\
RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa05LNT0290200.1

TAGGATAACATGCAAAACTATATTAACAGGAGTGACAAGTTAGTGTAGCCAGTACAATTAACCTGAATAAATGCATTCTCATGATACATATGTACACAATTTTAGGCCATTAAGAGAACTCACGGTTGCCACACACTTCAGCATTTACCAGAGTATCCCATCTATTATTCCAAAGGTACAGTTGTCTGAAATTTTGGAATATTAAGGTTCACATGGCAGTTTTCGAAGCACGTCAGCATCTCGGATTTGATACAGCGGCAGAATTTCGCCGCTTAACCCTAGGGCCTTGATAGAAATCTATGGAATCGCTGTACTTTTACAGCATAAGCTTTCACAAAATCCGCCTTTTCAGGTATGGTTCCACTAGATGAAACTCTCCTCTTTCTTATATGAAATAAGAAATCTTCAGTATCAAGGACATAGGAAACCTTTGAGGATTTGCAGGATATCTTGCATTCAAGACCATTAGTAACCATGAAAGCATCAATGGCCTTCAAAGAAGCTTGAGAGTCATCGTTTCCCCCACGCTTCCGTTTATTCCTCCCAAGGAAGATATCGTCATACAATTTAGTATTAGAAATACTTGACAGATACTCATTATATAGATAAGACGAAAAATTTGGATCAATTGACACTGCAGTTACTTCAGGTTTTTCATGCCCATACTCCATTAGCTGAATTGATAATCTTGTAGGATTTGAACGCCGTTCAAATCGATATATGCTCTCATCATGGAGAAGTACACGCGCATTTTCATGATAAACTAGATCAAAGAATCTCCCAGGTGACCTGGATTTTTCGTATATGTAAAGTTGGAGCAGCTTGTTATCCATTTCGTCAGAAGCTATCGCTTGAAGCTGCTTTACAACTTTGTATATCAGCTTATCTAGAGTAAAAAGAACATATGACTGAGTCCCGATGATTGAACGGCAGTCATCTTCAAATTTGGTGTTGTCAGAAGAACCATCAAGCAAGTTATACAGTGCACTCATAAACTTTGAATATTGGTCTGGCAAGTTCGTATCCTTAGAAGCTTTCCATTTCTTTTCAGCTGAGGAGGAGTTAGTCTTAGCTGACAGTATTCTTTCATATAGGATCTGGTGTAGCCTGAACAAAACATAAAACGAGTCATTTCCATAAAATATACAAGAGAACTTCTCTTCATGATCATTTAAAGCTCTAGGAACATGCTTAGCAAGCGGTTTAACTGCATTGTGTGAGCGTTCTGAGAATGGAAGTGATATTCCTGCATCGGCATCTTGTGCCTCAGTGTTTTCCGCTGCCTCACCCTCACTTTCAGCCTTTGCATCAGGATCATCCTGATCCATATCATCTTCATCCTCATGATCTTCTCGAGAACACTCTTCACCATCACCAGATTCACTACCAGAGGCATCTTCACCAGCTTCAGATGCATTTTCACTGTCCTCCATCATCTGGGCACTTTCCTCACCTTCATCATCTGCATCAACATCATTCTCTCCAGCAAACTCGGTTGCATCCATAGGTCTACCCTGGAGGAGTCTCCTAGTAGAATCTTCCTTCGCTTTAGAAACTCCATCTACAGATACACCATCAAAAGGCCCAAAATTCTCCCCAACATCCCCATTAGGAGATAATTCCCCCTCTTCTCTTTCAACCTTTGAATGATTATGGGATCCACAATATTCATTAATTGGACAGTGTTTGTTGTCCTTGCTGTTGAAAGACCCTGGAATCCTAATTTCTCCACTCCCCATAATTGCTTCATTGCCACCCTTAGCTTCAGACACAACCTCACCTCCAGCTGGAGTAGCACTGCAAGCGTTTATACCTGGTTTAACCTCCATATTTGCTCTACTATGATTCTGTTCAGGCCGAGAAAGGTGACTGCTCTCCACTGATCTTTCAGTGGAAATGTTTTGTGCATATACCGCTGGAACCACATCAACAGCAGGAGTGGTATTTTGCAGCCTTCTATCTAACATAGTTTTAGGTCTTTCCTCATCCCTGCAAACAGTTCGTTCAGCATCCTGCAAGCTATTTTGCGCATCTGCTGCAACTCCACCCACCAATATAGCACGAGAACATGAAGCTTGTTCCTTTGGAACAATTTCATCACTATGAGCATGCTTAACAGTAACTGTGCCGTTTGTTGATGCATTATTAATTTCAACATTTGCAGGACCAGCCTTTGTGCTTCTGCTATTGTGTTTTTCATCTTCAACACCATGGCCTCGAGGATGAACACCCAAAATAGGCTCCAGAAATGTAGCCCAGATTTTCATCACTTTGTCAACTTGATCCGAAGAACTGCAGACTTCTCCACAAGAGTACTTGATGATCTGATAAAGATCTTCATGAATTTCTGGGTCTACATACTCAAATGACATATTGGGAACTATTGGCCGCCTATTCCCAGAAGCAATAGTAAGAAGCATATCATCCTCCTTCCTTTTCTTCTCATTAACTTCTTTGATTGCAGCTAATAGAGCTTTTGTACTCAGATTCTTTGTGTCCTGTTGTTTGAAATAGAAGCTGCGATGATCAAGGGACTTGTGATAATTCTTAGCGTATATTTCAGCCCAAACTTTATTAAAATCTGACCGGCACCTTGACCATTCCTCTTGCTTTTGCTTAAGCCTAGTTAAAATAACTGGAAGTGCAACACTAGCGTTTTTGCGAAGAACATCCATGACATCAAGCCCATGGTCACCATATAACCGTTCAATACACCTCAGATTCAATGGAGTCAAATGCTCGTCTATGCGTATAGGGCTGTCTGGTTTGATTGAGTTGTCCTGCATCTTTTCTATCAGCTCCTCAACACGCTTAATTGCCACAATAACAGATTCCAACAGCATGTCCAACTCAAATCTGTCATCTTCACATCTAAACAAGCTTTCTTCATACTGATTCTTCCGCATGTGCTTAAACGAATAATCCTCACTTCCTGAGGTCACAGACACCCAGAGATCATTGAGAACTGAGGCTCCAAGGTCAGTTCTGCAACTTGCAGGAGGCATTGGGTAATTTTTAGGCAGAAGTCGGTAACTTGGAGTACACCGCTGACAATTTGAGAGGTCAAGTTCTGATATTGGCTTGCATAGGTTATACTTGTCTTTGCTAGAGAATGTAGTAGCTTTGTGGGTAGCGCCTTCCTTAGAATTGAGTGCAGATCCTTTTTCTACTATTTTAACTATTTGTGATGTTTTCCTTTTACTGAAGACTCCCTCCAGAAAGGCATCTATATTTTCGCACTGTTCCAGGAAGTCATTAAATCCATTCATAAGATCTGGATAGTGCTGCAGTATGTCGTTGACCAAGTTTTTCAATTCACTCCTTGTAATTATTTCCTGGCTGTATATGTGAAGGCATTTCAAAAACTCCTGGTAAGCTTCAGGCTCTAGCTTCTCCTTTACTTTCTCACAAAAACGGAACTCCTTTGTGTATGCACTCTTCAATGCATCCTTATCGTCGTATGGTGAAGTAGAGGTGCTAACCCCACCTTGTTGTGTGTCAGCAAGAGCACCATCCATCTTCCTTGCTAGTTTGCGCTTACGTTGTCCTCCATCCAAATCTTTGCTGTCATATTCAACGTCTTTCACGTCCGTTTCATAATCTTTTCTACTGCGATCAACCTTACCATCCCTTCCCTTGTCAACACGCCTTCTGTGGGGATCATCCTCAGGATCAGGGCGATCAATACTGAAGTCACGATCGACAGTTGATGGATAAGCCCTCTCCCTCTTAATGATCTGCGCGTTCCTTGCCGAGGGCATTAGTGGGCCCCTGTCGTCGTGTCTGCTTGAAACACCTCTAGGAACAGTTACCGGTTCTGGAGCGGTTGACGTATCAGGCAAGAAATGCTTGAACTCCTCGAGTAAATCGGGATAGTCACGGAAGAGCGCTGCAACCTCCCCGTAAACATCTTGGATGGACTTGTTATGCAAGCGGTACATGTTGAGGATGCCTAAGAAGGACTTGTAGACGTGGTCCTCCTGCTGGAAGCGAGCCTTGATCTTGTTGACGAAATTGATGGCCTCCATGAAGTCAACAGGCTTCTTCTCCAGGTCCTGGAGCTTGATGGCAAATCCCTTGGGCAAGAAGGCGTTGAAGCCAAGGATGAGCTCGTGGTGGCCATTGAAGAGGGTCTTGACACGGATGATGACGCCAGCGGTGTCGATCCTGCCGCTCTTGAAATCGCGCATGACCTCGAGGAACTCATCGTACTTGTCGCGCTTGTCCTGGAACTTATCCTTGACGGCCTTGAGGTAGAGAAGCGCGTCATTGGTGGTGAGCTTCTGGTTCTGGGAGGGCCCCTGCCCCTGCTGCGAGGGGGCGGGCGCGGGCGCGGGCGCCGGCATGGGCGACGGATCGGATCGGGCGAGGTTAGGACGCTTGAGGTGCTGAGACGCCGTGGGCGCTGCCTTCATCACCCACCCATCCACCGACCAAGGCAGACGGATTCCCTTATGGCCACGGCCGCCTGGATCTGCCCGACCGCAAACCCTAACTTCTATCCTCCTCCTAACTACTCCTATACGAGTATCCTGGCTAGAGTAGAGGATCGATCGCCTTTCTCCCTTCCTTCCTTCCTTGCTTGTTAGGGAGGAAGGCCAACTAGTAGTATATTGAAGAAGAAGAAGAGCCCTCGAGAGACGAACAGAAGAAGAAGAAGAAACAGGGGAAATGGAGTGAAATGATGAAACCTCTTCCTTCGATCGCCTCGCCTGCCCTGCCTGCCTTCCCCTTTTTTGTGTTTTTGTTGATCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.338504
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0290200.1 5 39314 G A
Osa05LNT0290200.1 5 40635 T C
Osa05LNT0290200.1 5 41109 G A
