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

>Osa02LNT0176500.1

GGCAAAATTGAAGCGACCCAGGCTTCTGCATTCCGTAATCTGGGCGCTGTGTTTTCCATTTTCTACAGAAAAAATAGCAACAGAGTATCGAACAGGAACTTCTGTACAGCATACAAGTACAACACGCCGGGGCCTTTTGCAATCGTCCCTTCGGGAGAAAAAAGAGAAGGGAATAGCTACACCTCCGGTCCTGACGCAAAGAGGTTGACAAGGCCTCGGAAAGCTTGAACAGATACCTCACAGGCCTGAAGAAGTTCTCCGTCCAAGTTCCAGACACTTTCGTCATGTGACGATATAAAAGTAAATGCTTGTGTCTTATGATGTTCGACAAACTTGAAGCTCAGAGGATCTGAGCCCTTCTTGGTAAATTGTGTTAGATGCCATAAGTAAAAGGGAAGAGGGCAATCTCTAATGAGCAGAAGATGAAGAAAACCATCAGATAGGTGTGCGTCAGCTACTAGACCATCAGGGGCTCTTTCGTTACGACATGAAATGACAGCTGCACCAACACTGAGAAAACGACCCTTGGACCAGACCCATTTTGGGGTCTCACAAGCTGTTCTGGAACTGTCTGGATTTTCATCTTCTGAATTCTGTTCAGATGTTGAAGTTCCTTTGCATATTAAACAATTTGTTCGGCAGATGGTTTTCCGATGTCTATTTTGATGGTATTGCAGTGTTTGGACTCCATTTGCATTATTCTCTGCCGATGCTGTAAGTGAATGAGTGTTTCCATTTTCAAGAAAAGCCACTTTTGCCTCATAAGATCTGTGCTTCAAAAATACCATTGTTCCAGAGAAGTCATATCGCGCAGGACCCATCCACCTGTACTTTTCACTCTCCCTTATAACTTCTCCATAAAATCCATATCCTGCAAACGAAGCAGCATAGCGCACAGTTGGTGAAACCTCAGCTGATGGGCTACTTTTCCATCTGACAACTTGAGCTATATCAAGTGATATCCTTCTGCCGAGGATAATAAGCAGAGCAGAAGTCACAGGATCTCGCTCCCCAGTTGTACTGAGAACAATAGCATCCGTTGAGCCAGAAGGAATTATTCCAAGCCTAAACCAATTATTTGGGAAGGAGACTAAAGGCACCTGATCTCCATTGCATGGTTCATCACTAGAATCTGATGACGAGATGTCCAATCCTGTAGATCGTGTGGTTGAAAGAAGGGGCTCATGATCATCAGGTGTGTTAGAACTTCCAGAGATGGCATTTGCATCATCTCCTGTGAGCTCACTATTGCTTAGATCATTATTTCTATGTTCTTGACACTTCATGTTGTTTCTGAAATATCCAAACCCTTCTGGAGTTGGAGGATAAGAATTTGTGTGCCTTGTACTTAGTAGCCCATTCAAAATTTCATTAAATAAACCATCACCACCCACTGCAATAACACCATCAAATTTCTTGAGATCTTTATCTGATAAAGATGCTAAAGTATCATATGCATGTCCTGCTCGCTGTGTGACTATCACCTTCGTTTTTACTTTTGCCCGCTCAAATAATGGAGCTACTGTTTCCCAATTCTTACACCCTCTACCTTTTCCACACAATGGATGGACAAATACCATGAGGCTCTTGGGCCTATCCTGTTCCTTATTTATGCACGTCTTTATATGCTCCACCCAAGTTTTGCAGGTTTGCTGGTCTTTATGACCAAAAATATATTCACAAGGTACCCATGGAGATGGTCTTTTTCTTGGTCTTGTGACCGTGTGTATGACAAATCGGTTCATCTCAGTATTTATCTTGCCTTGAACGGTAGCTCTTGCATTCCAAGGTTCACATACAGGACCCACCTCAAGAAGCTCTACAGCATAGACATCTGAAAACTTAAGCTTGCTCTCTAACTTAGGTTGCATTATGATAGATGACCAACATGAAGAACTCACTTCCTTCCGTTTCTTCGATTCAAGAACCCGAAGACCGGAAGCTACGAATTTCCTGACTCCATCCTGGTGAAGGGGCTGGAAGGAGAGGCCGTCGTCGCCGACGGCCACCGTGACCTCCCCGACGCCGTCCAGGAAGAGCGCCTCGCCGCCGCCTTCCATGGCCTTTCCCGCTTGCTGTTGCTTGGTCTCACGACTCCTCCCCGGTCACCCGCGGTGGGGGAAGAGGAGGGGCAAATGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.980943
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0176500.1 2 26506011 C A
Osa02LNT0176500.1 2 26506172 A G
Osa02LNT0176500.1 2 26506545 C T
Osa02LNT0176500.1 2 26507772 C T
Osa02LNT0176500.1 2 26507964 T A
Osa02LNT0176500.1 2 26508376 T G
Osa02LNT0176500.1 2 26505189 A G
Osa02LNT0176500.1 2 26508503 T C
Osa02LNT0176500.1 2 26508664 C T
Osa02LNT0176500.1 2 26509651 T C
Osa02LNT0176500.1 2 26510059 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
Osa02LNT0176500.1 osa-miR5814 Translation 5.0 22.235 1 24
Osa02LNT0176500.1 osa-miR1437b-5p Cleavage 4.0 20.398 1 21
Osa02LNT0176500.1 osa-miR7693-3p Translation 5.0 15.694 1 22
Osa02LNT0176500.1 osa-miR172d-5p Cleavage 4.5 19.136 1 20
Osa02LNT0176500.1 osa-miR1857-5p Cleavage 4.0 8.981 1 21
Osa02LNT0176500.1 osa-miR1857-5p Translation 4.5 12.358 1 21
Osa02LNT0176500.1 osa-miR1846a-5p Cleavage 5.0 20.747 1 21
Osa02LNT0176500.1 osa-miR1846b-5p Cleavage 5.0 20.747 1 21
Osa02LNT0176500.1 osa-miR1860-5p Translation 5.0 14.901 1 21
Osa02LNT0176500.1 osa-miR1846c-5p Cleavage 5.0 20.747 1 21
Osa02LNT0176500.1 osa-miR2869 Cleavage 5.0 17.506 1 21
Osa02LNT0176500.1 osa-miR5155 Cleavage 4.5 17.746 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0176500.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0176500.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0176500.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0176500.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0176500.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0176500.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0176500.1 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0176500.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0176500.1 2 T2-2tiller Morphological trait Culm/leaf C424 C747
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