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

>Osa03LNT0245500.2

AAACCCAACTCTAAGTGACCCTATATAACATCAATAATATCCAATACATGATACATTCATCTATTGTCACAGCTATTCTTCCTCCTGACTAAATGTGTTATGTACACTCACAAATCAACATTCCTACACTGACATATAGCCCCAACAAAATGGCCACTGATCTAACCAACATCAAATCAAATCAAATGGAGTGTACCCAGCCCAATGGAGTGTACACCAGTTGCTGATCTAAAAATGCCACCACCTTTTCCTTTTGTTCTCCATAACTGGTAACTCTCCTTCTGGATATATCGAGTTGTAGTGCACCTCAGCCCAAAAACTCAAGCATATAACTCTTTCTGATTTCTGAACAACAGGAAGGATTTCAATGTAGCAAGTATCTCTGAATGATGTCAGGATGAAAATCTTTACACCATACGAGTCTGCAGCAGCCTGCAATGTAACGTGGTCACCCCACTCCCCGTTCTTTATCATCTTTTTTAGATATTCCCTATAATCCATAGGGACATATCCTGCATAAATTTCCGGATAAGACTCAAGCTGTTTCACTATTTGTTGCCGAACAAATCTGTGGTGTTCAGTGGTGCGGTAAAATTGATCGGACAATGCTCGGAACTGACAATTGCCATCCCCTTCAACCTTGAGCTCAGCAAGATCATACAGCTCCAACCTGTGAAGGAGTCTTTGGTGATCTGAAAAGGCTTCATCAACAGAAGGAATGTCCCCGTTAGTTTTTGGAACATGAGGAATGGGAATCATGTCGTGTAATCTTTTGCCAACTTGGCCATCTAGAGCAGAGAAATCATCGACAAACTCGATTAAGCAGTCATGGGCATTATGATTATTAGTATTAGTATAATCTGCAGGGGTTGAACAAGAACTAAAGGGGGGTGGTGGTGGTGGCGCATCATCTTGTTCGTCTTCCTTTAGTGGAGGAGCTGTAGAAAAAACAAGAAAGATTAATACTGTAGTGTACAAGAGCGGAGGAAAGGGAAGAGGGAATACCAGAGGGGGGGAGATGGAGGATGGAGGAGGATAGGGATTGGGATTGGGCGTAGGAAAGCTCCTCCTGGAGGGCGTGGGCGATCATCTCATCGCAGTCGACGCTGCTGGTGCGTTGTTGGTAGTGTAGGGCAGCGGCGGGTGGAAGAAGAAGGTGAAGGCTCCATCGGAGAACATCCGGATCCTGCTCGTACACAACCATGGCCTCTTCTTCTTCCTCGATTCTTCTCCTTAATTCCCTTGGTTCTCAAAACAATTGGATTGGATAGGATTGGTCGTAACTATGAAGAAGGATCTGACAAGATGGGCGGGGCGGGGCGGCGG

Coding Potentia
Explanation CPC Score
noncoding -1.13471
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0245500.2 3 36286874 C A
Osa03LNT0245500.2 3 36288617 A T
Osa03LNT0245500.2 3 36289087 G A
Osa03LNT0245500.2 3 36289098 C T
Osa03LNT0245500.2 3 36289174 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
Osa03LNT0245500.2 osa-miR5532 Translation 4.5 15.772 1 22
Osa03LNT0245500.2 osa-miR5512b Translation 4.5 14.141 1 21
Osa03LNT0245500.2 osa-miR815a Cleavage 4.0 19.041 1 21
Osa03LNT0245500.2 osa-miR815b Cleavage 4.0 19.041 1 21
Osa03LNT0245500.2 osa-miR815c Cleavage 4.0 19.041 1 21
Osa03LNT0245500.2 osa-miR1869 Translation 4.5 10.133 1 24
Osa03LNT0245500.2 osa-miR2866 Translation 5.0 17.757 1 20
Osa03LNT0245500.2 osa-miR5161 Translation 4.0 15.335 1 20
Osa03LNT0245500.2 osa-miR5512a Translation 4.5 14.141 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0245500.2 3 nan Resistance or Tolerance Drought tolerance R1925 RG1356
Osa03LNT0245500.2 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0245500.2 3 Qsbn3b Morphological trait Panicle/flower RM227 RM85
Osa03LNT0245500.2 3 Qsnp3b Morphological trait Panicle/flower RM227 RM85
Osa03LNT0245500.2 3 nan Morphological trait Root R1925 RG1356
Osa03LNT0245500.2 3 qLT3-1 Morphological trait Shoot/Seedling RM227 R1925
Osa03LNT0245500.2 3 qPL3-1 Morphological trait Panicle/flower R1925 RM227
Osa03LNT0245500.2 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0245500.2 3 QSn3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0245500.2 3 qSV-3-2 Physiological trait Germination/dormancy RM227 RM85
Osa03LNT0245500.2 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
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