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

>Osa01LNT0023000.1

GTTGCTAGCAAAATTTTGCTACTCACGCACTGCACAAGAGCTTGTGCCTGTCACCAATCGTTGCTGCTTGCTGCAGTTGCCTGATTAAGTGAGGTGCTAACGTCGCCGGCCCTGACAGAGGAAGAGCTCTGATTGAGTGAAGTGCTAACGCCGCCGGCGCTGACAGAGGAAGAGCTCTATGTGCGTCTATAGCACTGTGTCCTTCGATCAATTTCGTATATCGCTGCGTCTGATATATAACCTCGCCAACGGTATCAGTTGCGATCTCGCGCGCGACTAGGATGAGCAGCCATCTCCTTCCGTCCGCGTGCGTCGCGTCGACCATGCCCATTCCCCTCCGCATCCGCACGCCGCGATCTCCTCCTCGCCTCTCACGCGCGACGCGATCTCCCCCTCCGCTCTCGCCTGTGATTTTAACGAGCAGGTAGAAAATTAGTTGGGAAGGGCCCACTAATGATGATGTGGAAAAATTTTAAATTTTTGGGAACCAAATTTTAGTCATCTATTGGAGAAGAGGGTGTATTTTAGGCTAAATATGTTTTTGGCTGTCCCCAATACAGGATTTTTGGGAGTTTAATTTTAGTCATCTATTGGAGATGCTCTAAGCGGGCTCATGGATTGGCCCGCTTGCATCCCTACTCTCAGGTTCCATGAATCCTAGCCAAAAGTTCATCAGAGAACAGTGCTTTGTCATTTTGAGCACACAGCTGTGAAGACTTAGGCCCATGCTATTTGAAGTTTCTGATGGCTGAGAAGTATTGACCAAACTGGAGTGTGGACACAAATTTCCTGCCCCAAATGTCCAGTGATTCAGTCCATGTTAGATGTAATAACAGAGAAACTGAGGCAACTTCTGACATTCTGAGTATCCGTGAACCGTGATTGGCATAAACATATAGCTTCAGCTGCCCTTTATGCCACTTGTGAAGCTTCTGCTTCGAGGTGCAGACGTGCAGCTTCTGTTCATTGTTAGCATGCATTATGGCATCATGATTGATTCATTCTGGGAATTGGCAAATTTGCACAGGTTGGCCAGAAAGAAGCTCTCTGTCTGCTGCAGCTCACCATCATCTTCCCCGAGGTCAGCATGTTTTCGCTGTAAACCGCAGCGAGGAAGGCGGAGACCACCTGGTGCTGGAGTGAGTTCCACTCAGCTATGTGCAGCAAACTCACTTATGTGCATGGCGTCATCAGCAGTCCACTTGGCTCACCCTAGACAAAAGAACCTCGAATTCAAGCAAAAGCCATAATTTTCACTTCATAATAAACTCAGTAATTTCAAGCCTGAAGATTAATTGTCATCAACAGTGAGATCAATGTTGGTGTCACCCAGTCACTGTCAATAGCAACTCGGTACGGGCGTGCTTGTTATCCAAGCTGAAGTACCTGGGGTTGCCCAGGTCAGCAAAGTACCTGGGGTTGAAGAAAATCTTTAAATCTTACCCATGATACACTCCTAAAAAGTTTCTGAAAACTGCTTGGCCCCATCTTTATTACATCATCTGTTGGAACCCTTATTCTCTGAAGCACTTATCTATTCTCTGTGCTATTTATGTAGCTAAGAGAACAATTCAAGTTATGTTACAAATGCATTATAGCAACTTCAAATAATATATATGGAATGTGCAGCTTCAAACAAGTTACATGTTCGCTGAACTCAAGGAGCAGGTTTGTCAAACAAGAGATGTACACCATATGACCAACACCTACTCTGCCTAGCGACCTGCTCTCCACGGAAGCCGGCGGCGAGGGCGCCGCCAATCTGGCCGGAGCTAAAAGTTTCCCGCCGGCCGGCCGCCGTCGCCGTCACCGATGCCGCGGAGACTACGCCCGTGGGACCCAGATCGTCCGCCCAAAGGGCACACCCGCAGCCGGCTGATCGCCGCCGGACGTCGGGAAGCGGCGCCGTCGGAGGAGAGCGAGAGACAAGGGGAGGGGGAAGC

Coding Potentia
Explanation CPC Score
noncoding -1.16049
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0023000.1 1 20381590 A C
Osa01LNT0023000.1 1 20383132 G T
Osa01LNT0023000.1 1 20384255 G A
Osa01LNT0023000.1 1 20384367 A G
Osa01LNT0023000.1 1 20384268 G A
Osa01LNT0023000.1 1 20382068 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
Osa01LNT0023000.1 osa-miR169q Translation 5.0 22.819 1 21
Osa01LNT0023000.1 osa-miR419 Cleavage 4.0 22.468 1 21
Osa01LNT0023000.1 osa-miR812f Cleavage 4.0 13.345 1 24
Osa01LNT0023000.1 osa-miR812f Cleavage 5.0 13.38 1 24
Osa01LNT0023000.1 osa-miR2926 Cleavage 4.5 24.367 1 20
Osa01LNT0023000.1 osa-miR2931 Cleavage 4.5 19.755 1 20
Osa01LNT0023000.1 osa-miR3979-5p Cleavage 4.5 22.382 1 20
Osa01LNT0023000.1 osa-miR5494 Cleavage 4.5 22.538 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0023000.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0023000.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0023000.1 1 nan Morphological trait Root RM23 RM306
Osa01LNT0023000.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0023000.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0023000.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0023000.1 1 qNVB-1-1 Morphological trait Culm/leaf R2159 C178
Osa01LNT0023000.1 1 nan Physiological trait Source activity RG532 RM472
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