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

>Osa04LNT0265500.2

AGGGTACATCACGCTTTCACAACTTTTTGCCAGATTCCGGCATAACATCACTAGTGTTTGCCGGACACTGACATCCCATTTTAGGTTGCAGGAATATTTATCCAGTTAGGCCTTTCAGATGTTTTAGATTTACAAAGGAAGGTGACAAGGAGACACTACAGATAAAACAATGTTCGTGTCTACATTCCAATTTGAACAGCGCGTCAACGGGCTGTGTCAAGAGGAGGCCAACCAGAAAACTGTGGTCAGAAACGACGAGGGAAAACGCAATCTGGACATTGAAGGCGCGAGCACAACTTCACCAACTGCAATTCGATGAAGATAATCCATCTACAGGATCTAGAGATCCATCTACTCTGATTCACCAGGGTGTAATCCACATTCTAATCTGACGGCTTCCAGGAGCTGAGGTGATATCACCTCCTTTTCAACTTGTTCTGTACTATTATTTCCACTTAAGCTATTCTGGGCCACATCTGCTCCCCAACCCCTGTACAAAATCACTTTGTTGGGCTCCCGCGACACTAGAACCGATCCAGTTGCTTCCTCTAGTTCTGAAATCAACTGCTGAATTGGAGTTCCGTCTGCTCGGTTCTTGATATTCACAATAGCAAGAGGATGCTTCTTGAAGTGTGTTTTTATTGCTTTTGCGACTCCTGTGATGACATTGTTCCTCCCAACAGCGAGTACTGGCCGTTTCTTCATTTTCAGAGCTTGCTTCCTTAGCATGAGCCTTTCTCGGTTTGAAAGTGGAGCAGCTGCGGAAGGCAACTGAGAAGATTTCTCATCCAATTTCAGCTCGTGTACAGGTGTAAGGGTTCCTACAAATTTTGAGCCACTTACTCTGTGACTATCTGAATTGTGCATCACAGAAGAACTAAGTGGACTTTGGTGTGTACTCTCAGATGAAGTACTTGTACTCTCAGTCAGACAGGAACTTGTAGTTTCAGACAGATCATCTGTATGCTTGCTGAAACATAACAACTTGTTCTGCATAACATCCAAGGGAACTCCAGATTTGGTTAAAACTGAGGTTCCCTCTGTTTCACTTTCACCTGAAGAACACTCTACAACCACTGACTTGGCACACTCAGGAAGAACTTCAGACATTCTTTTTTGTCCACTAATGTTCCAGAATTAACATTGAGATCAAGAATGCCTTGGTTGTGGTGGCCTGAGTTCATTCCATTAGTTGGAGTAACAGGTTGAACCTCCATTTGTTTAAAAAACATCTGATCCTTCAAGTAGTCTATATTCTTTGAAAGATTAAGCACATGAAGCTTCAGGGACTTATAACGCTGATACTCCACAGAACGCTTCAAAGCATCCTTTTTATTTAACAAAGATTTTGGCCTGAGAGTTGATGGCCTCTGATAGTTCTTTCCCCGATATATTATAATTGCATGTGCTTTGCTCACTCTTTCCACTGCCACCAATATACCACCACTCTCAGCCTCTAGAGTTCGAGCAGCATATTCAACATCTTTAATGTTGTGTTCTTTACATATAATTTTGACAAGTTCTCGGTACTTCCAGTGAAGGTGCATATTTTCAACAGTTCCATCAAAAACTCCTCTCCTTCCTAGCAATAAGAATGATTTCATCTTTAAACCAACTTTCCTCAACATGTACCTCTCCTCTTCTGAGATAACCTCTCTAGTTTCAGCTCTAGAAGGCTCAGACGACATTTCTAGCTCTTCAATAAGCTTTTCAGTCTTCTCTTTCTCTGCAATTGCCTGAGATAATCTGGCCTCAACATTCTGGGCAAACACATTAAGAGATTCTGCTCTATTATCTGAAACTGCAGTTTCATCTTTATGCTTCTTTTCATAGCATTCATGCCCATCTAGTGAGACATCAGTAGCCATCTTCAGTTTAGAAGAATTTTGCGGTGTGCTTTTGTCAAAATTAAGCTTAGGGTTACTGATTGTAGAATTGCCATACTTTCTACGCTTTTCTATTGCAAGAGAGACAGCTGTGGGCAGGAAATCTTTCCCTCTGTAGAATACAATTGACTCATTATCCCTTGATAAAAGGGTCCCACCTGTCAAGCCCTTCAGTTTCTCAGAAATGAGATCACTATCAATGTTCTCTGCACCTCTCTTAATTGCAACCTTTGCTACCTCACATCTTTCCCATAGTTTGATCATAGATGCAGCCAACCCTTGAAGGTTACTACTTCGTCCAAGTGCGTAATGGTAGGGTAGGGGACGAGCTAGTCTCCTAAGGATTGTCATTTCTCTATCAGTTAACCTCGGTGGTACTCCTGAAGGAAGCAGACGAAAAGGCCTACGGTATCCAGGAACAATTGCTGGCAACAAATCAGCATCCACTGGAAGAGGGTCATACCCCCACCAATCAGAAAACCGTGGACCCAACCCATCCAATAATTTGTCAGCTTCCTCTGCGAGTTTGACCTCCCCAGGTAATTGTAACCGAAACTTATTTGGAGAACCAACACCAGCAACTAAGGTTGACCGAGCTCGACCACTGATCTCGCTAGGACGAGACACATTAGTGCTTGTATGTAATATTGCTTGCTGATCTTTTGTAGCACTGTTAATGCTTTGCTCTGCAGATCCAATGTCTAAATTTCCCTCAAGCGCATCAACACCAAACCGTCTAGTAAGATCATCGCCCTCCTCAGTATGATTGCTACCATGTTCTGCAGGATTATCAGAATCCTCTTCACTGCCACTTTGTTCGGAAGCTATTATAGCAAGATCCGCGTCCTCGTCATCAGAACTTGTATGCTCTGATGACTCATCCATGTCATTCTTCATTTCTCTATCATGGAAGTAAGGATACTTATAGTCAGTTCCTCTATATAATATGATGGTGCTTCCAGATCTCCAAATGACTAAGCCTCCAGTTTTTCTCTCGAGAATCTCGTGCGTGCGCTTCATGTTCATGGCGGAGACGTCGTCGCACCTGATCTTCACGAGCTCCGCGTTGCGCCACCGCTCGTGTATCCCGTTCACGATCCCCTCCGTCACCCCGGCCTTCCCGACCTTGAGCCTGTTCCGCAGCCGAATCCCGGCCCCCTGAAGCCGCCGCAGCTCGTCCCTCGGCAGCGCCAGCTCCGCGGCGGACGGCGGCGCCGACGCCGCGGCGCTACTATCCCTCCCGCCGCGCCTCCTGCGGCGAGACGCGGCGGCCCCCTCCCCATCGCCCGTGGCCCAGCTCGGGTCTAGGGTGGAGCCGACGCGGTGGCGCGGGAGCTGGGCCGGCGTGGGAACGAATATCTCGCCGGGGGACGCGCCGGCGCCCGCCTCCGGCGCCGCCGGACCGGGGGCCGCCTCCGGGTGGTCGGCCTCGAGGTAGCCGAGGCTGCGGAGCTTGTCGGAGATGCGGCGGAGAGCCGACTTGGCGAGGAGCTCCGGCGAGGGGGAGGCGTGGATGGGAGGGAGGAGGAG

