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

>Osa04LNT0274400.2

GGCAAAGTAAGAATTGGATCAGCTGATCTTGAAAGAGACCTGTTACAATATTCGGTCTTCGGGTCCAACTTATCACCAAATATATACATGTATACACTAAACATTTCTCTACTATACAAAATTTCTTCTATTAGCGCCTACAGGCTAAAACCATAAATCACATTGGTAAGAGATGAGGCAATAAAAATACGCCATTGTTATGAGATGAATTATCTTGAATCTGTTGTCTTACTTCATTGACATGGAAATGGTAACAATGTTTGGTACCTTTCCAATATTTACTGCACAGGTACCTCCAGGAATCCCATATAATACTTCATTATTGCATTGCTGCATCTTTCCTGTAGTAGATGGAACTGCCATGTAATTATAATCCCTGCTACTCCTCTAGTTTGTAGACCTAAATGCCATGCACATTGGTGGGCTGATCTTGGCCAAAGCAAGCAAGGACGCAGGGAAGATCCAAAGACCATCCCCGCATATCAAACCAGATGCAACTGCTGGCACCATTAGTGCTGCTTTGCTTTTGTCAATTATATGCCAGGTGAAGACTATCAGGCTCCCGATACACATGTCGATGGCAAAGCTTGCACCAACCAGGAAAGGAACCCCCATTGCCATCGGTAGGGGAACCCATCTCCCATACTTCGGTGGGCAAAGGTCCCTCGTAAGGTTAGCTGCCACTGCAAAGCCAAAAAACCCATAGCAGAGCTGCAAGCAATGCTGGGGCAGAGCAGAGAAGCCCTCAACACCAAGAATCGCCATGTTTCGGTAGACTAGAGCATATGGTGCTTTCCAGTACCCTTCTGGGTTGCCAATGTCAAAGGCACTGTAGAACAAGAAGAAAGTTAGTGGTGAAATTACACAACCCATGACAGTTCCAATGGCCTGAGCAATAATCATCGATCTCGGTGATGTTAATGTTAGATGTCCCGTCTTGAAATCATGCATCAGATCAGCAGATATGGACACCAGCGATTTCACCAAACCACAGCCTACTAGGCCAGCAACTACACCAGAGTCTTTCCCAGCCCAGGCTGCAAGAATGAAGAGGGCAATCTTTCCATAATTGTAGGCCATATTGATGTCAGTTAGGCCTGCTCCATAGGCATTGCAGAAACCAAGGGCAGGCGCCAATAAGTATGCTATGACAACATAATACCACTTCATCTCATGGAACATCATGGGAATGGCAATTACTGCAATAAAAGTTAATCCAAGATAACCAGAGAAGGCTAGCCAGGAAGGAATATTGTCTGTTGTAAAAACTTCATTACGATGAAGTTCATCGAGCACTGGCATGTCTTCCCCCTTCTTTGCATTCTTCAGTTTTGAGCTATCAAACAGATTCTTAATAGTGAGTGCAACTATCTTCACAAAATTGTATAGGCCATCACCTAGGATGAGAGCTACACAGATGAAGGCCTTGTACCCTTGCAGGCTTTTCATGCTGCTTTCAGGTATATCTGCTGAATACCAATCCCCTTTCAAATCACTGATCAGTGGCCACATTACTCCCCATGAGAGAATGGCGCCGAGTAGGAGAGACAGATTAACAAGGTGGGAGCAAATCATCCCTGCCCCAACATATGTGAGACTGAAATCGAAGAAGAATGTTTGTTGCCAAGCTTTTAGTCCAAAAGTTGGAAACTGCGAGAACCCACAATTGTCTCCACCAGAGTAAAACCACTGGAAGAAGCTCCAAAAGAAACTCATAGCAAAATATTTGGTGAATCCATTTACTTGCTGCTTTGCCATTGCATCCCCATGAGGTGTGTGGAATCCATTTATAAGCACAGCTGTTGCAGTCCCACTTGGGTAAGTTAATTTGTAGTCAATTATCATGACCTTCCTAAGAGGGACGAGAGCGAGAAGTCCGACGAAGCTGACGGCGAGAAGGAATCCAGTCATCCACGCAATGCCGGGCTCCTTGTAGCTCCCCGGCACGTTGCCCTCCGTGTCCTCGCCCGCCATCTCGTAAGTCCTCTTGTTGAGCCCAAGCAAGTAAGAACCAAACCCACCTCCAACTGCGATGCTGTAGCAGGCGACGGCGCAGGTCTGGACGACGGTGTTCTCCTGCCGCGTGAACGGGCGGGCGGCGAAGCCGAGGCGGGCGAGCGCCTGCGTCCAGCCGCGGAGGACGACGAAGGCGATGAGCGCGGCTGAGACGTTGAGCGTGGGGACGAGGCCCGTGGTAAGGTTCAGCTTCATCACGATGACGCTGTACATGGCGCCCACGGCCAGGCTCGCCACCAGCCCGCGCGCCGTCAGCTGCTCCCGCCACGGCGGCGGCGCGCCGCCGCCGCCGCGGGCATGCGTGGCCCCCTCCTCGGCGTCGCCGCCGCCGTCGAGCCCGGCCATCTCCTCCTCCCGCGGGTGCGCTACCACCAGCTCGAGGCGCGGCGGCCCGGGCTGCCGCTTCCTCCGCCTCTCCTGCTGAATTAGCCTGGATTCTCTCTTGCTCTTGCTCCAACTGAAAAGACAAGAACAGCGAGCCAAACGAAACTGAAGGTGAGAAAGAGAACTGAATAGCACGTCACAAAAGAAAGGGGAAGTGATTGGCAAAGAGAAATAGCGTATACTTGGTTTTGTTTCGTCAGAAAAGGAAGCAAGGAGGTTTGGTAATGTTTTTATCTACCAATATAATCACTAGTAGAAGAAATAGAATTTATCTC

