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

>Osa11LNT0102700.3

GATCCGAATGAGGCCACATAAATATCTATATGAGTCTTTCAAACCCCATTTAGTTTTAAAGGGGAGATTCATGAGCTAGCAATTATATATACATTTCTCAAAATCTTACCCCTCAAAATTTCACTTGACATGCTGATGGCTTTGATCACATGCGGACATGCCCACATATAACTTAGGTAATGAACTCAAAATTTGAGACAGAATACAGATGAATGTTTTGTACATCGCACGGGTTGTGAAAAGAGGGTGTAGAGAGCTATAAAATTCACCTCTGACCTCTTCGTTCCCAGCTTCCCAAAAAACCAGAAGATGTTGGAGTATGCCACAGCTAAACCATGTGTTTCCAAGAGTATAGCATAGCAAACTCCAACTTGAAGAACGGTCATTGGCCTCGAGGATACTGACCCACTCAAATCTGAGCAGCTACTAGTCTGCAGAGTGACCTTGTCCCTTGCAGCCGCTATGCAAAAGGAGAAACAGACTCCAAACCAGGTCTTTTGCATAATAGGCACCAAACGACCTCCTAATCCCGCTAAAAGATAACGGATGGAATATGTGGAGATCAAACCTTTGGTATCAGCATTGTGATATACCCGTAACGCCAGACAGAAGCTCCACACGGTCTCTCTTTAGATCCTCATGTGAGCAGTGAGCTCTCCGGGATCATTGACAGCTCCAAAATCAACACTATTAATCGCGGCAGTTCCATCCGCATGAGGTAGTTTCATCAAACACGTTATGAAGGGCAGGGCATGGGGGCATTCCGATGGCTTTCTGCAAAGTCCCTGACAATACGCTTAAGGGTTCTTCCGCCTTTCCCTTGCATGTAAGCATGGTTGTTTCTGACATTATCACCAGTCCTACTGTGAAGATAGTCTGAGGCTGCATCATGAAGTACGCTGAGCCATAAAGGAACTATCATCTCAGCTTCCCCTTGCCTTAGGTACTCTGAGGGCATAGATTTCACCGCTGATTGCAGCCATCGACAAAGGGAATCCCAAGAAATAATGGCCTTCCACGTTGTTCTCTCACAGAGGCTGCACACTGCTGCCAACTGCTGCAATATTGTTGCAGATTTATGCACCTGTTGGAAAGAAAGAAATGTGAATATCATGCAAAGTCTCTATGGCCATATATCCTGCCCTCTGAGTGGACCATATTTATAAAAGAATCAAATCATAGATATGATCAATGGTACTAAACTGGAAAAGCAACAGAAAGTAAACTTTAAGCAAGTAATCATTATGGTCAGGGTGCAAACATAAGCGAGGGAAAAGGTAAAAAGATGGCCTTTGAAGCACAAGCATAGGAGCAATTGTGTGGAAGCAATGGTACGATGGTGCTCTTTGAAACTGTACCCACCCTTGACAAGGCCGATACACCAAGTAGAGCATAAAGTACATTTGACATGAGACCTTCACCGCAGCGTGCCAAAATTTGAGCTAGCACCACACCAGGTGATCCATCAGAGGGGTGCTCTCGAGATTCTAGTGCAGCAGCGAGGCTAACATCAAGAAAACCTACATGTGTCATGGCAAATGATCAAATGAGCACAAAAATATACTAGGTGCTACACGATGTTTCAAGTGCAATAGCTTGAGCTGAATGCTGAAGCATATGTCACAGTAACAGATTAAGGTATGTAAACGGTATGAACAGTGCAGCAAGTACAAATAGATCTTTTAACTCCAAAGGGATTATAAGTGTGATGAAAAGAATAACGCTTTCTACCACCAACTCACATTACAGTGATACACTAGTTCCAACAGACATAATAATGTAACAAACCTTATCCAGAAAGTAGCTGAAAAGGCATCCATGACTTTGCAGGGGAAAAACACTAACTTGACATGATTGCTTACCAGTAGACCACAATCCAAGCATTATTTTTCTTTGCATATACTTTATCTTCTCAGGGGAATAAATTTCTTTAAATTAAAAAACCAACAGGCCCAATAGGACATTATCCTTTTTGCTGAAATGAATGAGCAGTATGCATTCATTGTTTCCCCTTTATGCAACTGGCTAATTTACTAACATTCCATGACAAAAAAACAAATGCTCTAAGAAAAAAGGTGTTCAATTGATAAAGAAAAAAATATATACATAAAGGTGGATAGATATCCTCACATGACATATATGACATCGCAGCAAGTGCTGCTCCTCGGTGCATTGCTGTAGAGCATATAGCTGCCTTTTGAAATGACAACTCAAGCAGGGAGCCAGATGCGACAATAGCTTCCTTTGGGCAGCAGCGAATAAATGTGGATGTAAAGTTTGCATAGGCTTCAACAAGATCAGGTTCTTGATCACATGTGTAAGAAGAATTCAAAGTAGATATTGAAGCTGCGGAGCTAAGTGCTTCGAAAGTTCTGACACATAAAGCAACATATTCTTCCTTGTGACCAAATTCTTCAATAACACTGGCAGCTGTTCTTAAGAAGCAGTCATGCCTTTGAAACAGTAAGAAATTTGTTGATAAGCATTCCAGAACTTTAGGTAACAAAATCTGGAAGTGTTGTCCACAAGAATGTATGGCTGAAGAAAGAGAACGACATGCAGCTGCAGATAAACTAACATTCTCCATATGAGATGATCGGGAAAGTCTTTCAAGAAGTGGCCAGAATATACCAAGAAGAACCAAAACCGTGTCATCATCAATCAGACTAGATGTAATTGATGTCGCCAAATGGCCAAATAGAGCACCCATCCTGTAGAGACCATGGACAGCAAGGTTCAATGCTTCTGTGTAAGCAGCTGGATTTTGACGCAGAGATTGATCTCTGTCTATGTCAATAAGCTTCTCCACTGCTGTGTAGCTGGAACAAAGTAACCTTGCTAGTGAACTTTTCCTTAACTCTTTGTCAAGAACAGAACATAAAGCATGTGTAATTGCAGTAATGATCTCTTCCTCATCCTCTATTCGCAGATTCCCCGCATCCATGCCCTCACTGATCCAGAAAAGAATTTCCAGATTCTGAGGCTCGTTCATGAATGAAGAACCATCCTCACAAAGTTTACGCAAAGCTAATGAGCAAGCATTTGATGATATGGATTTTGAAATCCCTGAAGCACAGAACAGGAGTAATGGTTTAATATTACTTTGAGAGGATGCCAACAACTTTGAGTAAGAACCAATGACATCACCAAATGATTTGTATACCAAGGATAGGCATCCATTAAGTTCGCTGTGTGCTCTGCTGGACAGAATGTTCACAAAATGCATTATGATTGAAAAATCGAAGGGGCTTCCATCTTGTAAAATTGTGTCAGCGACCATGCTAAGTGCATACATTCGAACTTCTACCTCTTTCCAAGGAATTGATTGGCTAGCCAAACCCCATCCACCAGAAAAAAGCTTATTAATATATGCAGGAGCACCTAGAAGCAAGCAAATATCAACAAGAAGCTCCTCCAAGTTCATTCTGAACTGTGCTAGTCCATCAGGTATGCATAATTCCCCATCAGTGCCATGTTCATCAGTGTCAATCTGAGCACGAAAAAGAAGTGCATCAAGCAGTGAAGAAAACACAGGGGAAAATATCTCTTGTGCAGCATTCCTTTTTTCTGTTTGTGCATCACTATCAAGTATAAAATGTGCTAAACTGCACCAAAATTGCAAGGTTGAATCTGCAATCTCCCAATCATCACTAGAAAAGGCTACACATCACAAACAATTCAATAGATTGACCTCAAAAGTGCATCGGCAAGAGCAAGTGCTTGAACACTCCCTTCTGCAACCAAAGCAGGTGCTGCCTGACCAACTTCACACATCAAACAAACAAGACCAGCAATAGTCTTCTCGCTTCTGTTGGCAAGAGCTGGCAGAAGAAGAGCTTCTCTAATATATGGCATTTTACTTAGAAATGCCTGAGGTAGATCTTGGTGATGACTGACAAGCTCGGTCATAACCTCTACGGCCACATCAAACGAGAAGGACACCTGCAGCGAGTTGAACGCGAAGGTGAGAAGTGGGTGAGCCGCGAGCGCCGCCGCCGGCATCTCCGAGAAGCATCCCACGCGGACCCAGCTCAGTAGGCAGCGCAGGATTCTGCGGTTGCGCTCGTGGAGGGGGACCCCGTCGGCGGCGGCGGCGGTGTTCTCGGATTGGGCGAGGAGGAACTCGAGCACGGCGGGCGCGTGCGCCATGAGCTCGCGGGTGAACCTGCAGCGCGCCGCGGCGTCCACCCCGGTGTCCCCGCTCTGGTCCTGCACGACCTCCTCGGGGAGCACAGTGAGCAGCTCCATCACGGCGGGGTCGGGGAGGTGCCGCATCCGCGCGAAGAGGCCGTCCACCCCGCCCTCGGCGCGGAGCGCCAGCGCCGCGAGCGCCAGGGAGATCTGCGTGAGCAGCCGCGGCGGGCCGAGGCAGAACCGCCCCGCCGCGAGGAGGAGCGCGTCGAGGAGGTGGGCAACCTCCTGCGGCGTGGGGCAACCACCGGCGGCGGCGGGGGGGCACTGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.755206
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0102700.3 11 19971783 C T
Osa11LNT0102700.3 11 19972281 C A
Osa11LNT0102700.3 11 19973109 C T
Osa11LNT0102700.3 11 19971074 C T
Osa11LNT0102700.3 11 19971959 A C
Osa11LNT0102700.3 11 19972020 G A
Osa11LNT0102700.3 11 19972180 T C
Osa11LNT0102700.3 11 19973248 A T
Osa11LNT0102700.3 11 19973305 G A
Osa11LNT0102700.3 11 19973533 G A
Osa11LNT0102700.3 11 19973858 G A
Osa11LNT0102700.3 11 19974425 T C
Osa11LNT0102700.3 11 19974510 A T
Osa11LNT0102700.3 11 19975159 C A
Osa11LNT0102700.3 11 19975738 A G
Osa11LNT0102700.3 11 19975870 C A
Osa11LNT0102700.3 11 19976366 G A
Osa11LNT0102700.3 11 19976804 T C
Osa11LNT0102700.3 11 19977399 G A
Osa11LNT0102700.3 11 19977432 A C
Osa11LNT0102700.3 11 19977469 A G
Osa11LNT0102700.3 11 19977895 A G
Osa11LNT0102700.3 11 19978055 A G
Osa11LNT0102700.3 11 19978679 T A
Osa11LNT0102700.3 11 19978741 C T
Osa11LNT0102700.3 11 19979453 C T
Osa11LNT0102700.3 11 19979915 A G
Osa11LNT0102700.3 11 19980411 A T
Osa11LNT0102700.3 11 19980926 C T
Osa11LNT0102700.3 11 19980967 C T
Osa11LNT0102700.3 11 19981234 T C
Osa11LNT0102700.3 11 19981248 T C
Osa11LNT0102700.3 11 19981268 T C
Osa11LNT0102700.3 11 19981526 A C
