCCAGCCTCCTTAAGCTATAGTATTACGTTGTGAATTGAGTTACTGCATGCTATTCCAGAGAGCAGAGAATTTATGCCCTCAATGATGCATTGGCCGGCTGTCAAGTTGCCCCGCTCATTTTCCTGAACTTCAGAGGGAGGAAATTGCTTGAATCGGCGTTCCTCTTCTTGCCAAAACTGCTAGGTGTGACACCAGTCGGTGAGACCAAGGAAGTGGTGGTGTTTCGCCGAAACCTCCCCATGTTCCAATATGAGAATCCATCATGTTGGCTTCCAGAACTAGGAGAACGCATAGCAAAATTTCTTGGTATCACACTTTGCTGTCGGTCATGGATATCCTGAAGAGTTCTTATGGGAACCATGTCCACAGCATGGCTAGGGTAAGCAGCAGCTGCAACTCCCATTGCAAAAGGAGATGAGCTGCCGCCGGGAATCATCCGCGACGACGGCCCCGGGAACCCGCCGCTGCCGCTGCTGCTGCCAACCTCGAAAAGTGGCATGGTAGGCGAGAACTCCCCGAAGTCGGTCACCGGCGGCGACGGCGACGGCGCGGGTAGGCGGAAGAACGGCGAGAGCATAGGTGGTCCAGTTCCGCCGCCGCCGCCGCCGCCGCTGCGGACGGGGGAGGCGGCGTCCCACGCGGCGAGCGGCGCGCCACGCAGCGGGCGCGGGCTCCAGCGGAAGGGACCGAATCCGGGGGCGCCCATCGGGGGAGGCGGCGGCGGCGGCGTGCGGGACTCGTCGGTGGAGACGGCGTCGTGGTGGTGCTGCGGCTGCGGGAGCGGAGGCGGGGGCGGGGGAGGGGGCGGCTGGTGGGGGAGGAGGTGGAGGCGGCGGATCCAGACGGAGTTGAGCGGGTCGGGGTGCTGCTGCTGCGGCGGCGGGAGGCGGCGGTGGTGGTGGTAGGACGGCGGCAGCGCGGAGCTGTGGCTCCCGACGGAGCTCCGCAGCGCGAGGTGCTCCGACATGGCGGCGGCGGCGGAGGGCGGGATCGCCGGAGACCGCGAGGAGGACCCCGAAGGCGAAGGCTAGCTTAAGCTAGCCCTCGCACAGCTCTGGTCGTGTGGCTGGGCTCACCTAGGATGGAGGCGAGGTGGGGAGGAAGCAAGCAAGCGGGGGGAGGAATATAAGCTGCCGGGAGGTCGCCGTCGCCGGCGTCGTGGTCGTCGTCGTCGGCGTCGCGGGGAGTGGAGGAAGTGAAGCGAGAGCCGAGAGAAGAGGGTGATGAGGGGATAGGGGTGGACACGAACACACGACCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.947141
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0228500.2 3 27435295 A G
Osa03LNT0228500.2 3 27432348 A G
Osa03LNT0228500.2 3 27432429 G A
Osa03LNT0228500.2 3 27432500 A G
Osa03LNT0228500.2 3 27433081 A G
Osa03LNT0228500.2 3 27433122 C A
Osa03LNT0228500.2 3 27433309 C T
Osa03LNT0228500.2 3 27436513 A G
Osa03LNT0228500.2 3 27433336 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0228500.2 osa-miR5833 Translation 3.5 24.957 1 21
Osa03LNT0228500.2 osa-miR413 Cleavage 4.5 20.162 1 21
Osa03LNT0228500.2 osa-miR1854-5p Cleavage 4.5 20.613 1 21
Osa03LNT0228500.2 osa-miR2877 Cleavage 4.0 17.907 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0228500.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0228500.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0228500.2 3 QFlw3 Morphological trait Culm/leaf RZ474 C746
Osa03LNT0228500.2 3 Yd3-13 Morphological trait Seed RZ403 CDO337
Osa03LNT0228500.2 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0228500.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0228500.2 3 qSB-3 Resistance or Tolerance Bacterial blight resistance R250 C746
Osa03LNT0228500.2 3 nan Morphological trait Panicle/flower RZ448 RZ403
Osa03LNT0228500.2 3 nan Resistance or Tolerance Blast resistance RM16 RM168
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