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

>Osa04LNT0267900.2

TCTGCAGCTGCAAATTTTCCATTCAATGTGACCATAGCTGGCTGGTTGCAGCAGATTGGGCACCAACTTTATAACTGCCAATAACAAACAATATAGCTTGACAAACAAATAATAACACATCCTGTATGTGAAAATTTCAATCTTGGACCAAAATATATGTTGTACTACAAATAATAAACATTAAACAGGTCTGATAAATCAGAGAGAAAGCTTTGTCCATCTAAAATTAAATGGAACTAATGTACATTGGACCACAGCCATAAATAGTTAAGGAAACAAATCTTGGTTCATCTAAAATTATATGGAAACAGCATTGTCCGATTGAGATGATGTTTGCACTCTTCTTCTAACATGGCACCGGCTGCAAGGTTCCAGAACAGTCAAATTAACTGTAGATGGAACTTTATCCTCAATGTATGTTCTGATAGCCGCGAGCCCCCTTGGAGCTTCCGTGAGAACACCATCTATCATGGGAAAACACCGCCTATACTTATCTTGATCACACCTAGGACCATAAATGGTATCCAATGTAAGACACTCAAGTGACACCGCATTATTGAGGATATAACATGTTAGTTCCACCAAGCTCTTCGCAGAGCTGAAACCAGTGATCTTCACACTCTTGAGGTGGCCATGGTGGTGTTCAGGTATGTGTCTCAGTTGTGAATCCGTGAAAATCGATTCATTCACCATACGTAGAGTCACATTTAATATCAAAGTCTCCAAGGAAGGAGATGCATTGATAAAAGAAACCAGAGAGAAATAGTCATATGGCCGGGAAATGGTCGATCCTGTTATCATACGAATGGTCAGGTGCTTAAGGTAGATGAATTTGGTAGGTAGCATTGGTGCATCAACCACCTCATTCACTGATTCAATGACAAGAGTTTCAAGATTTGGCATAATGGATGGCAGATTGGCACGAGCATCATGGATTGCACATCCCATGTCTAGTTTCTTCATTTGCAGCGTTTCCACAACTGAGAAGTTAACCCTGAATCCTCTATGGAAAAAACTAGAGAGATTTGGAGCTTTGCTCTCTATCACTTTCAAGCTTGAGCATTCAAAAACACTAAGTCTGCTGGGCTGCTGTAGGGCGAAAGGTATCTTCAGGCAAGTTATCTTCGTGCATTGAGTGAGCTCTAAATGCTCCAAAGCAAGAGAGTTGGAAAGAAGGCACTCTAACTCAGCCCATGTAGCTCACTAACCACAGAGACAGACTTGTTAGGCTTCTCAAGGGGGCAAGTTCAGGTGTGGGATGGAGGGCACAAAATCGAAGTTTAATGTACCGAAGTGAGTCTCGAACCCCATCAGACAAAAGTGAGCATGGGAAGTTGTATTGTTTGTTTGTGTCAAACAAAAAAAGGGTGAGTTCTTCGATCCCTGGTTTAAGAGCAATCTGAAGCCAACTGTCAAGATAACTAGTGCCATCGAACCCACACATGCCACTGTAGTCAAGCTTGAACGTTTTCAAGCTAATGCCTGAGTGGTTCCTGAGAATGCACCCAATTTTTCCGTGGAAATTCTCGCCAAACGCATTTCTCTTCAAGCCAATCGTGTCTTTATTAAAGATAAGATTGGGATGACACCTCCAAGAACGTAGAAAAGCACGAGATACGCAAGCAGCACGAGCAGCTTCACGCATTGACATAAAGGAATGTATACGAGACAATATGTCCTCAGGAAGATATGGGATTGAATTTCTCATCATTTTGCCAGCTTGAGAATGACCATCGCCATCATGTTCACACGGTGATATCTTTCTTTTACCCGTTGAGGCAATAAACCCAGCTGAGCGGGCTCGGATTTGCGGCCGGCGATGCCGCCGCCGCCGCCGGCCGCGCCGCTGGGACATGAGCCGGTTCGGCGCCAACATCCCCAAAGACGAGCTCACGAAGATACCCCCTTCCTCCCTCGGATCTGACCGAGAAATCACTTCCGTTTCCCCCTCCTTCAGATCTCTCCTCTTCTCCTCTCCTGCCAATTTGCGGTTCGGTTTTGAACTCAAATTCGCACCGGCGACGGCGACGGCGACGGCGCCGGCGAACGGCGGGCGGAGCTATCTACTCGCCTACAGAACGACAAAAGTAACCAAACCCTATTCAGTGTGGGGACTGGGGAGTGGTTTGATCTTCTTTTTTTTTTTTTTTTGGCTTTTGGAGATGATCTCTTGCTCCGGTCTTATTGGATTGCGGAATAAGTCTATTCTGACTCCCTCTTGGGCTTGTTGAATCGCATCCCCAACTGTAAAACCAACCAGGTATAACGTCTCCCCCAACTTTAAAAAGGAATAAGTCAACTTTGGATCCCTCTATTTTGTCGCCCAGTCCGATTTTCATCCCTTGACCGCAAAACGGGTACAACCCGTCCCCCAACTTACAAAAACCGGACAAACGAGATCCCTCGGCGGTTTTGGCTGACGTGGCGCCTACGTGGCTTGTTTGACTAGGTCTCCGTCCCACGTGGCATTGACGTGGCGCTTACGTGGCAATTATATCTAGAAATAATAAAAAGCGTGGCCCCACATGTCAGCTGCACACAAAAAATATTTTTAAAATGGTGGGACCCACGTGGGCCCCACGTGTCAGCCTCACTCCTCTCTTCTTCCCACTCCCCCCTCTCTCTCTCCTTCCTGG

