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

>Osa02LNT0166600.1

CTTTACAATTCCTTCGAAACTTTACAATTCCTTTGAAACGAATAAGCCCTAAGGTCTACTCCCTCCGTCCCAAAAAAAGGCAAACAGTAGGTTTCCGTGCCAATGTTTGATTGTCCGTCTTATATGAAAATTTTTTATAATTAGTATTTTTATTGTTGTTAAATGATAAAGCATGATTAATACTTTATGCGTGGCTTATCCTTTTAATTTTTTTCATAATTTTTTTTAAATAAGACAGACGGTCAAACGTTGGACACGGAAACTAGGGTTTGTCTTTTTTTGGACGGAGGGAGTAGGTTGTCCAGTGTCCACCCAAATAATCACATTGAAACAACAGCCACAGCCCACAGGCCATCCAATTATGCAATTAGAACATAGAACATGGTGCCATGGTGGTATGAAAAGTCACTGGAAATAAAAGCCATTCACATCTTCTGGCTGCTGCACAAGTAGTTAGCTTCGAGTTTGAGAATGAAAGGGACACTGGGGTAAAAGGGAGTGGAGGAAGGATGCAGAATCTGTAAAATGAATGAACACGTACAGCACCTTTCTACGACAGAATCCAGTAGACTTGTAGCCAACCCTTGCATAGAATCATATTATTGAATCTCCATCACGCAACGTGGTAATCTATAAGATGTCAAAAATGCTCTTACTCTTATTATTACAGTATCAAGTGTCTTGTGATGTGTGCTTGAAATCTCCAAGCGCAGGAAGGAGCAAAGCAAAATCACAAAATAGATGCAAGCTGATACTTGCTTGAACCTCATTTCAACCAAAAACAATCACGCGCACATGCAAAGTAGAAAAGAAGTCAATTCTCAATCCCTTCTTGAACAAACAAATACTACATAGTGGAAAGTGGAAACTTTATAATGGTGCACACGCACACTTGCTTGATTGTTGATGCTACACACCAACCAGATGATATTATGCTTCAGCAATCAACAAATTCTACAGTTGGTGAAAAATGATATGCAATCCAAATACAAATAATAGGCTCCCAAAAGGATATCCTATGGGGGAAACATTTTGTCACTAAGTGACTTCACACACATCTCAGTTGTTTTCCAACTTGTCCAATGGAAGATGTGCAACTATCATATTCACAAAAGAAAGAATACAACTAAGTAGAAACACACCACTAGAAGAGAACTAAAACAAAGCCAAAGATGATACTTAATAAAGATGCACCCATAAGCACCAAGGCCTTATTGTTGTGGCACTATTCACAGAAGACACAAGGTTTCATTTTATTTTATGTTTTGAAGGATAACTCAGGGCATCTATTCATTTGCTGCAGCTACAACTGTTACAGAAAGCCAGAAAAAGGCCGATTCTATTTGACCACATGGCATCAATAACTGTTACAAGCTACAGTAGATTATCAAACCACCCACACCAGCAAACCATAGTACCGGACCCTAAAAGGCTAAAACTCTACCTAATAAAACGACAAACAATGAGGCCATAGGATATGAATTGAAGTGAACCAATGGAAGACATAACAATGCAACTACTGGTCTCTGAAGATTGCACATACTAAATTGAAAGTACCAATATGTTCACCACATGACAAGGATCTTCTTAAAAGTGTGCCATCCAGGGTGATAGCGAGAACACTTGGCTTTGATAGCATGTCAAGTTTCATGCATTTAGTTCTACTTCAACAGCACAACATGAGAAACACCGTAGATCTCATTATCCATGCTGGCCTTCTTTGTTCTTGTCGATGTCCCCTTACTAACAGGGTTGGAACAAAGAAATCAGACCCTGAGGATCTGCAGTTTAGTGGAGAATGCAATAGCGACCCAGTCAGGCTGGGTCGCTGACCATTGGAGCTGCTCAATCTCTGCCCCAGCAGTGTACGCCAATATGGGATCAAGACCGCCCTCAGCTGCCGCAGCAGCTGCAGCATTGCCATTTCCATTGCCACCATTGTTGCTCCCAGTGCCCATGGATGACAGGTCCCATATAAGGGCCTGCGAGTCATCCCCAGCTGTGCAAATGTGACAAGAGGAGTGTGGCGCCCATGCTATGGCGTTGACGGGCGAATGGTGGCGGTGGAGCTCGACCACCGGTAGTGTTGGGTAGCGGATATCAAGCACGACCACCTTGGGGCTATCCATGATGATGGTTGCCATGTACCTAGGGTCCTGCTTGTTCCACCCTAACCTAACCAGCGGTGTTGGCGAGGCAGCGCCGCCATCTGCACCTGCCGAATTGGAGCTGCCGCCAGAACCGGACTCGTAGATAATTGTGGAATGCTCCTTGTCCCGGAGATCAAACACGCGAACGGAGCCGTCGGCGGAGACGGATGCAAAGACGCCGGCACCGCCCCAGGCGATGTCGTAGACCTCCTTGTCATGGGCAATGAGCTGGGTGTCGACGGCCTCCCGCTCGACGTCCCAGATGGTGCAGGTGGTGTCGATGGAGGAGGTCCCGATGCGGCGGGGGTCGGCGTCGTTCCAGTCGAAGGAGGTGAGCGGGCCGCAGTAGTCGCTGTTGCGGTTGCCGTTGAGCTCGCAGCGCAGCTCGACGTCGGGCGAGGCGGTGCCGTTGCAGCGGACGGAGCCGGAGTTGGAGCTGGCGGCGGCGGCGGCGGCGGCCTCGTCCGGGGAGGGGATGCGCCAGATGCGGAGGTGGTCGGCGGAGGTGGCGAGGAGGTCGGGGCGGACGGAGTGCGGGTCCGGGACGAACATGGTCTTGGTGGGAGGGTAGGGGTGGTCGAAGGTGAGGACGGGGGCGATGTCGCCGGAGGACTCGTCGAGCTGGACCACCTGGACGTGGTTGTTGTGCTGCTCGAGCAGGCTGGCGATGGCGAGCCGGTACTTCTTGTCGCGCCGCACGCTCCAGTTCATGCCGTAGATGTGCCACCCGGCCTCGTACGTGTAGATCTCCGACCGCTTCGCCTCCCCGCCGCCGCCGCCGCGGCCCCCGCCGTTCCCCTGCTCCTGATCCGCCCACGCCTCGCCGTCCCCACCCGCGCCGCCTCCTCCCATGGCGCCGCCGCCGCCGAAGCCGAGTTGTTGGGGGGAGGGGATTGGGTGGGGGATGCGGATTTTTGGGGGGGGGGGGGGGGGGGGGTTCTACTTTCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.0240898
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0166600.1 2 19179027 C T
Osa02LNT0166600.1 2 19176937 T C
Osa02LNT0166600.1 2 19176659 T G
Osa02LNT0166600.1 2 19176802 A G
Osa02LNT0166600.1 2 19178445 G A
Osa02LNT0166600.1 2 19178883 A G
Osa02LNT0166600.1 2 19179446 A C
Osa02LNT0166600.1 2 19178412 A T
Osa02LNT0166600.1 2 19176732 C T
Osa02LNT0166600.1 2 19177144 C A
Osa02LNT0166600.1 2 19176600 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
Osa02LNT0166600.1 osa-miR812p Cleavage 4.0 11.768 1 24
Osa02LNT0166600.1 osa-miR812s Cleavage 0.5 11.793 1 24
Osa02LNT0166600.1 osa-miR5799 Cleavage 2.5 11.793 1 24
Osa02LNT0166600.1 osa-miR5819 Cleavage 3.0 16.236 1 21
Osa02LNT0166600.1 osa-miR5825 Translation 4.5 11.307 1 24
Osa02LNT0166600.1 osa-miR171i-5p Translation 4.5 12.979 1 21
Osa02LNT0166600.1 osa-miR812a Cleavage 2.0 11.768 1 22
Osa02LNT0166600.1 osa-miR812b Cleavage 2.0 11.768 1 22
Osa02LNT0166600.1 osa-miR812c Cleavage 2.0 11.768 1 22
Osa02LNT0166600.1 osa-miR812d Cleavage 2.0 11.768 1 22
Osa02LNT0166600.1 osa-miR812e Cleavage 2.0 11.768 1 22
Osa02LNT0166600.1 osa-miR1439 Cleavage 2.5 10.837 1 21
Osa02LNT0166600.1 osa-miR812g Cleavage 4.0 11.793 1 24
Osa02LNT0166600.1 osa-miR812h Cleavage 4.0 11.793 1 24
Osa02LNT0166600.1 osa-miR812i Cleavage 4.0 11.793 1 24
Osa02LNT0166600.1 osa-miR812j Cleavage 4.0 11.793 1 24
Osa02LNT0166600.1 osa-miR2094-5p Translation 4.0 15.855 1 21
Osa02LNT0166600.1 osa-miR2866 Cleavage 4.5 18.585 1 20
Osa02LNT0166600.1 osa-miR2874 Cleavage 4.5 14.244 1 24
Osa02LNT0166600.1 osa-miR812o-5p Cleavage 1.0 13.911 1 21
Osa02LNT0166600.1 osa-miR5489 Cleavage 4.5 20.473 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0166600.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0166600.1 2 nan Morphological trait Root RG171 RG157
Osa02LNT0166600.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0166600.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0166600.1 2 2-3SY Physiological trait Source activity RG171 RG157
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