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

>Osa02LNT0158800.1

GGGAATTTTTAACCAATCAGGAAATTCCAAGCAGTTGATATCCTCATTCAGATATCAGGAAGTGTTAAGTGAAATGGATATTCAACACAGATGCTCCAATTATGTACATTAACTCCAGATAGATAGTAGTAGGATAAACTAATATGAACAGAGGTAAGCATAATTATGCATACGATAGATGAGATGGCAAAGGATGCTACTATCTTAAAGACCAAAACAAGTTGCCAGAGCAAATCATCAAACGAATGTGCACTTCCAAAGCCTGCTCCCTATCTTTGTTTGTTCTTTAGAACTCTAGCCATTGACGCAGCAGTGAAGAGAGCTTCTTTCTCAAACGGCGAGAGCTGCATATCCGGGTTGATTTTTCTCATATTATGAAAAGCAGATACAAAACTCTCAGATATCTGTAGGAGAGTCGCTCCAATCTTCTTTGTTGTATCACTATCTTTGCTAGAATCACATTCCAGATGAAGGCAGACCTGGTATGCGTTTGCTAAGAGCAGCTGGACAACTTCTGAACTCATCTTTTTAACAATGGCTTTTGTGGTTGCAGCCGTTGAAAATAAAGTCAGTACATTTTCCAATGTCAAATCGTGTTGTGAATTATCAGATCTCCGAGTACGAACTGCAGGCTTGCCACAATATTTTGAAAAGTACTGAAGTATAATCTCCAATTTCCACTTCCATTCCACAAAGATCTGATATAATTTAAGAATAAATAATTAATTTACTAAGAAAGGACAAGCTGAAAAGAAGAATTATACAACTGGAGTACTGAGAGGCCCTGATCGGCACCCTTGGCTGCATCACCGCAGCCATGCATCAGGCTAGTGCAGTCAAGCACTGAAGCTGCTGGTTGTGGTGCAGCTGCAGCCAAGACATCCGATCAAGCCAAAAATGGTGGGCGCGAACAAAAATAAAGTTAATAACTTTAATCTCATTTTCCAAAAAAAATTTCTCTGGCACTCACAACAGTACAGAGTTTCAGGTACAAATTTTATGCACCAGACTCAGCTCAAGTCTCTGTCGTTATTAAACACCATGGTTGACAATGTGCCTGAACTGTTATTAAGAATGCAAGATTACCAGCTACTTATGGTTAAAAGAATCGAATGTTGTACTAGAGAAAATAGGAGCTGGCCAATCAAGAAATGTGCCTGCTCATTGACAACCATTTTAGTGGCCAAATAAAATACCCTTACTCTTACATCATATGCCTTTACAAAAATGACTTATGACGTGCATTTGAGCAAGGCCAGAAATGGTCCGCTACTCAAGTAGGAGTAGGTTTTTTACATTTTACTCCAATGTGACATATTTTCAGCCTATTCCATATCAAGTGTTCACCACTCACATTTCTCCTTTTGCCCTCCCTCTCCCTCTCTGTATTTCCCTTTTTTTTACTCCGAGTCGTCAGGAGCTACAAATATCTCAGGGGCCTTCACAGCCCTATAACGAGTGCATCACACAAACAATTAAGGAGTTCCAGGGAAAATAACAACAGCACAGCTGCCTTAGTAACAGCACAAAGAAATTAATTAGACAGTAAGCTTCTAAAGTTTCATCAAGGCTTCCAATATATGAGCTCTCTGTTCTTTTTATTTATTGAGTATAGATTATTCCCCACTGCAATTATTAAGACACTTGAGAATGTGTAACATGTGGTTGTGGTTCCTAGGCCACATACCTGAGAGACATGGAGTGGCAAATCCTCAAGTTTAGTAGTGTACCTCTATACAGTAGCAAATTGTCATAACCCATCCCCCTTTATGAACAATTAGCACGTGGCGAGCTACATATACTGAAGTGGAAATTTACAGGTAGCATGTAGGAACTGTGAATAGGTTTTTATCAAGTTATTGATGCATGACCAACTGATGCAAGCTGAGAATTACTCAATTACAATAACAAAGAATTGTAGATATTTAGGGTAAGACAGGGACAAATAGATGGAATGATTTGCAGTTACCAGAAGAAATGGAGATAAATAGCTTATGTTGTAAGTTAGCTCATCTAAAATAACGTCCAAGATAGGATTCCTGCACCCATCAGCTCTTGAAGTCAGACCCATTGTGTCTGCTTCTTTTCTAATCAAGTCAAGGTTCATAACCATAGTGAAAAGTTTCTGAACTGATGCAAGAGCTTTTCTTTCGAATTCAAAAGATATGATAGCTAAGGAAGATTCTAGATCAGGTGCTGATTTAGCAGAACCTTCTTTGGAAGATATGCCATCTTCAACTCCCTGATTATATTGATTGAGCAGAAAAGATATGCAGTTCTTTACTAAAGATTTGAATGCCACCTTCCGTGAAACCAGAAGCATCTGTAGAAGAGATTCCCTGAAAATTACCCAGTCTAATGACTCTTTATATGCAATCTGACGAGGTACAAAATCAGCCTCAAGGGTGCTGACAAGATATTCAAGCAGCACCATGTTCTTTATATGCTCAATTCCATTATTAGCATCTGTGTCATTAGCTGTTTCAACCATATCCTCGATTAATGATGAAAATCTCTTCAAAAGGGAAAACCAGAATTAGATATCTCACATGCAGAAAAATCAGGATTCAGAAGGCCAAATACGTTGATATGTAGGATCAATAAGTTTGGATATACTTAAATATAGTAACTTAAAATAAAAATAGGCTCAAAAGGCAACTGTAATTCCCAGTTCTTGACAATATACAGTACCATGTACCAACAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.842559
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0158800.1 2 12340504 C T
Osa02LNT0158800.1 2 12340806 A C
Osa02LNT0158800.1 2 12340990 A G
Osa02LNT0158800.1 2 12342543 A G
Osa02LNT0158800.1 2 12343232 C T
Osa02LNT0158800.1 2 12343419 A G
Osa02LNT0158800.1 2 12345631 T G
Osa02LNT0158800.1 2 12344059 C T
Osa02LNT0158800.1 2 12343747 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0158800.1 osa-miR5817 Cleavage 4.0 15.667 1 24
Osa02LNT0158800.1 osa-miR5834 Translation 5.0 13.335 1 21
Osa02LNT0158800.1 osa-miR172a Cleavage 4.5 10.41 1 21
Osa02LNT0158800.1 osa-miR172b Cleavage 4.5 10.41 1 21
Osa02LNT0158800.1 osa-miR172c Cleavage 3.5 10.41 1 21
Osa02LNT0158800.1 osa-miR172d-3p Cleavage 4.5 10.41 1 21
Osa02LNT0158800.1 osa-miR417 Translation 4.5 23.645 1 21
Osa02LNT0158800.1 osa-miR417 Cleavage 4.0 17.824 1 21
Osa02LNT0158800.1 osa-miR1851 Cleavage 4.0 16.022 1 21
Osa02LNT0158800.1 osa-miR1875 Cleavage 3.5 19.368 1 24
Osa02LNT0158800.1 osa-miR2872 Translation 4.5 12.958 1 21
Osa02LNT0158800.1 osa-miR2873b Cleavage 4.5 14.998 1 21
Osa02LNT0158800.1 osa-miR2873b Translation 5.0 16.619 1 21
Osa02LNT0158800.1 osa-miR5151 Cleavage 4.5 9.511 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0158800.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0158800.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0158800.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0158800.1 2 tgw2 Morphological trait Seed RM290 RM550
Osa02LNT0158800.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
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