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

>Osa05LNT0315100.2

CTCAGCACTACCAGTAATAAATAAATCAAATGTTCTAATTATACAACCATAGGGGAGGATTTCGCCTCGCTACTCATCCATCATCTGTCAGTTATGAGTTAAAATGTCACATGGAGATCAAAATTCTAGCAGTAACAGATTGCCGCGCGAATGCCAACACCATCATGAAAGCTTTGCTCATGAAAAATTTAAGTTGTGAAGGCATGGATTGATTGATTTCTCTTGGAGGGTCAAGGAGGAGGAGGAACAAGCATCCAGTCATTGTTTCATCCGTTTCATGCCACCATTACTGAATGGAGAAGCACTACCAGGATGTGGGCTTTCCTCTCTAAGTGGTGAGTTCAACAAAGCAAGTTCTCGGAGTTGCTGTCTCTTGTAGTAATCTTGCGATTCATCCACTGGTTTCAACAACTCTTCTAGGATTTCTTGTGCTTTTGCGAGTCTAGCGTCAATGACATTGGCAGGTAACTCGGCTTCAATCAAGATATGCAGGGGATCATCCAAGTGTTCATACCCAGCCCTTCCCTTAAGTTGCTCCTCCTTGTTAGGGTCTTTAATTGAGCCCTTTCCTCTTATGAAAACACGACAACCTGTAGAGGCCTCAATCCTCTTCAACGAATTTCCCCTTGGTCCAAGAAGGCGACCAATAAAATTGAAATTAGGGTAAGCATCTGTCGGTATTTCCAACCGCAAGATCTTCTTGACAATGTAAGAAGAGGGACTTTGTGGTGCTCCTTGCCAACCTGGTCCTTGAGAGAAACTTACTCTCTGCTCAATGTGAGAATAACAAGGTTAGGTGCCACAGGAGTTAGGGTATGGAGAATACAATAAATGTAGCACTGAACAAGAAGGCCAAACATAGCTGAAGATCCACAGGAAATGGAACCATAGAAGTAAGGAAATCAGCCTGATGTTCTTATAACTAGCTATGCTATTCATCCCTAGTTCATAAAATCTACTCAAGAATATGCTATGAAATTTCTTGTTAAGAGGCATATCTATTTATTCCCGTGCGACTACGTAATACAGAATTGAGTTGCAAAAAAAAATTAAGATCTTGATAATAAGTATGGCAATACATCCTTCGGTAAAAGAATAGTTACACTTCCTAATAATTACTCCTTAAGGTCAATATTACTTGTCATTTCCGACAAGCAAATTGTCCTAAAAGCGGGTCAGTTCAATTGTCTGAAACGACATATATTTCCCTCCAGAGAGAGAATTCGTTAAGCATTTTAAGAGTTAATCATATGATTTGCTAAATGTTATTGAAGTTCACCAATCCAGTTGCATAATATAATTTGAAAGGCACATGGAAAAACAAGGAACGAAAAACAACATTCTCTGTTGGAATGTATTGGTAGTAGTGCCACATAGAATGGAAAGTCAAGGTTTCTCAACCAACTTAACTTAGAGCTCTGAACACTCTCTTCATTGCATTTGCACAATGCAGAGACTATATGATTTGGACAAGAGAAGTAACAGTTTAGGGCAGGTTATTCGTTTGGTTGCCTATGTAAGGAAGATATCTAAGTATTTTGACCACACTGGCACACTGTCCAAGAAATGGCCAGCCAAAATTGGTAAACTTTAATTTTTTTTGCCAGGATGAGAAAAATAATACGACATCCATTGCTCTGTTGCTGTAAAGCAGTGGAAGTGTTGTAAGATAGAGGGACTTACATCAGAGTCTCTGGACTGATGATTGTCTGCTATTAGGAGCATGATAGGTCTAACAACTAACACCAGAAGTGACAGTGCTGAACAAAAAAAATGTGCGCCCTATGGTAAAGCACAATGTTGAGGTGACTGAGATTATGTGTTCAAGTCACAATAAAGTCTTCTCTTCCTTTTCTTCTGAAGGAAACTAATCCTCTGAATCAAATATGGGTAGTTCCACATACATAGCATCATTTGTTTTTTCAGAGCGGGCAGTGCTAATGATACAAAATAGTTGTATATAACAAAATTTCTTCATTCTAAAAGGATTTTAACGACTCAAGCACCAGAGCTTCTGGACTTTGAAGTTTCAATGTTGCACTCGTTTCTCTTATATCATTGATATAACGTTTACAGGTATTGTGGCGATAACTTATTCAGAAGTCCAAAGGTTAAGAGGCGGCAGGGGAGAAGTGGATCTTGCATGACAAAAGTCAAGATGAGCTGATCAAAATGTTACCCATTCCAAATAAAAATCACTGACCTCTTCTATAAACCACACGAGGTTCGATGTAGAAAAGCTATATGATGGCCATAGGCTACCTGTTGTGACATGTATAGTAATCATTCTTTTAAGGGTATACATAATACTCTTTAAAAGCCAGTTTTACTTCAAGAGGACCTTGATGGATTAAATTGATGGCACCCTATAAATTGAGGACCTTGCGCATTCATTTGTTTCCATCCTTGCATATCGCAATTCTAATAAGTATAACGCAACTTATCAGTGATATTTTACATAGCAGTCCTTTTGTAGAAATGTTTAACAGCTCCTGCAGATTAGTGATCAAATACGATACATGACTGCATATAGCGTGTTCGTGTACTTGGATAACTAATGCTCACCTCTGGACGCATCCCATTCCATGGACCAAAAGCATTACCACAGAAATTGGGCACGATGTGCGACGGATGCATCTGATTTGGGCTTGCAGGTTGCGACCTCTCGAAGTCCCCTACGCCGGGTTGCCGAAACATCCCAGACACTCGCATTATCTCTTGATTCAACAGCCTGCTGCAGATTGGGAGCACCTGCATGAACGGCCCCAGCTTCTGATGCTCCTGCAACAACTCCGCCAAGTACTGCCCGCCGCTGGCAGCGTCGGGCGGGACGGGGGGCCTGACCTGCGGCGACATGGCCCGCCCGGGAGAGAAGCAGCCGTCCGTACCGTGCAGCCCGTCCATGGCGATGGCGGCGGCGGCGGCGGCGGCCCCAGCCACCCCTCGGATTGGGGAGGAGGAAACCAAAGAAGGGACGGGACGAGGGGGAGGACGGGGGTGGAGTCGAGTCGAGTCGAGTCGGGGAGGGGGAGAGACGAGAGAGAGGTGTT

