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

>Osa02LNT0171100.1

CACTCTCAGAACCAGAACAGCACACTTGCAAACAAAGCCATGAAATTCGCTCCCCTACGTAAGTTTTGGTGACCCTTCCAATTTTGGTGGGGTCATGAGGCTTTTTGTCAGCCATATCGCCGTCTCTCTGGACGACACAGCACCTTCCCCAAACGGTCTGAGAACGCCAGCAAGCTCCTCAAGCCTCTCCTGCTTCAGCAGCTTGGCGCAAAGCTCGAGTAGCGACTCCAGTGCGTCAGCTCTCTGCTGCACTATGTTCAGATGGTCCCACTCGGCAGGAGTGCTATCTGAATGTGCCAATTTCACCGCGCTCTTCGGTGATGATTCTTCTGTAACGATGGGAACGTCTCCTGTGCCTGGTTTTGATCCTTGGTGAGTGTGTGCTTTCACTTCCTTTCTCTGCTCTTGCACTACTCCAATGGTCAGTTCCTCCTTTGGTATTGGTGCCTCATTAGGCTTCTGAATTGCACCAGAGACTGGCACGACATCTACTGTGCTGCTGGTTCTTACAGCTTTAAGAAAGATGGCCTCATCAATCTGTCGATCGGTTATTGTCATCAAATTTTCCTCTATCTGTTGAAAAAGCGTCAAATCATCGATGTTTTGATATGCTTTGTTTCTAGCTTGAGGATCCACAGATACTTGTGAAATGCAGGCGTCCTGGGTACCAACTGTTGAAACATCTGAAATATATGTGGAGTTGTCTCTTGTATCCACAGCTTGCTCTGCAGCGGTTTCTAATGCTTCACTGGATCCATTGGTTTTGATGATTCGCTTTCTGCCACTGCCTGGTTTTCTTGACTGCTGCTTGTCTCCCAGGTTACTTTTGGTGGGCTTCACTGGAAGGTAGATTGGGGAGCAGCTGCATGATTCAGCTAGATAAGGCTGCAAATATGGGTGCCTCAATAGTTCTCCAGCAGTGGGTCTATGTTCTGGGTTTTTCCTTAGCATGCTCTTCACTATCTGCTTCAGTGATGATGAATATATCGGTGGCATTGGAGATATTGAAGATCTGTTTATTTTGTTAATTAATGATGCCATGTCTGCAGCTTTGAATGCAGGGCGGTGTGCTAAGATCTCAAACATACAGCATCCAAGTGACCATATATCAGATTTGTAACCATAAGGTATGTCTGCTAGTATTTCTGGGCACATGTAGTTTGGGGTTCCCACAATCGTCGATGCAAGGTCCTCCATGAGCAATTTTGCTAGCCCAAAATCAGCAAGACGGATGTTATTATCCTTTGTTAACAAAATGTTGGAACACTTGAGGTCACGGTGGAGCACACGGTTGCAGTGCAGATAGTCAAGGGCCAAGAGCAATTGTGTGAACCATCGGCACACCCTCTCTTCAGAGAAAAGGACACCCCTTGCCTTCTTGATCCTCTCTGCCATGTCACCTCCTTCACAGTAACTTGTCACAATGCATGCCGAGGTCCCTTCATCAACCCAACCGTCCTTGTACTCGACGATGTACGGGTTGCTGAGGCTCGCCATCAGGGACATCTCCTGGTACGCCGTGCGCTGGAACTTGTCGTTCTGCTTGGACAGCCGGATCTTCTTCATCACGTACCTCTTGCGCTCGCCCTTGTGGACGACGAGGTATGCGGAGCCGTAGGCGCCCCGGCCGATCTGCTCCACCACCTCGTACTGCTCCATGGCTCTGGCTCTGGCTCTGGCTCTGCTCCCAGGTGCGTCCTCCTTCCTCCTCCTCCTCCCTACTCTGTTCTTGCTGGCTACTGTTGCTTGGGCTGGGGGACTAGAAATGATGCTTCTGCTCTCTGCTCTGCGCCTCGCTCGCGGACCTCGTGATAATACGCGCGCGCGCACGCGTGCGGGAGGGTCGCAATAATGGCGGGCGCGAGGTTGAGGGCGTGTGTCTGGTAGGCAGCCTCTGCCCTGTCCAGTGGACGGAGACGACGGAGACGGAGACCGAGACGAACGCAGCACCGCGCAACCACTGCTGCTGCTACTTGCCTCTGGGCTTTTGCGTGTGCGTCGCTGTTGCGCGTTTTAGCTTTTTGTTAACGGGAGGGGAGGGGTGGTGGTTAAGGATTAAGGCGTGTTTTGTATGGGACTAACCAACTAGTATAATCAAAATCAATCTCTTTCTCTCTTTCTTTAGGAAGGAGGAGAGTGATCGTACTGCCTACGTGTAATTAGTAGTGGAGGGAACGTTTGCTCGCGTCTGCGGGCGGGCGGTGGGTCCCACGTGGCGGTGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.966429
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0171100.1 2 22822617 T C
Osa02LNT0171100.1 2 22823889 G T
Osa02LNT0171100.1 2 22826110 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
Osa02LNT0171100.1 osa-miR5798 Translation 5.0 22.623 1 21
Osa02LNT0171100.1 osa-miR5805 Cleavage 5.0 21.739 1 24
Osa02LNT0171100.1 osa-miR5820 Translation 4.0 11.668 1 21
Osa02LNT0171100.1 osa-miR5837.2 Cleavage 5.0 18.348 1 21
Osa02LNT0171100.1 osa-miR399a Translation 4.0 22.537 1 21
Osa02LNT0171100.1 osa-miR399b Translation 4.0 22.537 1 21
Osa02LNT0171100.1 osa-miR399c Translation 4.0 22.537 1 21
Osa02LNT0171100.1 osa-miR399d Translation 4.5 22.537 1 21
Osa02LNT0171100.1 osa-miR399h Translation 5.0 22.537 1 21
Osa02LNT0171100.1 osa-miR399i Translation 4.0 22.537 1 21
Osa02LNT0171100.1 osa-miR399j Translation 4.5 22.537 1 21
Osa02LNT0171100.1 osa-miR160e-3p Cleavage 4.0 17.77 1 21
Osa02LNT0171100.1 osa-miR1861b Cleavage 5.0 23.451 1 22
Osa02LNT0171100.1 osa-miR1861f Cleavage 5.0 23.451 1 22
Osa02LNT0171100.1 osa-miR1861i Cleavage 5.0 23.451 1 22
Osa02LNT0171100.1 osa-miR1861l Cleavage 5.0 23.451 1 22
Osa02LNT0171100.1 osa-miR395x Translation 4.5 21.185 1 21
Osa02LNT0171100.1 osa-miR5076 Translation 4.5 17.202 1 22
Osa02LNT0171100.1 osa-miR5796 Cleavage 4.5 22.835 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0171100.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0171100.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0171100.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0171100.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0171100.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0171100.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0171100.1 2 qCA-2 Resistance or Tolerance Blast resistance RG25 RZ961
Osa02LNT0171100.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
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