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

>Osa01LNT0019900.1

GGCTTATCTCCGCCTCTCCCTCCTCTTCCCACGCGCCGCCGCCGCCGCCGCCGCTGCCGCCTTGGCTCCTTCGCTCGTCCGCGCTGCAGCCTGCAGCTTGTGGACGCCGGCTCCTCGGCGAGGATGTCGACCGAGGGGTGCTCCTCGTATCTTTGTCGGCTGCCAGGCCCTCCGACTTTAGCAGTTGGCGGTGCTGCCGGCGGCGAGTTGGTCGAAACCTCCTCGTCTTCTGGACCGCCGCATGCTTCCCCTCCGCATCGGAGTACTGCCTCCACCTCCCTCTCCTCCAATCCTCCCCGGCCCAGTTCCACCGCCGTCCCTCCCCTTTTCCTCCCCGGCCAAGTGCCACCGCCTCCTCCTTCTCCACCTTACTATCCCCAGCGACGCCGCCGCCGCCATATCTCCTTACATCTTCCCTTCATCTGGCCGATGCAAGCTGGGGACGACCAGATCCGGCGTTTTTGAGCTCAAAACCACCAGATCCATCCCCTAGCGCGGCAAGGGGGGAGGCCGCCATCTCCAGATCCAATAATGCCCCTCTTTTTCTTCTCCGGTCGTCTTGGTGGCGGCAGCATATGGCGGCCGTCCCTTCCGGGCTCAAAGAGGAGCGTCCGTGTGACCACCGCGCTCCAGGCCCGCGTTGTGAACGCTGTCCAGCTCCTTGGTGGCCACAAGACTACAAGAAGAATTATAGGTCAGGAGTGGAAGAGACGTGGTGAACCAAATATAACACATAAAGAAAAACTTGTACGGAATGGTGCTTGGCGTGGTTCTACCAGCAGATATTCTTTTTGCTACCATCTAGAGGAAGCTGATTTGCACCAGTGCCATCAAATACTCACCTGCACTTATCAGAGATGGAGATAAAATTGAGGCGGAATCCAAGATGGAAGTCGTTCTGGAAACAGAGCAAGGATCTGCTAAAGTCCGCATCTGCTATGACCGGGATCGGCAGAGTCCGAGTTGGACAAGGTTAGCCGATTGAGCCGAGTCCGACAATGTGACGCGGTACACATTGTCGGGTTGAGTTAATGAGCTTCATGAGGATTGTCATGCACGGATTGAGTCCTGAGACGGCAATTATATCTATTAATTAGGATATTTCATGTAATTTTCTTAGAGATATGTTTGGGCAAAAGTCTGCTGCAAAGACTTATGGTATCTTAGAGTTTGTTAGAGATAAGAGTCATGTCCGACACGAACATATTTTGTAATCTCGGGTATAAATAGACCCCGAGCCCTATGTAATACAACAACACACGTTCAATACAATCTCGGCGCATCGCCACCCTTTTACT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.045579
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0019900.1 1 16708247 G C
Osa01LNT0019900.1 1 16708546 C G
Osa01LNT0019900.1 1 16708572 A G
Osa01LNT0019900.1 1 16709000 A T
Osa01LNT0019900.1 1 16709439 T C
Osa01LNT0019900.1 1 16708311 T C
Osa01LNT0019900.1 1 16708635 G A
Osa01LNT0019900.1 1 16706837 C T
Osa01LNT0019900.1 1 16708849 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
Osa01LNT0019900.1 osa-miR5542 Cleavage 4.5 12.664 1 21
Osa01LNT0019900.1 osa-miR5819 Cleavage 4.5 11.97 1 21
Osa01LNT0019900.1 osa-miR1319b Cleavage 4.0 15.811 1 24
Osa01LNT0019900.1 osa-miR1425-5p Cleavage 4.0 18.138 1 21
Osa01LNT0019900.1 osa-miR2095-3p Translation 4.0 17.081 1 20
Osa01LNT0019900.1 osa-miR2095-3p Translation 5.0 17.284 1 20
Osa01LNT0019900.1 osa-miR5071 Cleavage 4.0 15.004 1 21
Osa01LNT0019900.1 osa-miR5524 Cleavage 4.5 18.258 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0019900.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0019900.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0019900.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0019900.1 1 qNVB-1-1 Morphological trait Culm/leaf R2159 C178
Osa01LNT0019900.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0019900.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0019900.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0019900.1 1 nan Morphological trait Root RM23 RM306
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