Coding Potentia
Explanation CPC Score
noncoding -1.07079
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0315100.2 5 23673505 T C
Osa05LNT0315100.2 5 23675123 G A
Osa05LNT0315100.2 5 23675245 A G
Osa05LNT0315100.2 5 23675313 A C
Osa05LNT0315100.2 5 23676036 C T
Osa05LNT0315100.2 5 23676044 C T
Osa05LNT0315100.2 5 23673829 A 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
Osa05LNT0315100.2 osa-miR5815 Translation 3.0 15.901 1 24
Osa05LNT0315100.2 osa-miR5816 Translation 5.0 22.146 1 24
Osa05LNT0315100.2 osa-miR169d Cleavage 4.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169e Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169f.1 Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169g Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169h Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169i-5p.1 Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169j Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169k Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169l Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR169m Cleavage 5.0 12.619 1 21
Osa05LNT0315100.2 osa-miR395w Cleavage 5.0 14.622 1 22
Osa05LNT0315100.2 osa-miR1320-5p Cleavage 4.0 8.101 1 21
Osa05LNT0315100.2 osa-miR2877 Translation 5.0 21.046 1 24
Osa05LNT0315100.2 osa-miR2922 Cleavage 4.0 15.911 1 20
Osa05LNT0315100.2 osa-miR2928 Translation 5.0 17.196 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0315100.2 5 qRFC-5 Physiological trait Eating quality RG470 RG474
Osa05LNT0315100.2 5 Eui Morphological trait Dwarf nan nan
Osa05LNT0315100.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0315100.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0315100.2 5 nan Resistance or Tolerance Drought tolerance C43 RZ70
Osa05LNT0315100.2 5 nan Resistance or Tolerance Drought tolerance C43 RZ70
Osa05LNT0315100.2 5 APAGE1 Physiological trait Eating quality nan nan
Osa05LNT0315100.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0315100.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0315100.2 5 QFla5 Morphological trait Culm/leaf RG470 RG346
Osa05LNT0315100.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0315100.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0315100.2 5 nan Physiological trait Eating quality RM163 RM31
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