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

>Osa03LNT0245100.2

GGAACGAAATATCCACAGGAGATATTGATGAATTCAAGCCGCAGCTACATTTGACGGCGAAAAAGAACAACACTACAGCCGGTAGTCGAGAATACCATGCATGGTTATACAACCAAACAACATGTTGTCAACAAGGAAGTTTAGACTAGTTTTGTTTGTCAAGAGCTAAAGTCTGTGCATTACGGCACAAACGTTTTACACACATTTCCTTGAGCTCTCTTTGCTCAACCCGACTCCTCCACAGCTTGTTATGTCGGCAAACTGTCATTTTTAATTACGGACTAGCACCTCCTCCCCTTCCAGGTGCTCTTGGCGCTTGTTCAGTTGCTGCCATGGGTGGCAACTTCTGCTGAAGTCTCACTACTGTAGAAACCAAAAGCTTGTCACCAACAATCTGTCTCAGCTGCTTCACTAGGTCAGGCCTGCTTATCTTTCTCCTCTTGAATTCTTCATAATATTTATGCACCAGATCCATGTCCGAACGGGGTACTTTAGCGGAAATAGCAGCAAAAAGCATTGAAAAGGGCATCCAAGGTGAACTAGGAGACCTTGGACTTGGAGCACGCCCAAGCATACATGCTTGTTGTTCATCACCTGAAGACGCAATGGTCTGTAGACTGTCATCCTTGGTTGGATTGTCTAGTGCACCAGAATTTCTTATCTCAGAGATATTGGATGCAGTATCTCCATTGTTCATGTAAGGTACTTTGATAATAACAGCATATTCAGCATAAATGTGCTTATGCACATTAGCATCCCATATGATGTAATGCTTTGGCCTTTGGAGATCATCCACACCACTGTCAAAACTTTCACTGGTTGGCTGGCATTGATTTGATCCAGGGAAAACCACCTCAACATTCCCCATTATAACACGGCACAACATCATCCTTATGATTCCATTTTCGTCAATATCAGATAAACCAACACAGATATTGGAGGAGTTTGCTGGAGCAAGATGAGCCCCAACACCATACATTGGACCCTGCAGAGGTTTTGCTATTTCCAAAGCACCATTCATCATCATCTCCTCCATAGTACCCTTAGTGCAAGCAAGCCATGCATAACGCTCATTTGCATTTCCCCGTTGATTTTTTGTGACTTGTACCTCCTTCTGGAAAAGACTATAACGGGACCTCCCAAGTTGATCTAGCATTGGGGTTCTATAAATACCGATGATGTCTTTTTCAGTAAATAGATGGCCTGATCCTTGAAACAACAAATTCCGAACAGCTGAATCAGCACGCTGGACACTTTGATTATTACGAGGAGCTTGCATGGCCCCATCAGCAGTTTCATTCATATGGCTTAAATGGCCCTTTTTATTTTCCCCAGAAACTTCACCACTTTCATTGAGTACCTTCTGTTTGTCCTCCACTACATTATTGACCTCCTGAACATCAGAAAGCACTGCATCAAAAGACGCTGAACTTGAGCTTTCAGCTGCAGACATCCCATCATGTTCATGAGCTTCATAACTACTGCTTAGATCATGAAAACTTTTCAAGAACTCATTTTTTCCATGCTGCAGAGGTTCAGATGGTATTACTCCAGCACATGAATCCGGAGAGAAGCATTTACCATGATCATCGATCCAAGCAATTGGCTTGCTTATGGCCATCACAGAATCTAAACAAACCATCTGCATGAAGTCCAACAGGATGTGCCTGTTCTGGAATACTGCACTAGTAATTGGCCTCTTCAACTGGAAGCTCTGCTGTACCGAATTGACAACATCCTCTGGGAAGTCTCTCCATCCACCATGTTGGTGAGACATCACACGAACAGGCATCCCGCTTATCTTGAAGTTATTGTACCTCTCCAGAATGTCATCGGCAGAGCACATCATCTTGGACTTCTTATGTCCAGTCGAATCAGGAAATAAAGCGAGATTCTGTTTTGGACCATTCTGAGAGAGGTTGGGGGCGTCATTGGCCTCAGCACATTGAGTAGCACCCACACGCTTCCTCTTGCGGATAGTAGAATCCAGCACATGTTCATCCAGTGCAATTGCATTCTTTGGTTCCATTTTTTTTTTTTACAAAAGACTCAACTAAGACTGGGTATTCATTTTCTTTACAGACTAACACCACTAAGTGAAAACAGTTAAGTTAATCTAGCTAATGAGACCTAGACAATGTTAGCATAGAGGTAGTTCCGATATAAGCCATGCTATCCAAAAGAGTAAGTGAAATACACCTGAGACCAAGAGGAAAAAAAAAGGAATAAAGATGGCATAAAGATGTATATATAAAGAGTACAAGAGACAGGCAATATTTAATTTATGTCTGGAACAATTATATATTCTTGCACATATCATTCATAGCCAACCCACGAGATTCTAGCTAAAACCTTTGTACCACAGGTGAATAAATTTGACGCAGGCCATACACCTCCTCAGATATCAACAGAAAAGTATAGGCCGTTTATTTTCCAAAAAGGATACGACAAACTATGCTTGTAAGGCTAAAATGTTGACTAACTAAAACAAAAGATAAGAGAAGATATATAAATCTTAGCATCAATTATAGAAAAAAAATACGAGTCCTGTTATACTAGATGGACATCATGTTAAACTACTGTGACCACCTAGCCTACGAGAACACTAGTCTTAGAGATCAGAAAGCACTCCAGACTGAAAGCAATTAAGAACATGGAAATCTTGTCAGCCATAGTTTATTTTCTTTAACAAAAAAAAAGTTTGATGGATGGCTATTTTAACTGAAAAAAATGTTTCTTCAGGACCCAACTCATCAAGAAATATGATAATAGTGCATCAGGCGTTTTACATGGCAATCATGTTATATTTCTTAAAGCATACATCCTGGTTGAGTGATGCGAACGTTAACTATAAAATCAATTCGTTTAAAAATAAGCCCCCATGGAGGGCATAAAATTAAACTCCTTTGTTAGTAACTCGCTATTAAAGGAGCTATACGATTAGCATGTATGGTACTCATCATTGTTGGCAGTAAGTATAAATCTGAAGAGGGGAAGGAGATTTTTCGGCATGCTCTGAAATGAAGGGCACAATTAATTGTGCTTCCCGCCACCATCAGTCGAAGCACAACTTCTGCTGGTGTGGCTGGTTGGCACAGAAGAAGGCGGCAACAGAAAATAATAGGAGAAGAAGATAACGGTGCTCCAGCAACAAGAAGAACATAATTCCATTGTTGGCCATGGTTCCTCCCCACGGACATTGGTGGAGAAACCAAGATGAAGGCCACAATACGATCCCATGGCACTGGAAAGCACGTAAGCACATCCATCACACGAGTTGTGAATATAGTAGCTGGATGATGACCGATGAACCCTTTTAGATGACATGTAATGAGTGAAGGATGAAGAGAACATACTAGCAACACAGGGAACTAGCAGTTAACATCCACCAATCGAGGTTAGATCCGGTAGGAGGTGGTCATCGCGTCGCGGGTAGAGATAGAATCGATTTCGATGTGGTTGAATCAAATCGAAAGGTAAAGGAAACCAGATAGAGATCGATAAGGGTGGTAGTAGAGAGGGCAGGATAGGCCTTGTAAAGAGGCGAATCCAATCCCGTGGGCCGGCGGGAGGGCGGCGGCGGTGGGGGAGATATTCCGGCGGGCGGCAATCCTAGCCTTGCCTTGCCTAGGGGCGGAGGAGGAGGATTCCGGTGGGCGAGAG

