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

>Osa03LNT0240100.2

AAATAATCCAAACACCATGCCACCACTTTATCATGAGCTGAACATAATACAGTACAGCGATGAGTATTCTGAAGTTCTCTACAAATTCCCATCGGGAAATGTCACTTTTTCAAGCCGTTGCCTATTGAACATGCTCACAATTCAACAACATTTATTAACATGGAAAAAAATAGTTTCCTGAAGTTCTCTATACGCCCCCAATGAATCATGACTCTTTATTCAAGTGGCTGTTTTTTTTTTGACACACTCATAATTCAATATTACCATTTGACAAGCAAGAGGGCATTTTTGAAGCGATTTTGAATTACCCTCACTGTTCGTATGGCTCTTCATCTCTACCTTGCTTTGGACTAAAGTCTACTATTGTTGTTGTTGTTGTGGTCCTTGTTGAATATGTCACGTCGGTCATAGCTTGCTGCGATTCGAGAGTTCTTTGCTCAGCTGATCCCTCAGTACTCTTCTTAGCAGCTTGTTTGAAGCTGTTCTTGGGAACTCAGGAACTATTTTGACATAGCTCACCTTGAAAAGAGGATTTAAGTTCTTTTGGATGGCTCTCTGAAATTTGCTCTTGAGAACATTTGCATCACATGGTGGTGATCTATCTTTTAGCACAGCCAAGATAGCCAGCTGTTCTGGTCCCCCACCAGCAGGTTTGATGCTAACCGCTGCTGTTTCTAGTAGAGCCTCATCGGCTCTATTACATATCCGCTCTATTTCCACGGAACTTGTCTTAATTCCTCCAAGATTCATAGTGTCATCTGCTCTTCCCTGCACAATATAGTAACCACCTACTGTCCTTTGGATTATATCTCCATGCCGTCGAAGTTGCCTTCCATTGTAAATGGGCATTCCATCAAAATAAACCTTATTGTTGTCAGCATTGAGAAGTCGATCTGTAGCGCCAAAATATAAAGGGAAGAGGCCCACTTCTCCAGCACAAGGTACATCATCAGGATATGGAGTTCCTTGTTCATCAAGTATGACAAACCCAGTGGACATGGATGCACCACTAAAAGCTCCAAAAGCTTGCGAACGCAGAAGACTGCCTTGAATGTATGACGATGCCAGCTCAGTACCCCCACAACATTCAATAATGGGCTTGTAAGAGGCACGCGAAGATAGCCATAGATCATCATCAATATCAGAAGCCTCTCCTGTCGTGGAGAGTACCCTGATTTTGGTCCAGTGAAGCCCTTCAGTAAAATTCCCAGCTTTCCATGACTTCACTAAGCTAGGTACACTTCCTAATATAGTGACACCAGCATCCTGTACAAACTTGCAAAAACCACGACCAAGTGGTGACCCATGATACAAAGCCAACGTTGCACCACTTAAAAAGCATGAGTACAAGAGTATAGGCCCCATAACCCATCCAAGATTAGTAGGCCAACAAAATATGTCCTGTGGCTGGATATCCAAATGCGCCCATGTATCACATGTGCATCTTATTGGAGAAAGTTGTGACCATGGGATAGCTTTTGGTTCTCCAGTTGTCCCTGAAGAAAATAGTATATTAGTTAGAGCGTCTGAAGGTTGATAAACTGTGGGATAAATGGACGACCTTCCAGCAGCACAAGAAAGGAAATCTTTCCAGGACATATCACCATTCCTTAGTGAAACCCCAAGAAAGCCTCCAGTTGCAGGAATTACAACAGCTTTAGATGAAGTCCCTTGCACAACACGGCTGTATAGTGGAACCTTCTTCCCTCCTCTAATTATGAAATCCTGAGTAAAAATAGCTTTCGCCTTTGACACACTCATGCGTGTACCAATCTCCTGAGGTGCAAAACTGTCTGCTATCGACACAACAACAAAACCACCAAGGACAATAGCCAAATATATGATGACTGCATTGCATGTCATAGGCATGTCTATTGCAATTCGATCCCCCTTTTGGAACATGGTATCAAGCGCAGTAGCAACTGTATGTTAGTCTGATAACATATACATACATCACTTGATTGTGAAGCTCCTTCAGTGACATACGGTTCACTGGGTGATTGTCAAGACCCTCATCCCTCCAAACAATAGCTGTGCTGTCATCTGTCCTGTTTTGGGAAGGCCAAGGTAACAGACAACATTCAGCAATATTAAGCACAGCACCTTGGAGCCATGTTCCCCCTTTCCTTGATTTATCTGATGTATCTAGAATTGACTTTGGTTCTTGTTGGAACTTGATTGAGATCTCCTTCAGCACCATTGACCAGTAGACCTCTTGATGCTCTACGGAGAACTTGTGGAAGAGGTGAAAACTTGAAACTGGGTCCTTATATGATGATCCTAACAACCTAGGACCATGTGCTTCCATCAGTCTACCAAGATTTGTTTGTTTAGTGTCAATCTGTGACGGGAACCAGTACGGCGGCGGGCCCCGGGCGGCGCGATCCCAGCCGGCGTAGACGGAGTAGTAGACGAGCTGGTGGAGCGCGTGCGGGTGCTCCGGCCGCAGCACCCCCGCCGCCACGGCCTCCCACGCGGCGTCAGG

Coding Potentia
Explanation CPC Score
noncoding -1.22556
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0240100.2 3 33634088 G C
Osa03LNT0240100.2 3 33632069 A C
Osa03LNT0240100.2 3 33635122 C A
Osa03LNT0240100.2 3 33635220 A G
Osa03LNT0240100.2 3 33635305 G A
Osa03LNT0240100.2 3 33635416 C T
Osa03LNT0240100.2 3 33635533 T C
Osa03LNT0240100.2 3 33635858 C T
Osa03LNT0240100.2 3 33633486 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0240100.2 osa-miR5534b Cleavage 5.0 16.948 1 21
Osa03LNT0240100.2 osa-miR5837.1 Translation 4.5 17.024 1 21
Osa03LNT0240100.2 osa-miR166c-5p Cleavage 5.0 18.525 1 20
Osa03LNT0240100.2 osa-miR1432-5p Cleavage 4.0 19.086 1 21
Osa03LNT0240100.2 osa-miR1850.1 Cleavage 4.0 12.245 1 21
Osa03LNT0240100.2 osa-miR1877 Cleavage 4.5 8.267 1 24
Osa03LNT0240100.2 osa-miR2122 Translation 3.0 17.941 1 22
Osa03LNT0240100.2 osa-miR5073 Cleavage 4.5 16.392 1 23
Osa03LNT0240100.2 osa-miR5144-5p Cleavage 2.5 23.733 1 21
Osa03LNT0240100.2 osa-miR5144-5p Cleavage 4.5 15.347 1 21
Osa03LNT0240100.2 osa-miR5522 Translation 4.0 14.953 1 21
Osa03LNT0240100.2 osa-miR2106 Cleavage 5.0 13.634 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0240100.2 3 nan Resistance or Tolerance Drought tolerance R1618 G164
Osa03LNT0240100.2 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
Osa03LNT0240100.2 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0240100.2 3 qSBR-3 Resistance or Tolerance Sheath blight resistance G249 G164
Osa03LNT0240100.2 3 QSn3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0240100.2 3 qPES-3 Morphological trait Panicle/flower G249 G164
Osa03LNT0240100.2 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