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

>Osa02LNT0178300.1

GGGAAGGAGACAGTACATCACTTAAGATAACATGATGTGCATATATATAGTTTTACTTCTAAAGGTAAAAATTAGAGGCAGGACAAAAGCTTCTTAATTACAAGGTTTTATAGATGCAGAAGAAATGGGCATAGGTTAATTCAGAAACTTGAATTGTCAGTACGAGACACGGTGATAACCTGCCAACCTTCTCACTGAGACTGCTGCCACGTTATTCGGTGATGGGCGATTGGTCCATGAAAGGTGCCTGTCACAACTCGCACGGAGTAAGCAGCACCCGGCTTCTTGCGCATCAAGAGCATCACTCTGTCCTAATAGTGTTCTTTCGTAGTGGTAAACACGCAAACACCGGAAACTCGAGCATCTCTGTGTACCAGCCTTGTGCTTCTGCAAAACCCGTCGCACGCTCAGCAGCCTGCTTGATATGATTCTGGAAATGATATGGACGTGCTGCTTAGTCTGCTGATAGTATGTCTTCCAGATGGTGAAGATCTAAGCTGACTTTTTTCATCAACTTTACTTTACCATGACCATGTCAGGTAACTTATCATTACAAAATGAAGCCATGGGAAATCACACAGCTATGGCCGACGAGGGAGGAATATTCTCAGAAACAGTAAGAAGAGCTACTTTGCTCCATGGTCTTCTTCCACTTGAGTGGGTCAGTTGACTGTGTCTCAGTGTCATGAATCCCTCTGCTGTTTAGTTCCCTGCTTACTGCACCACCTTGTCTTGTTTACTCTTTGTTCTCTTGCTGCTCGGCCAACAATGGAGCAGAGACTGCATTTGCAGGGCCATTGAACAAAGAGCTCGCCCTAGGGTTGGTGAGTGACGGTGATGGCTTTGGTGGTAGTGGGCTTGGGGACAAAGGCTTCAAGAATGCAATTCATTGCTTCCTGACGCTTTGCGTCACATAAGATGATGTGTGAATGCCAGGAAAGTATCAGCCTGAAATCTTAATTGAGGATAAGGCATCTCTTCCCAGTGAGGTACTCCGGTAAAAATGCAAATAAACTGTTGATTAAAATACTTTAGTATCTTCATTAGCATGACAAATAGATGTAGAACTATAGGGTAATATGCTAAGAAACCTAGGGAGATGAAATTTCCAAGACAAAACTGAAAGGGAAAGCTACAGAATGAGACCGGTGACTAAAGCAGACAGTTTTTTTTTTATCAGGGTAACAAAACGGGCATCATATGTAGTATAACAGATATCTCAAATACAGAAAGTAACATATGAGCAAATATATAGCATACTGATGTAACTCAATATGTACTCTGTGATTTTCTTTCCTTCGCAAAGCAGTAGTTTACATGTTCCAGCAAGAGAAGAAAGTGGCACTTACAGCTACAGGAGCGCCCCAATAACAGAGTGATTTCACACTATATTCAAGTCAGCAAATTGTTAGCTTGGACTGAGAATTACTGCTGTACAAAATGCTGGGCTGCTGGCACAGTTTTTTTAATACATAATCATGGATATGAGAAGGTTATAAGCACTAGGCTAGTGCAAATTTAAAAAGGAATACATGAAAAATAGCACTCATATTCAAAACTAAGATTAGCAATGAGCCCATGATATGAATAAATACTCAAATTAGCTATTGACAAGAACTCACAATGGATCACACCTTGGCACGTGTAAAAGGGGCATAGTGGAGTATAAGCTTAAAATGTGTCCCATCACAAGCAGCATGCCTCAAATAGCCTTTCTTCAAATCAATAATATCCTGGGGACCCGCACAGATTATAGAACAAAATAAAGACGAGCTTGAAATTTAATAACAGGACTTCAGTGGAAACTGGGATTGCTCATAACACTTGTCAGCATATGATCATCTGGTCCACACTCAAATGGTTGAGCAAATGGCCTCCAATCAGTAACACTAAATAAATACAAATAATTTATTTCCTGTGCTTTAGACTTGCCACAGCGGTGGTTCCTGCTGACAATTATGTGAACTCCACTTCCACTATTTAATTCTCAGAAAACTCATCCCTGATCACTTGCCTGATCTGACCCAAAAAAACTGGTAATCTTAGCAGTTAAATTAAGAGGAGGAGGAAGCGTGCCCTAATAATACTCAGTAACCTAATTGTCATCTGGGATCAGCTGACTGAAATTGGTTGTCTCATCGAGCTAAAGGAATGTTGTGAAAGGAACAGCAGGCACTTTTCGTCAGGTTCTTGTTTATAAGGGGATGACTAACTTTGGATATCATCGAACAAAGAATATGGTTTCCAATGCCGCCACCCTGTCTCCATTCGTGCAGTACACCAAGTCTGCACTCTGGGTAGCTAACTACACAAGCATGGACTGGAGAAATTTCCTTTCGCGTGCTCAAAGTTAGCAGTGTCAAATAGCAATTAGGTTGAGATGTCAACCCAAGTGCGGTGGCAAAGTTTTCAACTTGAGCTTTGACAAGAGACAGGAAGAATAACCAGTCGTATCCTATCCATGTATTTACAACATGCTTAAGATTTAAGAAGACCATAAACAAGCATTGCAGGGGCATCACGCCTACACATAAAGTTTTTCAAGTGGTTATATATAATATCTAAAGGAATGACTACACACGGACCCTCCACCTTTAGGAAAGGGAGAGAGACAAAACAAGGATAGGCAGCATTAAGCACGCGCATCACATATTCTAATAGAAGAGGAAAAGCACACCAGGAGGAGGCTCTGTGTACGGTGAACTTAATGACAGGCAATTGAAGGAGTAGCTTTGTTTACTCCAAGTTGACTCTCAGTGAAATGTGTCAACCACTAGAATAATATAAGAAAAGAAGCTTGGAGGCAAGGACAGACAGCTCATTCTCCCTCAATTTGAAAGATGTCGAGCGTGAAGCTTCCCCACTAACGACCTTAGTAGGTTGGTGGAGGATGACAGCGATCAGTGAAAATAGCATTTTGCAATGAGAAAAATAGCTGACCTCTAGAGACAACCGTGTGATAATACTGCATTCATGCATGACAAACTATGAGATGGATGTAAGCAGAGTTTTGGACTCTTCTTGAGCCTCCAAATCTCTTCCTGTCGTGACATGCTCACAGGTACAAGATCACTCTGGTTAAGTCAAAGACGTTAAGCACTTGGAATAGGAAGATGGTCAAAAGAAGAGTCATGTCTCTTGAAAGGTCTCACGGTGGATATCATGCTACACACTTACACCGAGGTCACTATACAAATTGGTGCAGGAGCTAGTGACTTCATCACCAACTGTAGTTAGCTTAGAGCCTAGAGGTGAATTTGACTACAGGACAAAATAGTAATTCATACATTATTAGAAATGTCAGTTCATAAATATGAAAAGATACTCCGGATGGACATGTTGAGACATATACAGAATACAAAATAAAATATGTGGATGCAGATTTACTGAGTCACTAATGATAACTGAAGATATAAAATATGACAGAACTAGAAAAGGACAGAGGAATAAAAGGTTACCTGGACACAGCAGTATGCTGTAGCTCTTTTGTAGCCAGCTCAAATGCATCCTCTGGAGTCAAGAACATCTCAATGTACCTAAAAATGGTTTCAGACATATCGATATTCTTCTTAAAAGAGGGCAATGGTGGTGGCAGATTCACTGCCTCCACCTCACCAAGTATAGTAACTTCTTATTTACCATCTACTCCATCATGTTTTATACCAACTACCCCATGTACTTTTATGTTATAAAATAATCCCTTTACATATATGATTATATCATATTTCACCTGTACAATATAACATCTACAGGTACAAAATTGTCCCAAAAACCTCACTATTAATTTGTTTTAATCCGTAGCAAAGCATGGGTATCTGGCTAGTTATAAACTAAAGTTGATGCAGATAGTAAAAGATACTATATGCAGATTCATTTGGCAAAGAATATGCATTAATATTAGAGGCAATCAAGAAGATTTACAGTGTCAAAAGGGCCCTAACATTGATCAAATATATAGTATTTGACATTTAAGTGCAACTGCATGATTAGTCCTCCACAGTTGAGAATCTAGGCTTAGGTTACAACGTTCAGTTGGAACTTGGAAGTGTCTGATGACTGATGGCATACAAAACAAATACTCTTAATCTTCATAGGATCCAAAGAGCAAGTCAGAATTCCGACTCCATACTTGTTCTTTTTTCCACCGGCCCAGCAAAGGAGTTTTTTTTTCAATGCTTTCATACTGCTCACCTCACTTGCCGCAGCCGCCGCCCGGGGTACCTCGCGCGGCTGCGCCTTTGGGTGGCGCCGCGGGAGGAACCTGGACTCGGTGGGAGCCACTGGTCGACGGCCGGTCGGCTGCTCGTCCGGCACCGTCGGCGCGGCGCAACTGTGC

Coding Potentia
Explanation CPC Score
noncoding -1.17507
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0178300.1 2 27274435 T G
Osa02LNT0178300.1 2 27273681 T A
Osa02LNT0178300.1 2 27273421 G A
Osa02LNT0178300.1 2 27273528 T C
