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

>Osa02LNT0169400.1

CACTTCGATTTTTTCTACTTTGGTACACGGCACCTGAGAAACAACTCCCCCCTACATCTAAATGCAAGCCACTCCGGTCTCTCCTTCCCTCTTCGCATCACCAAGTCACCAATGGTGACACCAAAAAATAGCCACATCTACCGAATACTCTGAACAAGTAACATTTCACCATTTCAGTTCAAGCTAGCACTTGTGTAGTTGCGTAGCCGTGTTGCCATCTCGTCAATCCAAACCACCAGAAATGAGTCGAGTCCATCAGCTAAGGTGAGTGAGACCATAATATGCCCTGTTTCCAACATTTCCAGATTGTCGCTGGAGCAAGATCTCTCCATCAATCATCAGCCTCGTTGAGCCTACGAGGGAGCATTCGCCTGTGCAAAGGTCACCATGCGAGCCTACCCTGTATGTTAAATATTTACGGGGCAGCGGGTTTCTTTCTTCGCTAGATTAGAGCACTCCAAACAGCAGAATCTCCTTCACCGCATCGAGCATGTACTTCCTTGATCCTCTCGACCGACTTGCATATGCCGCTGCAGCTCCAATCGAAAGACGCCACACAGACATTGCCAGCTTGTCCTTTCCACTCGCAATCTGGTGGAGTCCCGCAGCACATGTTTCTTTCATCGATATGATTCACTTCTAAACCAATAAACCATGAACCAAGTGATACATCTTCGTTCGCAAATTTGTGTAAGATAGGCTGGTTGATTGAAATGTAGGTCGCGAGGTCTTTTGAAATCGCGTATATCTGCCCAGTAGCATGACGGAAGTATTTGTTCCCTTCCTCCCCAAATTTCCAGTACTCAGGTTCATGGTACTTCACATTCTTGTCAGCGAGAACTGGGCCTGACTTCATGCATCCAATATACGTTCTTGGTTTTGATTTATGCCGAGCAAGGGTAGTGGCAAGCATTCCTAAGTTCACATGCACATCATCATCAACCTTCACATAAAAGTCAGCATCCCAAATACCAACTGCTGTAGAGAAGAAAATCTTTGTCTTAGCTGAGAGTTCATGATACCCTTCTACATGGTCTAGTCTAAGAAAGTCACGATGCTGAGCATCCTCTGAATCTATAGCTTTGTCCAATATACTGTTGGATGTAGCACTATGCCCTATAGTGAAGCGGATAACAATTCCCTTTTGATCTTCTAGTTGCTGCAGCTTTGCACCTTGAGGCATCCATGTCTCTCGCACTGAATCACGGCGCTTGCGGCTGCTGAATGCGGTGTTTACTCCAATTACAACAAATGCCTTCTTCCTTGGTTGGCTAGTTTCTGAGGTTACTGGTGAGCCACCAGCACGGAGAAGTTCCAGCGTGCTACGCTTAGCTGCAAGTTCCATCTGCAGCGTGGAGATGGACTTATCCAACAATTGTATGGCTTCGTGGGTCTTGGTTACCTCACCCATTATGTCCTTGTCTTCTCCATGCTTCCTCTTTGTATTGCAATCCTCTGATATGAGTTGCAACTCCCTATCCTGCCTCCGGCGTTGAGACATGATGTGGTTACTGGTATCAGGTGCCGTCCAAAAACGATCCGTGAAGAGCATGCCGAGGCCGAAGCAGAATGCGCAGAGCAGCAGCATCCTCCACCGCGCGGAGGACCGCCTGTCCACCGCGCCGCCCTTCCCCTTCATCATCATCGCCGCCAGCCGAGCTCCAGCGCCCCCCCCCCCCCCCCCCGGGATCTTGGCCGCCTCCAAATCGTCGGAACCAAAAAAAAAAAAAAACCCTGACCACCAACAAGACGAAGAACAAGAAGCTCCCCCCGTTGGCGCGGCAAGGCCCAAACCCGCGAGGAGATAGAGAAGAAGAACAGGGAGGGGTCAGAGATTGGCGGTGAGCCGACCGGAGAAGAGGAAGAGGAGAGATGAGGAGGAGGAGGAAGCAGCTGCTGGTTTTGCTTTGGTTTGCTTGGCTTCGCCGTCTCAAACAAACGAAACTATGGAGCGCGTGATGGCCTCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.939011
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0169400.1 2 21550825 G A
Osa02LNT0169400.1 2 21551540 C T
Osa02LNT0169400.1 2 21551595 A G
Osa02LNT0169400.1 2 21552169 C T
Osa02LNT0169400.1 2 21553902 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0169400.1 osa-miR166c-5p Translation 4.5 5.461 1 20
Osa02LNT0169400.1 osa-miR166l-5p Cleavage 3.5 15.539 1 21
Osa02LNT0169400.1 osa-miR171h Translation 4.5 24.503 1 21
Osa02LNT0169400.1 osa-miR529a Cleavage 4.5 17.478 1 20
Osa02LNT0169400.1 osa-miR530-3p Translation 3.5 19.456 1 21
Osa02LNT0169400.1 osa-miR2093-5p Cleavage 5.0 17.608 1 20
Osa02LNT0169400.1 osa-miR2094-5p Cleavage 5.0 18.875 1 21
Osa02LNT0169400.1 osa-miR2925 Cleavage 4.0 21.536 1 19
Osa02LNT0169400.1 osa-miR5150-3p Cleavage 4.5 16.184 1 24
Osa02LNT0169400.1 osa-miR2275d Cleavage 4.0 16.117 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0169400.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0169400.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0169400.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0169400.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0169400.1 2 qRTH-2 Morphological trait Root RM262 RM341
Osa02LNT0169400.1 2 qSTA-2 Morphological trait Root RM262 RM341
Osa02LNT0169400.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0169400.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
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