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

>Osa02LNT0163800.1

AGGGTACGAGAGGGGATCATAACATCCGTAGAAAGGCTGGATAGATTTCCGTGTACGGTCGTTCCCGTATATTGTCACGCTAGGCTTGTCACGCCCGGAATTTCTATCCAAAATTCCAAACGCTTCCATGTGTGTGAACCCTCGTCCAGGAATCAGCCGAGGCATACAATAACAAATTGATAATAGAGTACAATTATTACTATAATTAATAAGCGAATAAAATGTCATTACAGAGGTAGATAGTTCCTCTCAATCAATAAAGATCTAAGCAGCAGAAAATAAGATAAATGGCGCAGACGACTCCACTCCACAGGCAGCTTGACCAAGGCTACACCTAATCCTCCACACCATCAGCATCACTGTAGAACTCCTCCTCTTGCTGGCTTTGGAACTCTTCAAATTCTTCTCCTGCGAAAACGGACTCTCCAGAAACGTCGGAATCTAGCCCAACAAACATGTAGTATTCATCGTCGGAGTCATCATCCATGAAGGAATCCATATCATCATCATCGAAGGTGCATGATCGTGTACGATGATATGTAGAATGCTCAGTTTGCAGGCTCGATGTAGATGGCACATCACCGGTTGCTTCCAAGCAAGGCTTTGGATTTAGCAACGACGGGCTAGATCCCTCAGGGCACTCTAGTGCAATCGATTCAGCACATGGTTTGTCACGCCTAGCTGCATAGAGTGCGTTATGTCGTGCCAGATGAGCAGATCTTTCTCCAGGAGTAACATTTTGTCGACTTGGTCTACGACGAGCATTCATATCATGGATTTCCACATCTGGCATAGATTGCCTTACAACCCTACGACTGTCATTCAACTCTAGTCTCTGTTCATTTGTTAGTGATTGACGTCGTGTTCTCTATCGGTCCACCTTAGCTTGTTTTTGCTCCGGTGTAAGAGTTGCAGGCTTCTCCCTAGCTCGAGCTAGCTTTGACTGCAGTCGTTGTTTTGTCTGATTGGTTGGCGCACGCACCAATTCATTCTCTAGAGAGATGTCGTCATCATGGTCGCACTCATTTCGATCGTTGCCTTGAAAAATACCGGATTCATGCATTGGGCTATGGGTATTTTGGTTCCCACTTGTTACGATTGGATCATAATGATTTTCACATCCTGAATTATGAACAGTGAAGTCAGCACTATTCATGTTTAGGGTTGTTAATTGAGTGACGCGACTCATTGGAACTTCGTTGGGACCATAGTGAGCTACATTGTTGATGATTGTAAATGGGAGACGTCTGGGTGTGATATTGAGATGGGAAGCTTCTCTTTTTCCTTGATGCAGTGTGGAAGAATCATTATCTTCCAAGTGGCACTTCATTATATCAACAACACTTATATTTGAAATATCGCCAAGTGGGGCTGAAGCTTGAGTTTCCTCTTGAGTTTCCTCCTTCTTTCGTTTCCTTCTTTCACGTGCCTTCTTGTTCCTATCATCCTTTTGCTGTGGGGTCAATGCTGCGTAGCGGTCTCGAGCACGCTTTCTTTTTAGTTCAGCCACAGTAAGGTCACTAACATCTTCATGCGAACCTGTGCACATATGCACATTGCTGGGTGTATTGAAGGATGCACCGCGGTTTTCATTTGAAGAAGTTGGACTGGCACTTAACGACTTGTTTCCACCCCTGCCCCGTCTATTTGTCAAACCGGAACCACTTATATTTGTTATATCAGCAAGAGGGCCTGTTTTTGTACATGATTGTGTAGAGCCCCCAAGAATGTTATCCATTTCTCAATAACACGGCCAACTATGATATCACCAACCTCCGGCTTATACCTTTGTGGAGCGCGATGCGTGGGGGCACGGCGAAGAGGAGGACGGCGAAGAGGAGGGGGGCGCGGCGAAGAGGACGGAGCGGTGATGGGGGCGCCGGCGGTGGAGGCGCGGCGGGGCACGGTGAAGATGGGGGCGCCGGCGGTGGAGGCGCGGCGTGGCGCGGCGAAGAGGTGGGAGGCGCGGCGGCGAAGAGGACGGCGCGGTGATGGGGGCGCCGGCGGTGGAGGCGCGGCGGGGCGCGGTGAAGATGGGGGTGCCGGCGGTGGAGGCGAGTCGGTGTGCGGCGAAGAGGCGATGGGGGCGACGGCGGTGGAGGCGCGTCGGCGGTGCGCGGCGAAGAGGCGATGGGGGCGACGGCGATGGAGGCGCGGCGAAGAGGTGGGAGGCGCGGAGGCGAAGAGGACGGCGCGGCGGGGCGCAGCGAAGATGGGGGCTCCGGCGGTGGAGGCGAGACGGTGTGCGGCGAAGAGGCGGTGGGGGCGACGGCGGTGGAGGTGGGAGGCGCGGCGGAGGAAGATGCGCGAGGCGTCGGCGGAGCGCGATAGTTGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.170412