Coding Potentia
Explanation CPC Score
noncoding -1.24097
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0267900.2 4 23976991 T C
Osa04LNT0267900.2 4 23977251 G T
Osa04LNT0267900.2 4 23977385 C T
Osa04LNT0267900.2 4 23977524 A G
Osa04LNT0267900.2 4 23977627 A G
Osa04LNT0267900.2 4 23977805 A G
Osa04LNT0267900.2 4 23977871 A G
Osa04LNT0267900.2 4 23978815 G C
Osa04LNT0267900.2 4 23979366 G A
Osa04LNT0267900.2 4 23979496 A G
Osa04LNT0267900.2 4 23979711 A G
Osa04LNT0267900.2 4 23979842 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
Osa04LNT0267900.2 osa-miR5823 Cleavage 4.5 16.876 1 24
Osa04LNT0267900.2 osa-miR7695-3p Cleavage 5.0 24.027 1 21
Osa04LNT0267900.2 osa-miR166a-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166b-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166c-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166d-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166e-3p Translation 4.5 19.902 1 21
Osa04LNT0267900.2 osa-miR166f Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR395b Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395d Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395e Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395g Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395h Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395i Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395j Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395k Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395l Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395s Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395t Cleavage 4.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395c Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395a Cleavage 3.0 17.227 1 21
Osa04LNT0267900.2 osa-miR395f Cleavage 5.0 17.227 1 21
Osa04LNT0267900.2 osa-miR395u Cleavage 4.5 17.227 1 21
Osa04LNT0267900.2 osa-miR159c Cleavage 4.5 14.936 1 21
Osa04LNT0267900.2 osa-miR159d Cleavage 4.5 14.936 1 21
Osa04LNT0267900.2 osa-miR159e Cleavage 4.5 14.936 1 21
Osa04LNT0267900.2 osa-miR166k-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166l-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166g-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166h-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166m Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR166j-3p Translation 5.0 19.902 1 21
Osa04LNT0267900.2 osa-miR395m Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395n Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395o Cleavage 4.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395p Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395q Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395v Cleavage 4.5 17.227 1 21
Osa04LNT0267900.2 osa-miR395r Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR444b.2 Cleavage 5.0 13.135 1 21
Osa04LNT0267900.2 osa-miR444c.2 Cleavage 5.0 13.135 1 21
Osa04LNT0267900.2 osa-miR810b.1 Translation 4.5 21.601 1 21
Osa04LNT0267900.2 osa-miR1869 Translation 5.0 12.157 1 24
Osa04LNT0267900.2 osa-miR1862d Cleavage 4.5 19.861 1 24
Osa04LNT0267900.2 osa-miR1862e Cleavage 4.5 19.194 1 24
Osa04LNT0267900.2 osa-miR2118a Translation 5.0 16.695 1 22
Osa04LNT0267900.2 osa-miR2880 Translation 5.0 13.406 1 24
Osa04LNT0267900.2 osa-miR395y Cleavage 3.5 17.227 1 21
Osa04LNT0267900.2 osa-miR5148a Translation 5.0 13.181 1 24
Osa04LNT0267900.2 osa-miR5148b Translation 5.0 13.181 1 24
Osa04LNT0267900.2 osa-miR5148c Translation 5.0 13.181 1 24
Osa04LNT0267900.2 osa-miR5515 Cleavage 5.0 16.058 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0267900.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0267900.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0267900.2 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0267900.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0267900.2 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0267900.2 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0267900.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0267900.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0267900.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
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