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

>Osa02LNT0176900.1

CAGATCATACCAAAACAAGAAACTTGTCAGTTTGCCACTGTACATGTACATCCAAATCCTACTGGGGAAATAATGTTGTGCCTGAGAACAGTACTTGAAACCACAACAGAAGGGAAAGTACTATAATTTGGCCCTGACTGTTCGTGTCATGTTTAAGAACAGTGTTCAAATGCCAATCAGGTATACAGCCTGAAACTTCTATCATCTAAGGACGACAAACCACTGCTATTATATACAACAAATTTTCTGATTTCAGTAGTTGGCACTGCTTCTGAGTACTGACAGCATGTGCGCTCATTTTAGTCTCTCCGTGCTGGCATCTCGGCAAGAGGTTTCAAAACAATCGGCTTGCTTGGATCTACCACAAGTGAAGAACTCGTTTACAGAAAAGCCAGTGACCAGGGGAGCTTTCCTGTCCTAGACATCTTCACCATTGCTCTCTCAACACTAGCTATCTGATTGTCGGTTGCTGCATGCTCCTTGATTTTCTTCTTATCAGCTTTCTTTTGTGCATCTTTTATTGCCTTTTGCATCTTCTCTGCTGCTCTCGCTCTCTTCTTCTCCAACTTGATCTCAATTCTTTTCATCTTCTCCTTTGCCTGTGTAACCTGATTCATCTGCCATTCATCGATATCGGCCTCTTTCCTTCTCAGCTTGTCTATGAGCTTTTCAATCTCCGCATTCTTCCAGGCAACCAACTTGGCGTGGACAAAATTTTCCTTATGTTTTACCGCAGAACCCTGGGGCCATCTCCCCATTCTTTGCACTGCAACTGGGCTATTTTCGCCATCTGAATGGTTAAACGCACCGCCATTATGATCACTTCCCTCATAGGCACCACCAGCCTCAAAGTTCCAATCACGAGCTGAGGATATACGAGAAGACAGAGTATCAGCCTGCCAATCCGTTTGATCCACTGCTTCATCCTCTTCTTCACTGACTTTGGGCAATCTCCATTCATTGATAGCATCCATTGCCCCCAAACGCCTACGGTAATTATGTGAGGAGCGAGCTCGGCGCATCAATCTAGCTGGCGTGGCCTTGTGGATGAATCTTGGTGGCACTGGATTAGTTCTCTCAAATCTCCTATCCAGAAGGGAAGGTTGTCTGGGCGTTTGCAGTCTGATGTGTCGTGGTGTGGTAGACGGATTTATGAAATCTCCTCTGTTTGGCAGCCTTTCTTGGTCTTCTTCCAGCCGTGGCGTGACGAACGAGGAGGCGTCATCACCGTCGCGGCAGCCCTCCCCTCCATTGCTGCTCACGGGGCTGCAGATTGGGGACGGCGAGGCGGGGCGGTGGTCGGTGAGCGACCCGGCGCTCCACGCGGCGCAGCTGCCGTAGGAAGACGCCGGGCGGCGGCCGTAGGGCCCCCCGCGGCCGCCCATGGCGGCCATCGCGAGCAGCATCTGCGTGCTCCTCCCGACGGACGCCTCCGGCTCGGCCTCGGTGTCGGCGGCGTAGAACGCGGCGCCCTCGGAGGCGTCGGAGCGGGCGGGGGACGAGCCCGGCGAGACGCGGGACGCCGCGGTGGGCTCCGCGACGCAGGGGATCGGGATCGGGATCGCGGCGGCGGCCGCCATCTTCTCGCCGTTCTTCTTGCCCTCTTCCGGTGGCGGTGCCCTCCCCTTGATTTCTTCACTGACATGCGGGCCCGGTTCGTAGATAGCTGTGCACCGGCATCAGTTCGCTGCCCTTTTCCCTTCATCTCCCGTTCTCTTAACTGAACCAGCACTAAAATTAGAAGCACCACATGAACATTCAAGAAGCAGGATATCATCTGACAATATGAATACATCATTTGCGATGGTATGTGCAGCGAACACAAATTTTCTGTTGGCTCTACTGTTAGTCAGGAACTAACAAGTTCTGCCATAACTTATGAAACAATATTCCGTGCCATGTGTGGCTTTTAGCTTGCTACAACTCCGGCGCAAAGACAAATTTGCACCTCAATTGAGTTTTCATACTGTAAACTTGTGGGTATAGGGGAATTGGCAAGGCGCCTTTTGCCCTAAGTTGGAAGAATTTGTAACAACTTCTAAGATCAAGAATATTCCAGGAGCACGCAGAGCTTCTGGACTTGCAATCCTACTAAGCAGCAACACCTGTTGAATAGTTCAGCATCGTCCCTTTGACTCGTTGATGGCCTGGTAAGATCTGCTGCAAGAAAAGTTCAATCCATAGACAGATGAAGCGCAGCTCAGGGGAATGGAGCACCAAGGTGATCAGACTTCATACCCTTTTGCAAAGCACCCTGCCCTTCTTTCCCATTCCAGTGCCAGCGAGGCTTGCAGCGAGACGTGACTTGTTGTCAGGTCTCCACTTAAGCTCTTTGAAAGTGGAGAAAAGCTCTGAGAGGGCAGGGCTGATTTCCTCATCTTTGATTTTATCACAAGAGACAACTTTTAGGCTCTGCAGATCACTCCATGAGGTTATCACCGATTCTAGACCTCGAGTTGTCAGTTGTGAGCAACCTTCTAAGGAGAGGAACTTAACTCTCCTGCACAGTCCTGCCATGGCAAACATGTCATCTTCAAGGCCCCAGCAATTCTGGACCAATAACTCACGGGCACCCTCACAAACCAAAAGGAGAGCATGGAGGGCACGACGGTCACGCAGCTGGCACTGCTGAAGCTGCAGGCTCTCAAGCGTGAGGCAGGCACCAAGATGCTCCGCAGGCCCAGGATCGTCATCAATCCTGCAACATCCTTGCAACCTTAGGGTTTTGAGGTTGCCGCAGAAAGCGAGCGCAGCAAGCCACCCATTGTCCATCTTGTGGTTGGCGATGGTGAGCTCCTCAAGCATCGCACAGCACCGCCCCACAGCCGCGATGCCGTCATAGCTTCCCTCGCAACCAACAAGCTCCAGCTTCACTAATCTCTTGCATCCATGAGCAAGGATGGTGAGGCCGATGTCGGTGACACCACCATCTTCACTGGTGCCATATAACGCAGAGGAGGCTGCGACAAGGCGGAGGATCTGAAGATGCGCAAAGGCGGAGACTGGGCGGAGGGCGAGGTCGGTGCATCGGTGGAGCTCGAGCTCTTGCAAAGTTGCGCAGCCGCCAGCGATATCCATCAGACCCCCGGACTCCGAGGCGGCTGTGGCTGAGAGGCGGCGGAGGTTGGGGAAACTGGCGGCAACGGCAACAAGGCCCCTGTCGAGCACGTCATCTGCGAGGAAACGGCAGGCGACGAGCGGCGGGTCCGCGCCGGTGTCTAGGGTTAGCGACACCTCGGCGCAGGTGAGGAGAGGGGAGGTCGGGGACGGCACGGCCGGAGCGACAATGGACGCCGGGAACAGGTCGAGGTCCGCCAGTTCGGGGAAGCGGTGGTGTAGGCGGTGGGTCACAAAGGCCCAGTCCCTGACGACGAGGCGGCGGCGCAGGCGCCCCGCGAGGCGCATCCACCTCCTGCAGACCAGCGACGCGGCGCCCGTGAGGTGGGGCTCCGGGAGGCAGGCGAGGACGCGGAGGAGGAGCCCGTCCGAGAACTCTAGGGTTTGGTCCGGCGGCGCCACCGCCGCGGGCCGCGCCTGCTGCTGCTGCTTCTCCACCGGCGGCGGCGGCGGCGTCGTCATCTTCTTCCCGGACAGCGACCGCAGGTCAGGCCACCCCTTGAGGCCGTCGCGGTGCAGGCCCCGGCCACCGAGGACGCCGACCTCGGGCTCAGGCATTCACCGCGAACGGCGGCGCAGGGCCCCGCGTAGCCCCGGCCGCGCCGCGAGAGGAGAAGCCCCCGCAGTGCGGCCGGGCGCGGCGTCGGTCCGATTCGGGAGAGATTCCGGCGTGGTAGTGCGGCCGTGAGGGGATCTGAGGACTTTCCTTTTTTTTTTTTCAAAATTTTTGGGGGGGTTTGGGATTTGGAAATTTGCCTCGCCCCTCGCTGCTGGAGGAGCGGGATAAGAGAGAGGGTGGAGCGGAGGAGCCGTGGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.962019
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0176900.1 2 26626185 T C
Osa02LNT0176900.1 2 26631843 G C
Osa02LNT0176900.1 2 26632079 A C
Osa02LNT0176900.1 2 26627304 G A
Osa02LNT0176900.1 2 26627744 A G
Osa02LNT0176900.1 2 26629961 A G
Osa02LNT0176900.1 2 26630380 T C
Osa02LNT0176900.1 2 26630491 C T
Osa02LNT0176900.1 2 26631577 A G
Osa02LNT0176900.1 2 26626056 T 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
Osa02LNT0176900.1 osa-miR5804 Cleavage 4.0 11.561 1 21
Osa02LNT0176900.1 osa-miR5821 Cleavage 5.0 14.631 1 21
Osa02LNT0176900.1 osa-miR5828 Translation 5.0 14.574 1 21
Osa02LNT0176900.1 osa-miR171d-5p Translation 5.0 23.732 1 21
Osa02LNT0176900.1 osa-miR408-3p Translation 3.0 23.775 1 21
Osa02LNT0176900.1 osa-miR172d-5p Cleavage 4.5 17.627 1 20
Osa02LNT0176900.1 osa-miR529a Cleavage 3.5 24.63 1 20
Osa02LNT0176900.1 osa-miR529b Translation 3.0 7.74 1 21
Osa02LNT0176900.1 osa-miR1847.2 Cleavage 5.0 15.281 1 24
Osa02LNT0176900.1 osa-miR1876 Cleavage 5.0 14.009 1 24
Osa02LNT0176900.1 osa-miR2092-5p Cleavage 4.5 18.247 1 21
Osa02LNT0176900.1 osa-miR2874 Cleavage 4.5 10.143 1 24
Osa02LNT0176900.1 osa-miR2876-3p Cleavage 4.5 22.037 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0176900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0176900.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0176900.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0176900.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0176900.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0176900.1 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0176900.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0176900.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0176900.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0176900.1 2 T2-2tiller Morphological trait Culm/leaf C424 C747
Osa02LNT0176900.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
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