Coding Potentia
Explanation CPC Score
noncoding -1.22122
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0265500.2 4 23216031 G A
Osa04LNT0265500.2 4 23212521 T C
Osa04LNT0265500.2 4 23213378 A C
Osa04LNT0265500.2 4 23213721 A C
Osa04LNT0265500.2 4 23215002 T C
Osa04LNT0265500.2 4 23215522 T C
Osa04LNT0265500.2 4 23215691 T C
Osa04LNT0265500.2 4 23216197 G A
Osa04LNT0265500.2 4 23216848 T A
Osa04LNT0265500.2 4 23217196 G A
Osa04LNT0265500.2 4 23214110 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0265500.2 osa-miR5830 Cleavage 5.0 20.509 1 24
Osa04LNT0265500.2 osa-miR166b-5p Cleavage 5.0 17.427 1 21
Osa04LNT0265500.2 osa-miR166c-5p Cleavage 4.5 17.427 1 20
Osa04LNT0265500.2 osa-miR166d-5p Cleavage 5.0 17.427 1 21
Osa04LNT0265500.2 osa-miR395b Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395d Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395e Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395g Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395h Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395i Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395j Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395k Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395l Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395s Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395a Cleavage 4.5 9.708 1 21
Osa04LNT0265500.2 osa-miR395u Cleavage 3.5 9.708 1 21
Osa04LNT0265500.2 osa-miR164c Cleavage 4.5 17.901 1 21
Osa04LNT0265500.2 osa-miR167h-3p Cleavage 4.5 16.506 1 21
Osa04LNT0265500.2 osa-miR172a Cleavage 5.0 13.946 1 21
Osa04LNT0265500.2 osa-miR172d-3p Cleavage 5.0 13.946 1 21
Osa04LNT0265500.2 osa-miR444a-5p Translation 3.0 15.897 1 21
Osa04LNT0265500.2 osa-miR395m Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395n Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395p Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395q Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR395r Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR1435 Cleavage 5.0 13.031 1 20
Osa04LNT0265500.2 osa-miR1874-3p Cleavage 4.0 17.686 1 24
Osa04LNT0265500.2 osa-miR2090 Translation 5.0 11.663 1 22
Osa04LNT0265500.2 osa-miR395y Cleavage 5.0 9.708 1 21
Osa04LNT0265500.2 osa-miR1862f Translation 5.0 16.232 1 20
Osa04LNT0265500.2 osa-miR1862g Translation 5.0 16.232 1 20
Osa04LNT0265500.2 osa-miR3980a-3p Cleavage 5.0 18.08 1 21
Osa04LNT0265500.2 osa-miR3980b-3p Cleavage 5.0 18.08 1 21
Osa04LNT0265500.2 osa-miR5501 Cleavage 4.5 7.258 1 21
Osa04LNT0265500.2 osa-miR5501 Translation 5.0 18.629 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0265500.2 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0265500.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0265500.2 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0265500.2 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0265500.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0265500.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265500.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265500.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0265500.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
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