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

>Osa03LNT0194100.2

GAAATAATGCACTTCATATCTGAATAAATGAACCGGACGGTACAAATGTACAATGACGCCAGGCTCCAGCAGTATATGCAACTTCTGTTTACCAGAAGGAAAAGTAAGAAAACATATGCTCCGCGAGTTCTATACTTGTTCATGGTGTCATAGCAACGTTCCAGTTGTACACCTTTACATCGAAGGTGGCAGAATTCTCGAGTGCTTGTCTGAGTTCTTTGGCAGAGTTAAGATTCTTTCCAAGCATCAACGCAAAGCCGCCCCCACCAGCTCCAACAAGCTTGTAGCCGCAGCAGTAAGGGTCAGCAAATGCAAACAATTCGTCCACAAGCTTGTTGCTGCAAAAAGGATCTAGCTCCTGATGCAGCCTCCAGGCCTCCGACATTATGCCACCAAGCTCGTCTATTTCACCATTCATCAGGGCTTCCCTTCCAATTTTCGCCAACTCAGCAAGCCTCTTGATGCTAGATATCAACAGGCTATCACGGCGGAGATATCGAGTGACAACTTTCTGCAGGACCCGGTGGGCAAGCCTTACTTGACCAGTGAACACAACCAGGAGACGTTGTTGTAATTCTTGAATCAACTGCGGAGATGCCAGCAATGGAACAACATGCAAACGCAATGGCTGTCCTGGAAAACTCTGAGTGCACTTGATTCCAGGATATAGGCCACCAATTTGATCTTGCCATCCACCGCCTGTGCCCATTACTTGCTCTACTACCAGCACAGCTCTAGCAACAGTTGCATCACTTTCATCACCTTCTATAAGTTGGAATAGCCCCTTAACTACCGCAGCTGCTAATATGCTAGAAGTTCCCAGACCACTTCCACGAGGAACATTTGCCCATGTCCTAATGTTCAACCCTAATTTTGACAATCTTTCATGGTTTAGGACACCAGTCACAATAAGAGCAGACTTGACTAAACGGAATGAATCATTTTCTTTGAATGGTGAAGTAATAGAAGACAGGTCATCAATACAAACATTTCTGCCAGCATCATCTTCAATGAGAACTCCAAGGTGGTCCATTGTTGTCTCTATCATAGCACCAACTGGAAGGTTCCCTTCCAACCGTATTGCCATATTCAAAACACAACCTGGACGCTCCAAACTCCATGGAGGTGTATCACTCCAACCCCCGACAAAGTCGACACGGACCGGTAATTCCACAATAGCCTTCTTAGGATGCAGGTTACCATTACTTGAACACTTGGAATCGCTTGATGGCTCTACAAAATCATACATATGTGTTAACTAGATTGATATAAACATCAATATTGATAATGGTAAAATGAACCACATTTAGCTCGTTGCCTGGAAGACATAACTGCATTTTGAGAAAAGCGACAGAAAAAATAGCATTAAGTTTGTTGGTAGTGTACAGACTGTACCTTTAGATCCATATTTTATAGCTGATGCAGTTTCACTTGCTATGGAAGCCCACACTTTATCTTCAACAATAGCTGCAGTGGAAAGATCTCCAGAAGCTGTAAGCAGATCCATTTTGACCTGGTATCTTCTGCTCTGCGGAAGAACACCAGAATACTGATCCCCATGACTGGGACAAAGCGAAAGTAACTCATTACAGACTTCTACGCATGAATTTTCCTTTTGTAGCATTTCCTCACATAGTTGAAACAGGTTGCGCCCAAGCAAGCCATAGGTCATGCAAGCTTTAGCAATGTTGGTTGCTAGATCTGCTTGATGCTTGCTTGAATTCACACAGAGCTGATGGTAGTCAATCGAACGATGCAGCTCTTCTAAGCTGATCCTCCGTGATTCTTTCCACAGGGAAGCGACTTTGCCATCCAGGTCACATGTCGATCCCATAAGCCACATACCTACTTTCAGCGTTTCAGGTAGAGACATGACTGGAAAAAGCTTTGCATTCCATAAGCAGTTGTCTTCATTGGTTGAGCTCCACAGATCTGTATCCTGGATTTTAAGATGTTCCAAGACATTTCTCCATGGTTTGCCACAGAATGTCCCATCTTTCTTCATAGATACTTTTGGATTATCATGAAGGCCACAGTAAACCATTACTCTTTCCACAGAGTTTACCAAAGGGACTTCCCAGAGGCAATGTCGATCAGGTAATGTGAAGTATGAGCTAGTACTGATTATCTGAGACCTGTTCCCATGTAACTCATGTATATTCACCCCAACAACAATACATTGTGAGCCAATCCTAATTCTACCTGAAAGTGATGAATCATAGACCAATGAATCCTCTCCAACTGAGACCCCAGCAGAAATTTTACTGGACAAAATGACAGCTGTTGCCGCAATATCACAAGCAGTAGTCTCTGGTATCGAAGACATGTGCCTTCGCCCTACAAGTCCTGAATATGAGCCCGCCAAGTGATCAAGAACTTCAGCGGATGTGCCAAAATGTAAAAATGAGAAATCATATGAACAAAAGCTGAACATCCTGTGCTTTCCCAAAGCAGCAATTAGTTCCATGCCAAATGGACGGGTCCTTAACCATTCATGCCTGGAAGGCACCCATGCAGCAACAAGATCTTCGTATAAGCTCATCTCTTTTCTGCCAGTTATGAGCTCCTTGATCATGACATGGCTAGATGAATATGCAAGTCTAACAAGCTCCTGCCATGCTTTACCCCTGGCTGATATTATCCCTGTGTCAAGCAGTGCTCTCCCGTCATCTCGAATAGCCTGGCCCTCCACAAGCTCGTGCACTGTAGGCTTCTGGAGGAGATTATCAACCAAACACAGGGAATAGTTCTCCCCATCAGTTCCGTCCTTTGCCGCTACAACTACACCATGATTAGCAGCCACATCTAGAGTTGTTGGCACGGTGACGATGCAAGCAGCATCATCAGGAAGAACTAGGTTTGAAGCATCGAAGCATGGGAGAACATCCCCGGTCATTATGAAGATCCCACCTGATCATACTTGCGCTGGATGAGATCGCGAGAATGTGGTCGAAAAGCAGCGGAACAGGTCCATCAGGATTGTCTCCGGCCAAGTAAGGCAGAGGCAGGAAGGCCTTCCCCATGGGGTTCGCCCATGGAACCCTCTTGCTATCACCCCCAGCGTGAAGCAGCAGTACGTGTTTGTTCGCCATGAATCGTACCACCGAGCTGAGTGGGATGTCATCTGCTGAAGAATCACTTGCTTCGGGCAGCAATTCGGCGATCTCTTCCTTGGAAGCCTGGGCGATGAGATGGCGGACGAGGGAGGCGACGGCGTGGAGAGTGGCGGCGCCGGAGCCGATGCGCGCGGCGTCGGGGTCGGGGACGGCGAGGGCGGCGGTGGAGGCCGGGAAGCGGCCGAGGCGGCGGGCGCGCGCAAGCTGGCGGTCGTAGAGCGCGGCCTGCTCGGGGCTGGCCGCGGTGAGGACGACGGCGTCCCACGGCGGCACCCGCGACGGATCCCGCGCCGATAGCCGCAGCCGGCACCACGCCTTCCGCAGCACCGCCGCCGCCTCGTCCGCCGTGTGCGCCCTCCGCCGCCGCCGCCGGTGACGCTCGGCCGGCTCCATCGATCGAGCGACTTTTGCTCCTCGACTCTTATCTAGATCGGAGAATTTGGCCGTTGAAAGAAAGAAAGAAATATCTCGTCTAGACACCGACGCGACTCCACTCCACTGATCCACTCTACTGCCTTGCTTAGCCCTCGACGACTTGGCCAGTCTTCTCTTCCCGCTGCTACCGATGGCGATAGCGTTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.958196
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0194100.2 3 855083 C T
Osa03LNT0194100.2 3 855210 A C
Osa03LNT0194100.2 3 853403 A G
Osa03LNT0194100.2 3 854763 T C
Osa03LNT0194100.2 3 855432 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
Osa03LNT0194100.2 osa-miR5537 Cleavage 3.5 12.948 1 22
Osa03LNT0194100.2 osa-miR156a Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156b-5p Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156c-5p Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156d Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156e Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156f-5p Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156g-5p Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156h-5p Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156i Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR156j-5p Cleavage 5.0 18.185 1 20
Osa03LNT0194100.2 osa-miR172a Cleavage 5.0 17.373 1 21
Osa03LNT0194100.2 osa-miR172d-3p Cleavage 5.0 17.373 1 21
Osa03LNT0194100.2 osa-miR1861n Cleavage 4.5 15.297 1 22
Osa03LNT0194100.2 osa-miR2055 Translation 4.5 17.03 1 21
Osa03LNT0194100.2 osa-miR2876-5p Cleavage 5.0 14.726 1 21
Osa03LNT0194100.2 osa-miR2929 Cleavage 5.0 12.392 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0194100.2 3 qST3-2 Physiological trait Eating quality nan nan
Osa03LNT0194100.2 3 nan Resistance or Tolerance Other soil stress tolerance R1468A R1468B
Osa03LNT0194100.2 3 qZNT-3 Resistance or Tolerance Other soil stress tolerance R1468B C515
Osa03LNT0194100.2 3 qtl3.1 Resistance or Tolerance Drought tolerance RM7332 RM545
Osa03LNT0194100.2 3 nan Morphological trait Root RG104 RG348
Osa03LNT0194100.2 3 qRDW3-1 Resistance or Tolerance Drought tolerance RG348 RG104
Osa03LNT0194100.2 3 nan Morphological trait Root RG104 RG348
Osa03LNT0194100.2 3 qRTV3-1 Resistance or Tolerance Drought tolerance RG104 RG348
Osa03LNT0194100.2 3 dth3.1 Resistance or Tolerance Drought tolerance RG104 RZ329
Osa03LNT0194100.2 3 nan Resistance or Tolerance Drought tolerance RG104 RG348
Osa03LNT0194100.2 3 nan Resistance or Tolerance Drought tolerance RG104 RG348
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