Osa02LNT0178300.1 2 27276137 G A
Osa02LNT0178300.1 2 27276682 C T
Osa02LNT0178300.1 2 27277474 C T
Osa02LNT0178300.1 2 27278531 G A
Osa02LNT0178300.1 2 27278757 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
Osa02LNT0178300.1 osa-miR5544 Cleavage 5.0 18.098 1 22
Osa02LNT0178300.1 osa-miR5837.2 Cleavage 4.5 20.673 1 21
Osa02LNT0178300.1 osa-miR5512b Cleavage 5.0 16.031 1 21
Osa02LNT0178300.1 osa-miR395u Translation 4.5 22.603 1 21
Osa02LNT0178300.1 osa-miR399e Cleavage 4.5 21.347 1 21
Osa02LNT0178300.1 osa-miR399f Cleavage 4.5 21.347 1 21
Osa02LNT0178300.1 osa-miR399g Cleavage 4.5 21.347 1 21
Osa02LNT0178300.1 osa-miR399k Cleavage 4.0 21.347 1 21
Osa02LNT0178300.1 osa-miR319a-3p Cleavage 4.5 23.652 1 21
Osa02LNT0178300.1 osa-miR171i-3p Translation 5.0 9.046 1 21
Osa02LNT0178300.1 osa-miR1429-3p Cleavage 5.0 19.418 1 21
Osa02LNT0178300.1 osa-miR1849 Translation 5.0 14.592 1 21
Osa02LNT0178300.1 osa-miR1850.3 Cleavage 5.0 17.79 1 22
Osa02LNT0178300.1 osa-miR1854-3p Translation 4.5 19.225 1 22
Osa02LNT0178300.1 osa-miR1857-5p Translation 5.0 15.522 1 21
Osa02LNT0178300.1 osa-miR1857-5p Cleavage 4.5 11.603 1 21
Osa02LNT0178300.1 osa-miR2863a Cleavage 4.5 12.958 1 21
Osa02LNT0178300.1 osa-miR3979-5p Translation 3.5 18.143 1 20
Osa02LNT0178300.1 osa-miR5144-5p Cleavage 5.0 13.917 1 21
Osa02LNT0178300.1 osa-miR5499 Cleavage 4.0 16.116 1 21
Osa02LNT0178300.1 osa-miR5503 Cleavage 5.0 15.567 1 22
Osa02LNT0178300.1 osa-miR5510 Cleavage 4.5 22.743 1 21
Osa02LNT0178300.1 osa-miR5512a Cleavage 5.0 16.031 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0178300.1 2 T2-2tiller Morphological trait Culm/leaf C424 C747
Osa02LNT0178300.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0178300.1 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0178300.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0178300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0178300.1 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0178300.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0178300.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0178300.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0178300.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178300.1 2 nan Physiological trait Eating quality nan nan
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