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

>Osa02LNT0168100.1

GGATCTTGAAAAACTGTGCCAACATATTTTTTACTGATCAGTAATCCATTCTGGAATTTGAACATAATTAATCCTTGCAAGAAAAATATGTCAAATATAGTTGTTGTCGATGAAACAGTGTACAGGAGGTGTATTGAATTATATACTGCTAAGTCAAACAGAATCGTGAACGTGATGCCCCAAAAGATGGCTGGAAATCAAAACAATGAGAAGGAAAAGGAAAAAAAAACTTGTTACAAAAATGGAAAATAAAACTCATTACAATATAGGGGAGGGTCAAATTCCCAGCAAAAAATGCGACCAATATATCTTCATATGAAACAAGGTGCTGACTGTCTGATGAAAAATGATAACCTATGAGGCAGCTCAGTGTCCGTGTAAAGTGGTTGTTTTGCTTCAATGGCGCGACTGATAAAAACGAGGTCTGTTGGTGAACACCCGACCATTGGCTCTGACAAAATGTGTGATGCCAATGCAAAGACCAGCCCATAGAAGTGACAACACTAAATGGCGAACATCATTCCTGGCTTGTCTTAGTGACATCATCATGAACATAAGAGCTCCCATAACCAATGCAAAAGCAAGGCGGAAGGACGCATAATTCTCTAGAAGTCCTGCTTTGCTTGGACCTGCCATGTCGCGGCTAACAGATATAATGTAATGTCCTTGAAGTAGATCCATGGCATCCTGTTTAGTGCCATCTGCAAAGTTATTCAAGTAGTATCTAGCAAGTGAATTCCACAGATCATTCAGAATTCCCTGGGTACTTCTCTTCCCATACCGAACAAAATCGCCCTTCAATGCCGGAGTTCCAGAGTACTGAGTGCTTATTGAATCTCCATGGTTGGCCCATAAAACTTTGTATTTTGCATCAAAAGCTGGATGGTTGCTTATCGTATCATTAACACCGAGAACCCCTATTCGCTGAAGTTGGTTTTCTAGTATCTTTCCTCCAATCATGCTCTGAGTTACATTGGTGCGATCTAAGCAATCGACACAATTTGTCCTGATAGTGCCAGTCTGCTCCTCAATTTTTTCACCTTTACCATTCAAAAGGAAATACCTAACCCATAACATTATTAGCAAGATCAAGAAGGAGAAAATATATCCACCATGTTCCATAGTAATGAAAATGCTCTGTCCAAAGGCATAAGAGAGTTGGGATAGTACAGAGATGTACTGAAAATCTCAGACCTGGAACTTTTTCCCCTTTCTTTCTGTTAATAGAGCAAAAGAGAGGAGGGGAGCGGATGCTAAAACACCTAAACAAGGACTTAAAAACAGTATGACTAACACAAGTGACTATTGCTCTTCCCTTTGCCTACTATGCCAGAGAATTCAGTGCACGAAAATAATCTACATACTGCTGGAGTATTTGTGTTTTTAATGTATAGGTATTACTGCACAGTGATTGAGTAATCAACCAATATTCAGATGACTGAAACTCAGAAGTAGTAACAGAACCAATTGTTTGCTAAATAAAGTAACATGATGCAAGTGTCTGCTTTAGAAGTTTCATATGCCAAACCAAGAGTCAAGAACTAGTGCACCAAAAATTGACTCTGCATTCATTTGAAAGCATGTGTAGTCACGTGGTAAATAGCCTAATGATTTTGGGGGGTTGCTTAGCGAATGAAACCCAATAACAGAAAAAAAAAAGACAGCAAACAAATGCAGGGAAAAAGCAATGGATTAAGTAACACCAAAATACATGTCATGGGCACTGAGGCCAGAAAATGATAAACAGATCAAATGGAGCACTCTATAATGTATCTGCCAAAAATATACCTATGTTTCTTGAGATAATCTTCAATTTGATTGTAGAGCTGAGAAAGGCGCTCAAAGTGAATATGACCACAGATTCGATGGAAGTCAAAATGCACATATCTTATGTCTTCACTGAGAATAGGTTCAATAGATTTTGCATATCTGTCATGGAGGCGACCTTCACCACCGTGTGTATTGACAAGATCAACAGCCAATACAGCTCCATATTTCTTCTGTAAATCATGAAAGTGCTGCTCAAGTATGCGTGGCGCCTCCTCTTGTCTAACAATGTCAAAGCTAGGTTTATATGTCAAATCAACAATCTGCACCCACAAGAATGGTATGGACCCTCGAACTTGTACATAGGATGCTGTGAACCCTTTTGATTCCATTATCTGCTCTGATTCAACAAAGTTGGCAGCATAACCCTCTGGGTCAGCTCCACGTCTCCACATTCGTGTACCTATCCTCCGTGTGCACCTACGTGCAATCAGGGTCACATTTACCTTCTCCGATCCAACTTCTGCATGGATATTCTGAAAGCTGCCTTGAATGACTGGCAACAAGTACTGGTCCAGCTTGTTCTCAATTAGAGGTTCCAGCAAGTAACTGTTCCATAGAAATCTTGGTTCTGCCTGTCTCCAAAGCGGAAGTGATTTGAACTCATCACCAAGATTATGTAGCCTCTGCAAAGTAAGTGTTAAGTTGATATCATATGAGAAGTACAGGCCTATAGTCTTCTCTGCAGCATGCAGGAGTTCTGAAAATTCTGTTTCCATTTTACTCTGATTGCCAGAAGTGCTACGTGAGTTACTGCAGGGGAGAACTTTTAGTCCTGTCACTTTAAAAATTGCATGTCCCAAGTAGGATCCCACACAATCACGGCCTGTTATCACTAAAAAATATGATCCAACTGAAAGCTTGAGAACTCCTATCACACCATACACTGTTTGACATTTTGGTTTTGTAGAAGAGTCACGTGGTGGCAACTCTTCAACTAGATTCATTGAACCATCAGAACGGTTAGCTGACAGATACAAGTCAGCAAGACCATCAATCGGCTCAAATACATAGCGGTCTGGGAACTCCCATAGTCTCAGTCTTGTGTGAAGTTTAGAGGATGGACTTGAGTCATTTGCCCCACCCATGGAGGAATGCCCTTGGGAGTCGGAAACGAGGCGGCGAGCAGCTGCGGCGGCGGCAGCCGATCGGGGCGGGGAAGAGGCGCGGCGGTGGAACGGCGGGAGGAGGAGGAGGAGGCGGCGCCGGCGCCGGCGGGTGCGAGGCGGAGGCGATCTCTCGTCGATGGGGCGAGTGCGCAGCACGACGAGACGACTAGTAGTTGTTCGCTTTGTTCGGCGGCC

