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

>Osa01LNT0042700.1

GAACATTACCTTTTGCATATTTTATTATTGGATCACACAAAACAACGTCTATGTACACATTTCAGGCGTTTAACAAATCAAACTACATAACAAGCTCAACAAGTCTTGAAGCAATCAACTGAGATCTTGGTCCCTTGCTGGAACTCACTAGTGTTACAACAACAGCAGCAGCAGCAAGCATAATAGCACACAGAGCTTACAGGATATCTAGCACCAAAAAAAAAAGGAAGAACTGCCTAAGCTTTGGCATCTCCTTTAGGTTGACCAAGAAGAGATGGCCGGTAAAGTGAATGGCCCTGCGCCATCTCAATTCTTTCACGTGGATCATACATTGTTTCATCTCTTATGGCCTGAAGGATCGAATCAGGAGGAAGTTCCCTCTTGATCAAAATTTTGTACAGTGCCTTCAGGATTGGGCACATCTCAACCGGTGCAACAGATCTGTTGGCTTCAGGATGCATTACGCTTAAGCTATCCTGACTCAGGAGTTCATAAAATGCATTGACTGCAGAGACACCCTGAATGGTTCCTTTGCCTTTTATGCTGTCACCCATCTCTAGTGTCAGTTCACCTTTAGCTAGTTTCTGCCCATACCATGCATTACGACCCTTCAGCAATGTGACATAAGTGTCAGCCAATAATGGCCCAGCAAGTTTTTCAGGCTCTTCTTCCAAAAGGTGGGTTATGTAAATCATTTCAGATGTGCAAAGAGCAAAGTAAACGGATTTGCTGGTTGCACTCTCATTTGTTAGAGCTGCCACCATACCGGCACCAATGGCATACACATTTTTCAAACCTCCCATGACTTCATGTGTAATGAGATCACTATTATCCCATACAATAAAATGAGGCTGCCTCAAAAATTTAGCAAGAGGTTTTCTCCATTTGTCAGCTCCACATATACGAGCATTTGCATATTCTTTATTGTAAATTTCTGAAGCAATGTTAGGGCCTCCAAGATAAAGAATGTTTTCCAATGGAACCCCCGTTGCATTGCTAATCATCTGTGTGGGAGTTATGATCCGTGGCAGGGGATCCAGGGAGGCCTCTATCCCTTTGGCCAGAGAGAGGATGATGGGGGCAGTAATCCTCTCCTTCCAGTACCTCCCAATCTCCCCGAAGACTTCCCTGGTGTCCGTGGACGGCAGCCCGTTGATGACAATGTCGGCGTCCCAGACGGCCTCCTGGAGGTTGGTGACGACCTTGAGCGGGCAGAGCGGCGTGTCGATCATGTTGAGGCAGAAGCCGTCCCTGAGTATCTCGTCGGCGTAGAGGGTGCGGTCGCCGAGGCGGCCCTCGACGTACTTGAGGTAGGCGCAGCGGCGGATCAGGCGGCGGAGGACGTCCTCCCGGGCGTTGATGACCTCGAAGAGGTGCTCGGCGGTGGCGCGGTCGACGGCGCGGCCCGGGCGGCGCCAGATGCGGACCTGCACCTTGTCGCGGAGGTGTCCGTACGCGTCCTGCATCAGCGCGCAGAAGACGCTCCCCCAGGCCCCGGCGCCGACGCCGACGATCCGGAGCGGGTCGCCGTCGGCCTTGCCCAGCAGGCGCCGCAGCTCGTCCAGCTTCTCCTCCACGGTGGCCCCATTCCCGTGCCCGTTCGCCGCCGCCGCGCGCGGCGCGTCCTCCGCCCCGCCCATTGCTCCCTCCTCCACCTCTCCGCCTTCCCTTGTCGTCGCTGCAAGCAAAATCGAGCAGGCACCGGAGAGCCCAACGGCACACGCTACATAACCGACTACTTAATTACGGGGATCGGCGAGCGAACGAACCAAATCCCACAGAAAAGTATAGTAAAAACGACGCACTATTTTTTTTCCCTTCTCTATCTACTAAGACCAGCCTGCCCACCCCAGCATGTGACGCGATCTGAGGAGTCGTCCGCCAATTTTTGGTGGCTGCTGGTAGGTTTGGCCGCCGAATCACTGTCGGCCGGAGAGACCGAGGCGGCTTGGCTTGGCTTGGCTGCCGGCACCGCCCCGGGACGTTTGCCGCCTGTTGCGCCTCCGCTGCTCGCGTCGCGACCCGCGAACGAGGCGAAGCGAAAGCGAACAGGGTCGGGTGGAAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.183555
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0042700.1 1 33952632 A G
Osa01LNT0042700.1 1 33952684 A G
Osa01LNT0042700.1 1 33953844 A G
Osa01LNT0042700.1 1 33953862 A C
Osa01LNT0042700.1 1 33954287 T A
Osa01LNT0042700.1 1 33954425 A C
Osa01LNT0042700.1 1 33954633 A T
Osa01LNT0042700.1 1 33955648 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
Osa01LNT0042700.1 osa-miR5828 Translation 4.5 20.057 1 21
Osa01LNT0042700.1 osa-miR169d Translation 4.5 15.427 1 21
Osa01LNT0042700.1 osa-miR408-5p Cleavage 5.0 15.605 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0042700.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0042700.1 1 nan Morphological trait Root RM212 R2417
Osa01LNT0042700.1 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0042700.1 1 qLEJ-1 Morphological trait Shoot/Seedling RM212 RM297
Osa01LNT0042700.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0042700.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0042700.1 1 Pi35(t) Resistance or Tolerance Blast resistance RM1216 RM1003
Osa01LNT0042700.1 1 qLRC-1 Resistance or Tolerance Drought tolerance RM237 RM302
Osa01LNT0042700.1 1 dth1.1 Physiological trait Flowering RG541 RG109
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