Osa11LNT0102700.3 11 19981578 A T
Osa11LNT0102700.3 11 19981832 A T
Osa11LNT0102700.3 11 19982340 G A
Osa11LNT0102700.3 11 19983001 T C
Osa11LNT0102700.3 11 19977899 A G
Osa11LNT0102700.3 11 19983313 T G
Osa11LNT0102700.3 11 19972194 A T
Osa11LNT0102700.3 11 19982097 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
Osa11LNT0102700.3 osa-miR5788 Translation 4.0 20.473 1 21
Osa11LNT0102700.3 osa-miR5079b Cleavage 5.0 14.963 1 22
Osa11LNT0102700.3 osa-miR395b Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395e Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395g Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395i Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395l Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395t Cleavage 4.0 21.801 1 21
Osa11LNT0102700.3 osa-miR160e-3p Translation 4.0 21.405 1 21
Osa11LNT0102700.3 osa-miR395m Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395n Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395p Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395q Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR1425-3p Cleavage 5.0 20.365 1 21
Osa11LNT0102700.3 osa-miR1435 Cleavage 4.5 21.415 1 20
Osa11LNT0102700.3 osa-miR1866-5p Cleavage 4.0 19.486 1 24
Osa11LNT0102700.3 osa-miR2091-3p Translation 5.0 18.985 1 22
Osa11LNT0102700.3 osa-miR2098-3p Translation 5.0 20.449 1 20
Osa11LNT0102700.3 osa-miR2098-3p Cleavage 5.0 16.033 1 20
Osa11LNT0102700.3 osa-miR2275a Translation 5.0 21.513 1 22
Osa11LNT0102700.3 osa-miR2275b Translation 5.0 21.513 1 22
Osa11LNT0102700.3 osa-miR395y Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR5079a Cleavage 5.0 14.963 1 22
Osa11LNT0102700.3 osa-miR5161 Translation 3.0 11.928 1 20
Osa11LNT0102700.3 osa-miR5486 Cleavage 5.0 13.095 1 21
Osa11LNT0102700.3 osa-miR5498 Translation 4.0 23.399 1 21
Osa11LNT0102700.3 osa-miR5508 Translation 5.0 21.425 1 21
Osa11LNT0102700.3 osa-miR5515 Cleavage 3.5 24.177 1 21
Osa11LNT0102700.3 osa-miR395d Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395h Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395j Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395k Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395s Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395c Cleavage 4.5 21.801 1 21
Osa11LNT0102700.3 osa-miR395o Cleavage 4.0 21.801 1 21
Osa11LNT0102700.3 osa-miR395r Cleavage 4.5 21.801 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0102700.3 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0102700.3 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0102700.3 11 gw11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0102700.3 11 gpl11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0102700.3 11 yld11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0102700.3 11 nan Morphological trait Seed RM332 RM229
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