Osa05LNT0290200.1 5 40120 G A
Osa05LNT0290200.1 5 41995 T C
Osa05LNT0290200.1 5 42111 G A
Osa05LNT0290200.1 5 44370 T C
Osa05LNT0290200.1 5 44423 A C
Osa05LNT0290200.1 5 45070 A G
Osa05LNT0290200.1 5 45133 T C
Osa05LNT0290200.1 5 45884 A T
Osa05LNT0290200.1 5 46089 A G
Osa05LNT0290200.1 5 46203 A G
Osa05LNT0290200.1 5 44972 T C
Osa05LNT0290200.1 5 41821 T C
Osa05LNT0290200.1 5 44262 G T
Osa05LNT0290200.1 5 44806 G 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
Osa05LNT0290200.1 osa-miR5802 Translation 5.0 12.966 1 24
Osa05LNT0290200.1 osa-miR1319b Cleavage 4.0 19.296 1 24
Osa05LNT0290200.1 osa-miR5834 Translation 4.5 13.211 1 21
Osa05LNT0290200.1 osa-miR1861o Translation 4.0 19.205 1 22
Osa05LNT0290200.1 osa-miR5079b Cleavage 3.0 11.864 1 22
Osa05LNT0290200.1 osa-miR166k-5p Cleavage 4.5 23.412 1 21
Osa05LNT0290200.1 osa-miR172d-5p Cleavage 4.5 14.654 1 20
Osa05LNT0290200.1 osa-miR814a Translation 5.0 21.014 1 22
Osa05LNT0290200.1 osa-miR814b Translation 5.0 21.014 1 22
Osa05LNT0290200.1 osa-miR814c Translation 5.0 21.014 1 22
Osa05LNT0290200.1 osa-miR1428a-5p Cleavage 5.0 17.764 1 21
Osa05LNT0290200.1 osa-miR1856 Cleavage 5.0 22.975 1 21
Osa05LNT0290200.1 osa-miR1861a Translation 4.0 19.205 1 22
Osa05LNT0290200.1 osa-miR1861d Translation 5.0 19.205 1 22
Osa05LNT0290200.1 osa-miR1863a Translation 4.5 12.823 1 24
Osa05LNT0290200.1 osa-miR812g Translation 5.0 14.981 1 24
Osa05LNT0290200.1 osa-miR812h Translation 5.0 14.981 1 24
Osa05LNT0290200.1 osa-miR812i Translation 5.0 14.981 1 24
Osa05LNT0290200.1 osa-miR812j Translation 5.0 14.981 1 24
Osa05LNT0290200.1 osa-miR2093-3p Cleavage 4.5 16.935 1 20
Osa05LNT0290200.1 osa-miR2099-3p Translation 4.5 18.153 1 20
Osa05LNT0290200.1 osa-miR2923 Cleavage 4.5 22.331 1 22
Osa05LNT0290200.1 osa-miR395x Cleavage 5.0 15.42 1 21
Osa05LNT0290200.1 osa-miR3979-3p Cleavage 4.0 9.475 1 20
Osa05LNT0290200.1 osa-miR5079a Cleavage 3.0 11.864 1 22
Osa05LNT0290200.1 osa-miR5151 Translation 5.0 5.739 1 22
Osa05LNT0290200.1 osa-miR5152-5p Cleavage 4.5 18.576 1 21
Osa05LNT0290200.1 osa-miR5152-5p Cleavage 5.0 7.643 1 21
Osa05LNT0290200.1 osa-miR5487 Translation 4.0 17.237 1 21
Osa05LNT0290200.1 osa-miR5488 Translation 3.0 14.063 1 21
Osa05LNT0290200.1 osa-miR5499 Translation 5.0 15.004 1 21
Osa05LNT0290200.1 osa-miR5505 Cleavage 4.0 22.035 1 22
Osa05LNT0290200.1 osa-miR2275d Cleavage 4.0 17.507 1 22
Osa05LNT0290200.1 osa-miR5152-5p Translation 5.0 16.608 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
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