Coding Potentia
Explanation CPC Score
noncoding -1.08686
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0168100.1 2 20931673 T A
Osa02LNT0168100.1 2 20921451 G A
Osa02LNT0168100.1 2 20921854 C A
Osa02LNT0168100.1 2 20921920 A G
Osa02LNT0168100.1 2 20923622 G A
Osa02LNT0168100.1 2 20923739 G A
Osa02LNT0168100.1 2 20925069 G A
Osa02LNT0168100.1 2 20925135 C G
Osa02LNT0168100.1 2 20925574 A T
Osa02LNT0168100.1 2 20926127 C A
Osa02LNT0168100.1 2 20926160 A G
Osa02LNT0168100.1 2 20926289 T C
Osa02LNT0168100.1 2 20926495 A C
Osa02LNT0168100.1 2 20926703 C T
Osa02LNT0168100.1 2 20928188 T A
Osa02LNT0168100.1 2 20928749 A G
Osa02LNT0168100.1 2 20929588 A G
Osa02LNT0168100.1 2 20929970 T C
Osa02LNT0168100.1 2 20930563 A T
Osa02LNT0168100.1 2 20930061 A G
Osa02LNT0168100.1 2 20930117 T C
Osa02LNT0168100.1 2 20931913 A G
Osa02LNT0168100.1 2 20922900 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
Osa02LNT0168100.1 osa-miR5540 Translation 5.0 15.004 1 21
Osa02LNT0168100.1 osa-miR5807 Cleavage 4.0 21.785 1 24
Osa02LNT0168100.1 osa-miR531c Translation 4.5 23.571 1 24
Osa02LNT0168100.1 osa-miR156b-3p Translation 4.5 20.811 1 21
Osa02LNT0168100.1 osa-miR408-3p Cleavage 4.5 23.52 1 21
Osa02LNT0168100.1 osa-miR172d-5p Translation 4.0 12.794 1 20
Osa02LNT0168100.1 osa-miR531a Translation 4.5 23.571 1 24
Osa02LNT0168100.1 osa-miR395w Cleavage 4.5 14.1 1 22
Osa02LNT0168100.1 osa-miR531b Translation 4.5 23.571 1 20
Osa02LNT0168100.1 osa-miR1850.3 Translation 4.0 21.101 1 22
Osa02LNT0168100.1 osa-miR1850.3 Translation 5.0 16.31 1 22
Osa02LNT0168100.1 osa-miR5160 Translation 5.0 18.74 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0168100.1 2 qRTH-2 Morphological trait Root RM262 RM341
Osa02LNT0168100.1 2 qSTA-2 Morphological trait Root RM262 RM341
Osa02LNT0168100.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0168100.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0168100.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0168100.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0168100.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0168100.1 2 qSS-2 Physiological trait Sterility RM301 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