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

>Osa04LNT0248600.1

GATTCTAGGAGAAACTGCAGCTACTAGAAGCTCCCCAAACAGGCCCATAGTACACCCACTTAGATTCAGCTCACTCTAGAAAAACTAAGGCCAAGCCCAATAAAGAAACCAAACACATGCCAAGCCGGGAAGGAATTTCAGAAGGAAACCAACACGGCCTAAATAGGAAAAGAGAGGGATCGGACCACTGGCCAAAATTGGAAAACAGAAGTGATCCCTTGAGCGCCGCACACGACCGCTCGTGCGATAGCGTTTTTGAACTTTTTCCACCAGTTAATCACACGAACAAAAAGCATTTCGACTCCTAGGTCATACAAAACATACAATATGTGATTACATCACACCGATGGGATGAAAACGGTCCGAAACGTTTTCGGATTCCGAACATATTTTCAGAAATGGAAAGTGTCGAATGGAATTTTTTCGAGAAAGTTCAAAAAACGAAAACGAATTCAAATTTTGATGGTGTGAGAGATATTATTGTTTAAAAGATTAGAATTCTAAAAAAATATAACATTTCCACCATCAAATATAAGATATGGTGTCAGAGATATTATTGTTTAAAAGATTAGAATTCTAAAAATATCAATAGTATTTAGGTGGTGTTTAAACTCATATAGATGAAGATGAAGATTAAGTGTTTTACGAAATATGAGGTGGTATTAACGTATAATTAATTATGTTTTTAATTATTACAAAGTTGGAAAATATATTTATCTGGTATTTTAGAGCAACTTCCATATAAAAAGTTTTCTCATGAAACCCACCGTTAAGCAGTTTGAAAAACTTGCTACTATGTGTCTTTGTATGTGTCTTTGTGTGGACAAAGAGAAGTACTTTAGCCCCTGTGTCAACTTGTGACCATACACATGCACTTTTTAGCACATGTACTTTGCACGAGATTAAGACTTAAAATTTTATCTATGCACAAGTACTGTAGCAATACCGTTACTACTGCATGCTTTACGTTACTATAATTTCCTCGGTATGTTGCTGCCGAAAGTGTAGTACCAACCCATAAGTTTTGCATGTTATGAGTTTCGCAATAAAATAACTGAATTGTTCTATAGCGGAAGAGAAGAAATTATAAATCGGTCACCATATTCCTTTCCCACTAAGTTTAAAATTCTGTTTTGCATGTAGCCCGCTAATCATGAAGTTGGAAAAACCATTTCCCAATTACGTGACTTGGTTAATTGCATTAACCAAACAATTTAATAAACTGACAAACTATGTTCTAAATTTATTTAGTTGGATGACCGGGTCTGCATGCTAACCGGTCATTGTATCGTGATTACCTACGCTTTACTGCAGGAATTACTAAACAATTTTTAATATATTTTTTTCGAGAATCAAGCTATTAGTAAAAAGAAAAAAAAACAAAACATCAGGATTTATCAGCACTTATTATAAAACAAATAAATGATACTTACGCTTTAATATAAAGCATATTGATAAGTATATGTTAAATATCATAAAAATAAAAATGATAGATAGATTTGTGAAAATATTGTGCAAATAATGTGAGGGGTGATGATTGGATATACTTACATATCGATTTGTAGAATTAAATAAGGACAATTGCATCTACGATTTGTAGAATTAAATAAGGACAATTGCATCTATGCCCCTACTTTCAACCCCAACTGTTGTTTTACCCCTACGTTTTAGGGTTTGCAATTTTATCCCCAATTTTTAATAACGAACCAGCCGTTTACCCCCACTTGTAACGCATGTTTGGTGGGTCCCACGTTTAAGTGTTTAGAATTACAAATGGAAATTAAAAAAAGATTTATGAAATATCAATTTACCATTCTACCCTGAATGAATGGATATAGATGGAATCCCTCTCCTCCCCACCGACTGTGGTTGTGCCTATGAACACCCAGACCACCCTAGACCTAGAGGCGGTGGCGGTGGTGCAGGCATGCGCAAGGCGGTGGCGAGCGTCGGACAGCGCTCCGTCGAGACAGCAGCCAGGTGGCGGCCGTGGGGCGGGAGCAAGGCGGTGGCAGTTCTAGCGTGCGCGGCGAGCAGCGGCCAGGCACTGGCGGTTCTGGCATGTGCGATGATGGCTCGAGTCGACGACAGGTTTCCGGCGGGGCGGGCGGCGGCCACGGGGGTTCTGGCACAGCGAAGGCAGACGGCGGCAGGGCTTCCGGTGCGGTAAGGCAAGCGGCGGCGGGGCTTCCAACGCAGCGGTGGCAGGGGCCACCAGGGCTTCCGGCGCAGCAAGGCAGGCATCTGCCCCAGGCCTTCTGACGCAGCAGGCAGCGGCGGCGGTTGGGCTCTGTTGGAGGCAGGAAGAACAGAGGCTCGGTGTATGTGAGGTAAAGGTTAGGGGAAGGGCATCAATGGAGGAAATCCTTTCAATGGAGCATACTTGAAGAGATTAACATGTAATTTGATCTATTCTTATCATTGTGGTTCTCCCTTGATTCAGTTTGATTCGTTGGATAAATTACATTCGTTATTTGGGACTATGTGACACTAAGTAATGCTTGCTACTATATCTATGATTTCTATGTATTATGGTTTATTGTAAGGGCAAAAAATACAACAAATAGCCAAGGGTATAAATGTGCTTTTGCCCTAAAACTAACACCATCAAACTAGTTGTCAAAAGTGAGGGCAAATGTCTAGTTCGTTTTCAATAAAAGTTTAAACCTTAAAAAGTGGAGGTAAAACAACAGTTGGGGCTGAAAGTGGAGGCATGGATGCAATTTTCCCAATCAAATAAATTGTAGAAGATGTTGTATGTTTGCATGAGGCTAAATATGTAATTATTGTTAGTGGGTGATGATGTAGTATAGTTACATGTTGAGCTTTACACTTAGTGGTGCTACAACTTTATATAAAGTATAGATTCCCATAAACCATATCCGGTATAAGATATATTGTGAAGCAGATGAACGTTAGACTACCAGGGGATAACTACTCCCGATAGTAGGAAATAGATATTCAATGTATAAAAATATTATATATACACGTAAAAATTTCATACGTATAAAAAATATTATATATACATGTAAAAAAATCATACGTATATATTTTATATACATATAAACATTTCTTTTTTACATACATGTATTCTCGTACTGCACGGAACTAACCACGAACCACGTGGGGGAGAGAGGGGGGGCACGAGGCTAGTCGCTAAATATTGATTTAGCATTCCAATTTAACCACTTAACTGATATTCGCCACTAAACTTTTTAAACAAGATAAATTACCGATAAACACCATATAAAGTAGTTTTGGTCCCAGTGCAATCCAGTCAGCCAAGTCCATATCTATAACTAATATAGATATTCGTATTTTTCCGTTCGTCACCTCATAGGTATGGTGATTTTCGTCCCCCTCGCCTCCCCCAAATCCCAATCGGAATTCCATCACTCCCACCCAAAAAAATCCCAATCGGAATTCAATCAATCATACAAATAAAATAAAATCGGAGGAAGCATTATACACACAAATATATCCAAAAAAAAAGATCAAAGGAGAGGTCACCGTCGAACCGCAGCCGCCGCCGCCGTCGCAGGGACGCCAGGCCGCCGCAGCTCCCCTCCCGTTGGATCCGGCAGAGGGGAGGGGCACCGCCGCCGCTGGACGCCAGCGGGCCACCGACGCCTCCCCGAGCGCTACCGCCCCCGCCGCCGCCAGTGGTAGGGGAGGACGCCGCCGCGCCGCTGGTGGTGGTGAAGCCGCCGTCGCCGCTCGTGGAGGGAGGGCGCCGCCGCCGCCGCTGCTCGAGGGGAGGGCGCCGCCACTGCCGCTTGGGCTCTGGGGGAGAGGCGCCGCCGCTGCCGCTTGGGCACGGGGGTTGAGGCGTCGCCGCCGCCGCAGTCGCTCGGGGAGAGAGGCGTCGCCGCCGCCGCAGTCGCTTGGGGAGAGAGGTGCCGCCGCCGCCGCTTGGGCACGGGAGCATCGGGGGCGCGGAGGGGAGGGCGTCGAAGAGAGAGAAGGGAGAGAAGGAAATG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.866056
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0248600.1 4 4918023 A G
Osa04LNT0248600.1 4 4918065 T C
Osa04LNT0248600.1 4 4918296 G A
Osa04LNT0248600.1 4 4918325 T C
Osa04LNT0248600.1 4 4918701 A G
Osa04LNT0248600.1 4 4918749 A G
Osa04LNT0248600.1 4 4918978 T C
Osa04LNT0248600.1 4 4919158 G A
Osa04LNT0248600.1 4 4919400 C T
Osa04LNT0248600.1 4 4919415 A C
Osa04LNT0248600.1 4 4918003 G A
Osa04LNT0248600.1 4 4920805 A G
Osa04LNT0248600.1 4 4920866 C G
Osa04LNT0248600.1 4 4919633 A T
Osa04LNT0248600.1 4 4919951 T C
Osa04LNT0248600.1 4 4920215 T A
Osa04LNT0248600.1 4 4920252 T C
Osa04LNT0248600.1 4 4920396 C T
Osa04LNT0248600.1 4 4920503 A C
Osa04LNT0248600.1 4 4920597 C T
Osa04LNT0248600.1 4 4920259 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa04LNT0248600.1 DTM_#DNAt_MULE_japo_Os0709 Chr4 - 4919591 4920710 1119
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0248600.1 osa-miR5837.2 Cleavage 4.5 13.806 1 21
Osa04LNT0248600.1 osa-miR319a-3p Translation 5.0 18.928 1 21
Osa04LNT0248600.1 osa-miR529a Cleavage 5.0 22.583 1 20
Osa04LNT0248600.1 osa-miR1871 Cleavage 4.0 13.417 1 24
Osa04LNT0248600.1 osa-miR2095-3p Translation 4.5 23.174 1 20
Osa04LNT0248600.1 osa-miR2099-3p Cleavage 5.0 19.086 1 20
Osa04LNT0248600.1 osa-miR2863a Translation 4.5 15.166 1 21
Osa04LNT0248600.1 osa-miR2868 Cleavage 5.0 14.05 1 20
Osa04LNT0248600.1 osa-miR2863b Cleavage 4.5 12.887 1 21
Osa04LNT0248600.1 osa-miR2905 Translation 4.0 13.233 1 21
Osa04LNT0248600.1 osa-miR1863b Cleavage 5.0 13.491 1 24
Osa04LNT0248600.1 osa-miR5490 Cleavage 3.5 15.005 1 21
Osa04LNT0248600.1 osa-miR5504 Cleavage 5.0 21.254 1 21
Osa04LNT0248600.1 osa-miR5150-5p Translation 2.5 12.844 1 24
Osa04LNT0248600.1 osa-miR5158 Translation 5.0 21.171 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0248600.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0248600.1 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0248600.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
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