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0163800.1 2 16493588 T C
Osa02LNT0163800.1 2 16493663 C T
Osa02LNT0163800.1 2 16493666 T C
Osa02LNT0163800.1 2 16496986 A G
Osa02LNT0163800.1 2 16497025 A C
Osa02LNT0163800.1 2 16497083 A G
Osa02LNT0163800.1 2 16497235 C T
Osa02LNT0163800.1 2 16497523 G A
Osa02LNT0163800.1 2 16498063 C T
Osa02LNT0163800.1 2 16498124 T G
Osa02LNT0163800.1 2 16498244 T C
Osa02LNT0163800.1 2 16498267 A G
Osa02LNT0163800.1 2 16498402 C G
Osa02LNT0163800.1 2 16498431 T C
Osa02LNT0163800.1 2 16498524 A G
Osa02LNT0163800.1 2 16500665 C A
Osa02LNT0163800.1 2 16500983 A T
Osa02LNT0163800.1 2 16493448 A G
Osa02LNT0163800.1 2 16499271 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
Osa02LNT0163800.1 osa-miR5540 Translation 5.0 20.974 1 21
Osa02LNT0163800.1 osa-miR5806 Translation 5.0 18.227 1 21
Osa02LNT0163800.1 osa-miR5813 Cleavage 4.0 18.747 1 22
Osa02LNT0163800.1 osa-miR5834 Translation 4.5 15.561 1 21
Osa02LNT0163800.1 osa-miR164e Translation 5.0 9.583 1 21
Osa02LNT0163800.1 osa-miR408-3p Cleavage 4.0 15.407 1 21
Osa02LNT0163800.1 osa-miR414 Cleavage 4.0 19.416 1 21
Osa02LNT0163800.1 osa-miR414 Cleavage 5.0 22.362 1 21
Osa02LNT0163800.1 osa-miR1429-3p Cleavage 5.0 24.739 1 21
Osa02LNT0163800.1 osa-miR1851 Cleavage 4.5 12.166 1 21
Osa02LNT0163800.1 osa-miR2095-3p Cleavage 4.0 17.783 1 20
Osa02LNT0163800.1 osa-miR2875 Cleavage 3.0 18.221 1 24
Osa02LNT0163800.1 osa-miR2876-5p Translation 5.0 20.375 1 21
Osa02LNT0163800.1 osa-miR2922 Translation 4.0 17.688 1 20
Osa02LNT0163800.1 osa-miR3979-3p Cleavage 4.0 21.072 1 20
Osa02LNT0163800.1 osa-miR3980a-5p Translation 5.0 18.747 1 21
Osa02LNT0163800.1 osa-miR3980b-5p Translation 5.0 18.747 1 21
Osa02LNT0163800.1 osa-miR5339 Cleavage 4.5 17.778 1 21
Osa02LNT0163800.1 osa-miR5491 Translation 3.5 12.335 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0163800.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0163800.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0163800.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0163800.1 2 d50 Morphological trait Dwarf nan nan
Osa02LNT0163800.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
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