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

>Osa03LNT0238900.1

GCCAAGAAACCAAATTCAGATTACTGCTTGCAAACCAGCAAGAATTTCAGCCACAGAGTACAAGAAATCCTGCAGTGCCATTCTGCAAGATGATAAATTCAGGCAATTCATCACTACCCAGCAGATTACTACTGTTTCTTCCCCCAACTAATCTCTGAGAAAGGCAGCACACTCATCGACTCATCGTGGGGTTGGTTATTGAATCTATCTTCTCCAATCCCGGTTGACGGATTAACCAAAGCGAAAAACCGAAAGAAATTCAGTGCATGAAGTACAACAGGGAGATGATCAGATGACTGACGAGATCATGCTTCCCATCCTCTGAGAACGGTGGCGCGAGCGACACGGTTGACACCGAGGGTGAAGGCGCCCATGCGGAGGTCGCAGTGGTGGCTCCTGCACATCTCCTTCACATCCCTGAACCCACGGGTCATGTAGGTCTTCAGCTCATTGTTCACCTTCTCCTCGTCCCACATGAAACCCTGAATGTTCTGAACCCACTCGAAGTAGCTCACTGTGACACCACCGGAGTTCGCGAGGATGTCTGGAAGAATGAGAACGCCTTTCTTGGACAGGATCTCATCTGCCTCAGGGTCTGTGGGGTGGTTTGCAGCCTCAATGATGTACTTTGCTTTGATCTCATTTGCGTTGTCCTTGTTTATAACTCCACCAAGTGCTGCCGGGATGAGGACATCACATTCTTCAGTAAGCAGTGAGCGTGGGTCGATTGCATCGCCTCCGTCGAAACCCTTGATCCCGCGGTTCTCTGATGAGTGCTTCATTAGCTTTGCAATGTCAAGCCCATTGCTGTTCTTGACAGCTCCAGTGACATCACTGATGGCAATCACCTTGCCACCAGCTTCACTGATCAGCTGAGCAGCCCAGGATCCAACATTACCAAATCCCTGTATTACAAAACGCTGGCCAGCAATGCCCTTGCCATGCTCTGCAAGCAAGGCTTCAGTAGCAAACAGAACTCCCCTTCCAGTAGCTGCATCTCTTCCAAGTGATCCTCCAAGGTCAACAGGTTTTCCAGTCACCACAGCAGGTGAATAACCATGAAACTTTGAGTATTCGTCAAGTATCCACGCCATTGTCTGAGAGTTGGTTCCCATATCTGGAGCTGGAACATCTGTATGAATGCCAATCAAGTCGTGGATTTTCTGGGTGAAAACACGGGTAAGTCGCTCTAGCTCGGAGATGCTGAGATCTCCAGGGCTGCATCCTATTCCACCTTTAGCTCCTCCATATGGAATATTAGCCACGGCCGTCTTCCATGTCATTAGTTGTGCCAACGCATTGACCTCATCAGGATCAACCTCATGGTGGTATCTGATTCCACCCTTCATAGGTCCCCTAGCATTGTCGTGTTGGACCCTAAACCCAACATAAGATGCTAAAGTCCCATCATCTTTCGGAATTGTGCATTCAACCTTGATCTCCCTGAACGGGATGAGCAAGCTCTTCTCCAGCTTGGAGTCCAGGCCCAGCAGCTTGGCCGCCTGCTTGAAGTTCCTGCTCGTCGCTGCCAACGCATTCATCCTGTTCGACGAAATTCCCCTTCAGAGCCGCACACTTAGAAAACCAGACGAGCGAAGCCACGAAGCAATTAGTCGAGGATCTCGTCGTCTTAGCCAAGGAGACTTGGATTAGAGAATTTGGGCGATGACGCAGGGGATGGTTGGCAATTGGATCCACATATGATCCCAACTAGTTTGGGTTGGCCGCATCTCATTCTGTTCTTACATTCCAAATTCGATGCAAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.870018
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0238900.1 3 33039073 G A
Osa03LNT0238900.1 3 33041650 T C
Osa03LNT0238900.1 3 33041814 T C
Osa03LNT0238900.1 3 33041894 C T
Osa03LNT0238900.1 3 33042230 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
Osa03LNT0238900.1 osa-miR5789 Translation 5.0 12.857 1 21
Osa03LNT0238900.1 osa-miR5794 Translation 4.0 10.164 1 21
Osa03LNT0238900.1 osa-miR5802 Translation 5.0 16.737 1 24
Osa03LNT0238900.1 osa-miR1437b-3p Cleavage 4.0 22.13 1 24
Osa03LNT0238900.1 osa-miR2094-5p Cleavage 4.5 22.738 1 21
Osa03LNT0238900.1 osa-miR5076 Translation 4.0 10.599 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0238900.1 3 nan Resistance or Tolerance Drought tolerance R1618 G164
Osa03LNT0238900.1 3 qSBR-3 Resistance or Tolerance Sheath blight resistance G249 G164
Osa03LNT0238900.1 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
Osa03LNT0238900.1 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0238900.1 3 QSn3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0238900.1 3 qPES-3 Morphological trait Panicle/flower G249 G164
Osa03LNT0238900.1 3 QFll3 Morphological trait Culm/leaf G249 RG418
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