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

>Osa04LNT0289900.1

TTTTGGTCAATATTCTCTTTTTCTCCTCTCAGACACAAGCCTAAGAGGCACCCGAGATCAGCATGTGTTCCGTTCCGTGGTCGTCACAATTAGTACAAGTAGCATGCAAAATGTCACGCCTTAGTGACTACTAGCATGCAAGCATGGAATTTAAGCAAAAGAAACAGACATGCCCTACACTAGACAGACAGATCATCCAAGCAGATTACTTCCGTTGGACCCTTCCTCTCCAATGGCTCCGGAGAAGACTCGATCACGGTCAGCTTTTCGTCCAGCTCATTTATCTGCCTCCTTATCTTGTCTCCACGATCTGGTAGCTTCGCCACAAGCACCGTGTTTGCAAGGGTTTGCGAAAGCCGGTTGATTTTGGCCTTGATTTCCTCAGGACTTTCTGTGCTTGTGCTGTTCGGGGAGTATGTTCGAGCAATGAACTCTTTTGGCTTCATCGCATAGGCAGCACCATTGGCAACATAGTCAGATGAGGCTCCCTTGTAGTAGTGCTTGGCCATTGGCATAGCTCGACGACTGCTGTCCAAACCATCATTATCATTCAGTGTAGGTAAGATTGCTGTCTTAGAAAACAGAAGGCTGTGATGGCTCACGCCCGCTATGCCTTGTTGCTCCAGGAATTGTATATGCTTCCTCAAGGAGTCGTCCATCACAAGTTGTTGTCCATGCTCTTCTTGCAATTGCTTTTGTGTCAGCGAAACATCAAAACCTTGCTCAGGCAGACTGAAAAGCTCTTGAATATCCCTCTTGCTGAAATAACGAGTTTGTTCTTTGTGCTCTGTAGCTGTCCTAAACAGAGCCCCCTTGAAGACCTGCAATTTGTATATCTTTTCTTCGATGGTTCCAGATGTCATAAGGCGGTATACGATGACATCTTTCATCTGCCCAATTCGATAAGCACGATCAACACTTTGATTGTCCGTACTTGGATTCCAAGCAGGATCAACTACTATGACACGAGCTGCCTTGGTGAGTGTAAGTCCAAGCCCACCAACTTGTGTGGTCAGCAAAAATATTGGAGCTCCAGGACCCTCTTGGAAGTCCTTCACAATCCTTTCCCTCTCAGAAATCTTGGTGGTACCATCAATGCGCAAAAACTTATAGCCTTCTAATATTATAGCCTCCTGAATAATGTTTAGCATTTTACGAGTTTGCGAGAAGATTAAGACGTTGTGTCCCTCGCTAACAAGATTTTGGAGCAAGGACATCATAAAAGATAACTTGCACGAGACATCCTGACCAACTTGCAATTCAACGTCATCATCATCATGAGCCATATCTGCAAGGTTCATGGCCATTTTCTCAACCATTCCCATTTCTTGATTATTTAACATCGCATCCATGCCTTCCAAAACACCCTCAGCAGCTTTCTTAGTCAACAACAGCGGATGATCACATATTTTCTTCAATATCGTGATTGCGGCCAAGGGTGACCCTTGCATTGATGAATGAACTAGTTCACTGTTAAGAAAAGCTTCATATAATTGCCTCTGGCAAGATGTTAATTTCAGCCAGATAATTAGCTCATTCTTCTTAGCAAGCTTTTTATCTTCTCCCGTGCCGCTATCAAGAAACACTTCATTCTTCATGCGTCGCAAAAAGTATGGCTTTATCCGTTCTCTTAATTCCTTTGCTACATTTGAGCCTATGTGCTTTTGTCGATTGGTAGCATTCTTGTCATTTCCTTGAATGATAGCGTGCTCATACCTTGCTTTGAACTGCTCCTTATCACCCAAGACTTCTGGGCAACAGAAATAAAACAGAGCCCACATTTCCTTCAAGTTATTTTGTATGGGTGTTCCACTGATGACAATACGATGTGCACAGGGTATTTCAAATAGACTTTGAGCCCTCTGAGTCTTTGGATTCTTGATAATATGCCCCTCATCAAGAATAACATAGTTCCATAATGTTTCTTCCTCGTCATCAAAATCATTGGTGAAGTTGCCTTTTATCATCTTGAAATTGTTTCGAACAATGTCATATGTTGTTAAAAGGATTCCACCCTCCTTGAAGGCATATTTAAGCTCATAGTTGCGAGCATTTGCATTGGGACCAGAGTAGTCTCTGATCTTATCTTTGAGGCTCACAACTGAAAGTTCCTTGGTCCAATGAGTCAGAAGCGTCTTTGGAGCTACAACTAACACTCTCTTGATTAAACGGGAATGGAACAATCCAGCCAGGAATGCAGAAACCTGCATGGTCTTGCCAAGGCCCATGTCATCTCCAAGGATCCCTCCAGTTCCCCTACAATGCAGAACCCAAAGCCACCTGAGACCCTCACGCTGGTGGGGGTAAAGCATGTTGAATATCCTTCCTGGGAGATTGTAGGGCTTGCGCGTTACACCTGTCCCAGTGGGCTCCATCTTGAAGTCCTCTGTCTTCTCCCAACCAACATCATCAGCATGGTTTTCCTTCCCATTCTCTGCATCTTGGTCGATGTCGTCTTCATCGTCATAGTCCCCAAAAAATTTTGAGGCCTTGGATTCGGTTGTGGTTTTCCTTGACACCGTATCAAAGGCATAAGCTCCTTTGGCTTTCATCTTATCATCGTTGCCGCGGCCCCCAAAAGAAGAAGAGGCCTTGAACACCTTCCTGGTGACCTCCTCTTTAACACCAAAACCACCGTAGGCACCTCCCGCATCATCGTCGTCGTCATCACAGTCCACAAAGGATGAAGAGGGTTTGGTCCCATCATTAAGCTGAGACTGAGAGGGGTCGGGGTCGGCATGGAGGGCGCAGGGAAGTGGGGACACGTGGGGTCTGGGCCTTGCGGTGGGCCTGTCGACTGACAGGGAGTCGAGGCGGGTGGTGAGATCGTCCAGTATGTCGCGGATGCTGTCGTCGTCTCCGGCGGACTCATCGCCGGCGGTAGAGAGCTTGCAGAGGCGGCGGCGGCCGGCCAGCTTGACCTTGGCGGGTTCGGGCTCTGCGAGGAATTGAAGTGGATGGAGTTACTAGAAAACGGAACCGAGAGAGAGAGAGAGAAGGGTACCTTGAGGAGGCGGCGGCGGAGGGGGTTTAGGGTTAGGGTTAGGGTTAGGGTTTGGGTTTTGGGAGGGGCCCCGTTGGTGCGTGCGGGTGAGGCGGAGGAGGCGATCGTTGAGGCCGTTGGGTGTCGGAGCGGCGAGCGGCGTCGGCGCAGGAGGGGTGGGGTCGTCGTCCAGGTCGCCGCAGATGTCGAAGGGCGGAGGGGACGCCATCGATCTGCTTCCTTCCGAGTTCTGACGACGACGACGACGACGACGATGGAGGAATGGATTGGAGATTTCTCTCTTATCTTCTCTCGCTTGGGTTGGGTTGGGTGTTGGGTTGGTTCGGGGGAAGAGGGGACTGAGGAAGAAGAACTTCTCCGCGGCCTATGTACC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.851568
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0289900.1 4 35453130 A G
Osa04LNT0289900.1 4 35453335 A G
Osa04LNT0289900.1 4 35455250 T C
Osa04LNT0289900.1 4 35457475 T G
Osa04LNT0289900.1 4 35456065 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
Osa04LNT0289900.1 osa-miR5792 Translation 5.0 16.759 1 24
Osa04LNT0289900.1 osa-miR5792 Cleavage 4.5 11.624 1 24
Osa04LNT0289900.1 osa-miR5801 Translation 5.0 17.11 1 24
Osa04LNT0289900.1 osa-miR812t Cleavage 5.0 18.767 1 24
Osa04LNT0289900.1 osa-miR812u Cleavage 5.0 18.767 1 24
Osa04LNT0289900.1 osa-miR5812 Cleavage 5.0 17.484 1 24
Osa04LNT0289900.1 osa-miR5812 Translation 4.5 12.587 1 24
Osa04LNT0289900.1 osa-miR6252 Translation 4.5 14.186 1 23
Osa04LNT0289900.1 osa-miR396e-5p Cleavage 5.0 22.486 1 21
Osa04LNT0289900.1 osa-miR530-3p Cleavage 5.0 13.715 1 21
Osa04LNT0289900.1 osa-miR1866-5p Translation 4.5 11.37 1 24
Osa04LNT0289900.1 osa-miR2090 Cleavage 5.0 12.806 1 22
Osa04LNT0289900.1 osa-miR2118e Cleavage 5.0 24.748 1 22
Osa04LNT0289900.1 osa-miR2118h Translation 4.5 23.453 1 22
Osa04LNT0289900.1 osa-miR2118i Cleavage 5.0 24.748 1 22
Osa04LNT0289900.1 osa-miR2118k Translation 4.5 23.453 1 22
Osa04LNT0289900.1 osa-miR2118p Cleavage 5.0 24.748 1 22
Osa04LNT0289900.1 osa-miR2118r Cleavage 5.0 24.748 1 22
Osa04LNT0289900.1 osa-miR2863a Cleavage 3.5 12.127 1 21
Osa04LNT0289900.1 osa-miR812n-3p Cleavage 5.0 18.767 1 24
Osa04LNT0289900.1 osa-miR5499 Translation 4.0 8.851 1 21
Osa04LNT0289900.1 osa-miR5503 Translation 5.0 15.88 1 22
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