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

>Osa02LNT0166500.2

AACAGAACTATATGTAACATCAATATAACACCAGAACATGGTAGAGTTACTGACAAAAATGTTTTTTACCAGGTACGCACAAAGAGTCAACATGGGGTTCAAACCCTTAATTTCAAGACATGATCTTACACGCAGGTATGAAGAAGACGAATCCCAGATAGAAACCGCTAATCTGAGGAAACTCAGCACCATAACCAGAATATAGAAGAAAAAAAAACTACCACTCGCTTGATTTGAGCAGCAAGTTCGAAACTACGAACCTTTGACCTTTACACGAATCATACACAATTCAAATGTTTCTTCAGAGACAACAGTTTCCAATCTGCAGTGCCAAGCAATTCATGCCTCAATTCAATTGCCCTGCACCACATTGTCAACATGAGTAGCAACAAGACAAGTACGGACAATGCGCCACTGATATTAGACCTTGGCTACAAATTTCCAGCAGATCCATATTTCTTACTTGTAACATGTCCAGACTATCCATCTTTCCACCTTTTCACACATCAATGGCTTTAAAATTTGCATGATGATGTGGCCCAACAGCCAAAACCATACCAACAAGACCATTAGAATGTGCATCTTCTATCAACTAAGAATCACAAATAGACGGCACCATATATTAACTGATTGCTTGAATTTCTCTTGTTCTCATGTAGGTCATGAACTGCCCTGGTATTTCAGCAAGAAGTGACTGAACTGTCGAAATCCCACTGCCATGGGCATCCTTCATTGGGGCGAACTGTATCATATCCCTTGATGCCACTCTTCCTGTTGAGCTTTCTAGTCTCTCTCCTTTATTTGGATCTAGAAACTCCATTTCCTTGAAGTCCGCTCCACCAACTCCAACAACAAGAATGGACAAAGGAAAATCAGATGCCTTTATGATTGCATCGATAGTCTCTTGGAAATCAGTCACCACACCATCCGTGACTATTAACAGAACAAAGTATTTCTGCTGGTTGTTGGCAAGTGATTGGTTTGCTATTGCCGTAGCAGTGCTAACTACTGGACCAAATAGGGTGGGCCCAGCCAATGAGACATTACGAAGCGCACTGATATAAGCTGACATAATCCCTTGTATTCCCTCAACCTCAGGTTGATAGGTGCTACCATTCAGGTTGAAACAGTGGGAAACAGGACCATCAATAGGTCTAGCACCAAAGCCCCATGAGGGAAACCGCTTAGCTGGGTCATAGTACTGTAGTACATCTCCTACTTCCAGTATTGCTCTCTGATATGCATTTGGCCGACCAGTGGGATCAATATAATGCAAGGAATCTGGAAGCCGTGGATTTCCATTTGAAGCTGTGAAGTCTACGGCTACCATAAAATTCAATTGGCACCCAGCAGAAATATAATCTAGAAAAGTCTGTCTGTTGTTCTCAAGATATTTCTCCACATACACTTGACTCTTTAGTACCTCCTTACTGTGACTATCATGAGCAGTGCTGGCAGGAACAAAGAAATTTTCACCATCCTGACTATGATACATCTTTTCCAATTCTGCGACCGATTTTACTATCTTGCCTATTAGGTCATGTTTGCCGTTGCTACTGAAGTTGAAGCACTCTATGATTAAAGGGTTCTCCTTACTTCCAATCTGTTGGAGATTCAAGATCACTGGCTTCCACTTGGGATTGAGGTCGTTCTTCCTTACTTCCGTCTTACAAATTGGAACAGGCACTCCACTCTCTGATATTCTAGATATTAGTAAAAAGGGATCACTTTTTGAGAGAAGGTCCTTGATTTCAAGATCTGAACAGCGGAATACCATCTCCATTATTGCTTTTGAACCAGCACTTTCTTCTGCCTGAACATTTAGTTCACCAAATTTACTAGGATTTGGTAGGTTATGTTCGGAAACGCCAAGCTTTAGAGTCAACAGTCTGTTTTGTTTAGTGATAACCTCAGACAAAAGACAGACAGCCTCCCCAAGAAATTGTTGCTCTTCCAGTTTAAGCATCTTTTCATTGACATCATGAAACTGTGGATCAATGTCATATACCTGAAACACAATTGGTTGAAGAACCTCAAACTGGTAGTGCACGTTGATTCTTGCATTCCAAGATGGGTTCAAAGAATTCAATATTACTTCAGTACGCCCAAGTTCTTCAAGTGCTCCTTCTTTGCTTTTAGAATATACAATGACCATGGGATTGCTCTTGGTAAAGAATTCTTGGTCGCCCAAATTTGATGCAGAGAGAGATAACTGTTTCAACAGGTTATACAGAGTTCTTGTCAAAATAAAACACAATTAAACACACCCTCATCAGTTCGGTAATTGCATTTCTATCAGTAAATCCAAACAAGACATAAATTTATACAATGCACATGCATCATAATAGTCATCACATGAAGCAACATCACAGTATTAAATATTTGAAGTTTTTGGATTAACTACCAGGTCAGGTAGTATGAAATGACAGAAATACTTAGCCACACAACTTGCAGACTCCCAAGCGTTCAGGCACAAAATCTTACTAATAAACCACAAATACAGTAAATCATCTTTTACGCAACGTTATCAATTAGAAGAACATCAGCAGCCAACTGCTGCAGCCGTCAGAACATCAGAATGTTCAGTGCCGTGTCAAACCAAGAGCACACGGCATGCTCAGATTTCACGCCCGCTCCCAATCATCGTCGTGTAATGGTTTTTTATCCCGATCAACACGAAATCCCTCGGGTTTTTTCTCCTTTTTTTTTGTTTGTTTGTTTGCAAGGCTGAGAACAGGTAGCGGAGTAAATTAGCTGAGGCACAGACCACACGCATCCGCTAGTCCCGTCGCTGCAAGGCGCAAACCACGAGACTCACGCAGAACGGCGCGAAACTGGAGAACCGCCAGCGACGCACGCAACCGAAGCGCACCCGGCGCAATGGCACGGCCACCCACGCGCGCTCGCTCGCGAGCACCTGGCGGCGCGCTACTACTACTACTACTGCTATGGTGTGAAGCAGAATTAAACCGCATGGATGGGGCGTGAGGCGGTGTGTGCGTTGTGTGTGGGTTTTCCGCACCTCGACCTGCGTGGACGCGCCGGCGCCGCGGGAGCGGAGGAAGCGGTCGGCCGCGGCGGACGCGGCCTCCGCCGCCGCCGCAGCCGCGGCCGCCGCGGGGCCGACGGAGTGGCGGCCCGCGTGGCCGCCGCCGCCGCCCATCTCGTCGGAGCAGCAGTTCCCCATGGCTAGTGGCTCTCCTCGCCGTCGAGCAGGAGGGGGAGGAGGCGAGCGAGATCTACCGCCGACGCATCGATCTGGAGGTGGGAGGAAGAGGGAGAGCGAGAGCGAGAGGAGAGCAAGTGGAGTCGTGGAGACGACACGGAGACTTTGGACCCCTCAAACACTAGGCGAGGCCGAGAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.864822
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0166500.2 2 18996793 C T
Osa02LNT0166500.2 2 18995787 C A
Osa02LNT0166500.2 2 18997823 A C
Osa02LNT0166500.2 2 18999326 A G
Osa02LNT0166500.2 2 18999462 C T
Osa02LNT0166500.2 2 18996671 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
Osa02LNT0166500.2 osa-miR5534a Cleavage 4.5 10.733 1 21
Osa02LNT0166500.2 osa-miR5797 Cleavage 5.0 15.3 1 21
Osa02LNT0166500.2 osa-miR169f.2 Cleavage 4.0 13.391 1 21
Osa02LNT0166500.2 osa-miR171e-5p Translation 4.0 16.942 1 21
Osa02LNT0166500.2 osa-miR415 Cleavage 4.5 14.014 1 21
Osa02LNT0166500.2 osa-miR444b.1 Translation 5.0 13.622 1 21
Osa02LNT0166500.2 osa-miR444c.1 Translation 5.0 13.622 1 21
Osa02LNT0166500.2 osa-miR1428e-3p Translation 4.5 15.372 1 21
Osa02LNT0166500.2 osa-miR1865-5p Translation 4.5 21.273 1 24
Osa02LNT0166500.2 osa-miR2055 Translation 4.5 16.193 1 21
Osa02LNT0166500.2 osa-miR2093-5p Cleavage 5.0 15.848 1 20
Osa02LNT0166500.2 osa-miR2918 Cleavage 5.0 21.214 1 21
Osa02LNT0166500.2 osa-miR5154 Cleavage 5.0 19.336 1 24
Osa02LNT0166500.2 osa-miR5484 Translation 5.0 22.421 1 21
Osa02LNT0166500.2 osa-miR2918 Translation 4.0 17.537 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0166500.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0166500.2 2 nan Morphological trait Root RG171 RG157
Osa02LNT0166500.2 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0166500.2 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0166500.2 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