Coding Potentia
Explanation CPC Score
noncoding -1.28982
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0245100.2 3 36003355 A C
Osa03LNT0245100.2 3 36003635 T C
Osa03LNT0245100.2 3 36003646 T C
Osa03LNT0245100.2 3 36004608 C T
Osa03LNT0245100.2 3 36005191 T C
Osa03LNT0245100.2 3 36005441 G A
Osa03LNT0245100.2 3 36006352 A G
Osa03LNT0245100.2 3 36006754 T G
Osa03LNT0245100.2 3 36007038 G T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0245100.2 osa-miR5542 Translation 4.0 12.665 1 21
Osa03LNT0245100.2 osa-miR6255 Cleavage 4.0 15.558 1 22
Osa03LNT0245100.2 osa-miR395b Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395d Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395e Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395g Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395h Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395i Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395j Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395k Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395l Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395s Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395t Cleavage 2.5 9.375 1 21
Osa03LNT0245100.2 osa-miR395a Translation 4.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395f Cleavage 4.5 9.375 1 21
Osa03LNT0245100.2 osa-miR395u Cleavage 3.5 9.375 1 21
Osa03LNT0245100.2 osa-miR395u Translation 5.0 11.909 1 21
Osa03LNT0245100.2 osa-miR160f-3p Translation 5.0 14.136 1 21
Osa03LNT0245100.2 osa-miR171f-5p Translation 4.5 15.164 1 21
Osa03LNT0245100.2 osa-miR440 Cleavage 4.5 13.368 1 24
Osa03LNT0245100.2 osa-miR395m Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395n Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395p Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395q Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395v Cleavage 4.0 9.375 1 21
Osa03LNT0245100.2 osa-miR395w Cleavage 4.0 9.375 1 22
Osa03LNT0245100.2 osa-miR395r Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR1424 Translation 4.5 19.486 1 21
Osa03LNT0245100.2 osa-miR2101-5p Translation 4.5 14.589 1 22
Osa03LNT0245100.2 osa-miR2880 Cleavage 4.5 12.57 1 24
Osa03LNT0245100.2 osa-miR395y Cleavage 3.0 9.375 1 21
Osa03LNT0245100.2 osa-miR5151 Translation 4.0 12.861 1 22
Osa03LNT0245100.2 osa-miR5507 Cleavage 4.5 11.714 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0245100.2 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
Osa03LNT0245100.2 3 nan Resistance or Tolerance Drought tolerance R1925 RG1356
Osa03LNT0245100.2 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0245100.2 3 Qsbn3b Morphological trait Panicle/flower RM227 RM85
Osa03LNT0245100.2 3 Qsnp3b Morphological trait Panicle/flower RM227 RM85
Osa03LNT0245100.2 3 nan Morphological trait Root R1925 RG1356
Osa03LNT0245100.2 3 qLT3-1 Morphological trait Shoot/Seedling RM227 R1925
Osa03LNT0245100.2 3 qPL3-1 Morphological trait Panicle/flower R1925 RM227
Osa03LNT0245100.2 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0245100.2 3 QSn3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0245100.2 3 qSV-3-2 Physiological trait Germination/dormancy RM227 RM85
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