Coding Potentia
Explanation CPC Score
noncoding -1.0378
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0274400.2 4 27154633 C T
Osa04LNT0274400.2 4 27157067 T C
Osa04LNT0274400.2 4 27157540 A G
Osa04LNT0274400.2 4 27158479 G T
Osa04LNT0274400.2 4 27158907 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
Osa04LNT0274400.2 osa-miR7695-5p Translation 4.5 18.904 1 24
Osa04LNT0274400.2 osa-miR156a Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156b-5p Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156c-5p Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156d Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156e Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156f-5p Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156g-5p Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156h-5p Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156i Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR156j-5p Translation 4.5 19.369 1 20
Osa04LNT0274400.2 osa-miR418 Cleavage 4.5 11.671 1 21
Osa04LNT0274400.2 osa-miR395w Translation 4.5 14.388 1 22
Osa04LNT0274400.2 osa-miR1430 Cleavage 5.0 20.013 1 21
Osa04LNT0274400.2 osa-miR1441 Translation 4.0 17.124 1 21
Osa04LNT0274400.2 osa-miR1870-3p Cleavage 4.5 21.563 1 24
Osa04LNT0274400.2 osa-miR2867-3p Cleavage 5.0 19.673 1 20
Osa04LNT0274400.2 osa-miR2868 Cleavage 5.0 11.607 1 20
Osa04LNT0274400.2 osa-miR2876-5p Cleavage 3.5 17.626 1 21
Osa04LNT0274400.2 osa-miR5160 Cleavage 3.5 16.387 1 22
Osa04LNT0274400.2 osa-miR5493 Cleavage 5.0 22.476 1 21
Osa04LNT0274400.2 osa-miR5515 Cleavage 4.5 17.875 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0274400.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0274400.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0274400.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0274400.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0274400.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0274400.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0274400.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
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