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

>Osa02LNT0183800.1

TGTATCATGCACATGCAGTTATCAAATTGACAGAGATCATTTTCCAAGCGATTCTTGATATCCTTGTATCAAATTTTGTACAAGTTTCTAAACAAAAATCTATCCACGTTCTTATACTACTTATATGAAGCAATGGAGAAAATAACCAACACAAATAATGTATTATGTACAGTCTGCTTCTAACCTATACCTCCAAAAAACAACCAATGCAAACAATCATCATTTACAGTTACACGTCTCCATTCATTCTATTCCTCGTCACTACTTGAATCAGAGTCTGCATTGTCCTTCATAAAATGTGCCGGCAAGTTGGGGAATCTTGGCATGACCCTCTTCCTTTTGCTATCTACCTCTTCCGGTGGTTTCTGAGCCGGTGCTGGTGCGTCATCAGCTGCCCCCTTGGTTGTGGCCGCTGGGGCCGCCGGTTGTGATGATGACGGTGGTGGTGTTGGCTTCTTTTGCTGCTGCAATTTCCTCTTGATGTCTACACATGCCTGATCAACCATCCCCAGGAAGTCCCTAACTATGATGAACAGCTGGAGGGGATGTGCATTCTTGTCCTTGGTGGCACCAGTATGGTAATACTCCGTTGTCCGCTGCACCAGTTCAAGCACTTTCTCCTGGTTTCCTTTTAGTTCATTCAGTTCTTGTTCTGCAGCCTTCACAAATCCTCGCAACCCTCTTGCGAATCCATCGTCCCCATAGGTCTCCAAGAGCTTCTTGGTACCTGCCAGCCGGTTGCCCAGAATTGCGCACTCGTTGACAACAGTGTCATAGTCCACCAGTGCCGCCTTCTTCACATTGGCAAACTCAGTGCTGAGACCTCCAACAATCGGTAGCCCGAGGTTCAGGTATTCATTTTGCCTCTCCTCCCGTGATGGACCCTGACTTGTGGAGCTTGCTGCTGGGTTGCCACCATCGGTGCTCTTGGCAAGGCTGCCAGAGCGTCGAAGACTGTAGTTGCGGTTGATGGCTAGACGCTTCCCCTCTGAACGCACAACCTCCTCAATGACAAAGTGGAGCAAGGTGGTGCTCCCGTCTGTGCTCTTCACATCAGAAAGCTTGCGGAGTGCAGTAAGGTTGAAGGCCTGTGCATTACCGCGTGCTGTCCCAGCATTCATCCGATTGCCTGCCTTGAGCACAGCCTCGAGCAGTTTGAAGAACAGCCCCTTTGTCCTCAGCTCCTGGCTTGCCATCTCAAGAGTCCGGAGTGACTGCTTGAGCTGTGCAACCTCAGCAGCATAGTTTGCCTTGAAAAGCAGTGCATTGACGCGTGCAAATGGGCTGGGCACATCAAGGAGGAGCCGGAGTAGGAAGAACTCCGCTGGAGCAAGCCTGTCAGGGTTCCCAGAGAACTTCAGAAGTGTGTTCTCCTCTTCCTTGGAGATGTTGAGCCGAGACAGCTTCTCAAGGACCTCCGTGCTGAGCTCGGTATGGCCGTTTAGGAGGGCGTCAATGATTTCCTCTCGCCCCACGGTGAGGGACCGGAGGATGATGGAAATGTTGTGCGACTTGCGTGGCTCAAGCAAGAATATTTGCTCTGGCGAGTTCGAGCGTCCGAGGCCAGCTGAGGTGCTGCCACCAGAGGCATCCTTGGAGTCTGCAGGCTTTGTCTTGCGGTTTACCGCGGCGGTGCCAAACAGTGCCTCGATGATGCCTTCATCCAAGTTGAATGAGCCGCCGGTGATATTGTCCCACACCATGGAGTGATCGGTGGCCGCCACATTGACCTTGTCCCAATGCAGCGGCTTCAGCTTCGCCTGCTGATCCGCGGAACCGGTTGGGACGCCCGGCGCCGCCGGCGGCCTCGACGCGCCTCCCTTCGGCGGCGGTGGAGGCGGCCCACCTTTCTTTCCTCCCGGAGGAGGCGGCGGCGGCGGGGACGGGCCTTTGGGCGGTGGCGGCGGAGGTGGGCCTTTGGCAGGTGGCGGCGGAGGCGGGCCTTTGGGAGGTGGTGGCGGAGGTGCGGCTTTAGGCGGCGGCGGTGGGGGTGGCGCCGCGGCTGCTGGTTTGGGCGGTGGCGGTGGCGGCGGCGCGGGTGACGCGACGGCGGCGGCGGCGATAGATTGCGGTCGTGATGGGCTTTCCCTTCCAGGCGGCAGTGGCAGCGATGGAGATGGTGAGGCTGGTCGGGCGGCAGGGGCTGGTGCCGGAGATGGGGACGAGCGGGGTACCGAGCTGACGGCGGTGATCGCCGGCGTCGACGGTGGCCGCGCGTACGCCTCGGCGGCGGCCACAGAGAAGGACGAGGTGGAGCCGGCGCTGGGCGCGTACAGCGACTCGTCAAACTCAGCGGACGCGGAGTCGAGGGAGCCCCTCGGTATGAGCGGCTCCTGATCTATCCTGTTCTTCCTCGACCGCGGCGGCGACGGAGCCGACGACTCGTGGGCATCCTGCCTCCTCTCCGCGCGGTACGGCCGGGGCGGCGGCGGCTGCGGTGGACGCCGGCTCGCCGGGGGCTTCCTCCCCCTCCCGCCGTCGCCCTCCTTCTCGAACTCCCGCCAGTATATCGCGTCGAGGCCGTTCTCGTCCACCATGTTGCCCCGCGCCGGCCGCTTCGGCTCCCTCTCCGGCCGCTTCCCGGTGAGCGCGCCGCCCTGCGCTCCACCATAATGCTGCCCGGCCCCGCCCGCTTCGGTGAGCTCCCTCTTCTTCCCGTGCCGGAGGAACAGGAAGAAGGCGAGGCCCGACACCGCGAAGCTGCTCAGCGCCGTGCTCACCACGGCCACGGCGATGTCGCTCCGCTTCCCCGACGACGACGGCGGCGACGACGACGGGGTGGCCGTAGGCGTGCCGGGGGACGGAGACGGCGAGGTGATCGGCGGCGGCGTGGCGAAGGCCGGCGTCCGGGTGGACGGGAACCTCGTCTGGATGTTCTGCCCCTGCGCCGCGGCGAGCGGGGCGACGCCGACGAGGAGGAGGAGGAGGAGGAATAGGGGGAGAGGAGTCGGAGACGGAGCCGGAGCCATCGCTGCGGCGAAATGGAAAGTGACGGAGATGAGGCGAGGCGGTAGGATTGACTTAGCGGAATCGATGGGTTGAGCTTATCGTTGAGCTGGGCTGCGTCGCGTCGCGTGGCGTGCGTTTGACCTGGCCGGGTTGGGGGTTGGTTGTTTACTTGGTCGGGCGCCGGACGAGGGAGGACGGCTCATGGTTGGGTACTTGGGATGGGTCGTTGGGTGGGAAGAGAAGAGAATGGAAGGGAAGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.0905209
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0183800.1 2 30882418 A G
Osa02LNT0183800.1 2 30882594 A C
Osa02LNT0183800.1 2 30882749 T C
Osa02LNT0183800.1 2 30882903 A G
Osa02LNT0183800.1 2 30885254 C 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
Osa02LNT0183800.1 osa-miR6246 Cleavage 4.5 12.773 1 23
Osa02LNT0183800.1 osa-miR171a Cleavage 5.0 17.047 1 21
Osa02LNT0183800.1 osa-miR414 Cleavage 4.5 23.581 1 21
Osa02LNT0183800.1 osa-miR414 Translation 4.5 20.366 1 21
Osa02LNT0183800.1 osa-miR1856 Translation 5.0 17.486 1 21
Osa02LNT0183800.1 osa-miR2096-3p Cleavage 5.0 13.467 1 21
Osa02LNT0183800.1 osa-miR2118c Translation 5.0 17.647 1 22
Osa02LNT0183800.1 osa-miR2118q Translation 5.0 17.647 1 22
Osa02LNT0183800.1 osa-miR5490 Translation 4.0 8.053 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0183800.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0183800.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0183800.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0183800.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0183800.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0183800.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0183800.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0183800.1 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0183800.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0183800.1 2 nan Morphological trait Seed C747 C1445
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