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

>Osa04LNT0285600.2

AGAATAATACGAACAATCTGCGTTTCAAGAAAAAAACATAACAGTAATCTTCAAAACTACAAAAATAATCGCAAGCCAGTACACACCTACTGGGCGTTGGCGTTGCCAATTTTCCACAATCAAGATGGAATACATGAAATCGAAAGGTGGTACATGTCATATTTGCGTGGGTCGCTAGGCCTACAAAATAATTAAGTACATTGCTCTCTGCTAGGCTGCTAGCACAGAAGATTTAATATCCTCTGTATGGGCAAACCTCCAGCTTATCTACACTGGTGATCCGCGGGCATCTTGCTACCGTGGGAATGCGTTGTTCAATGAATCAGTAGAAGATGCAGCGATATGCCACACATCGCCTCACAAGGATGTCGAGGCATCTTGAAATCAAAAGTATCTTCTATCTTCTTTTGACTGGAGTTCTGGATCTGGAACGCTTCTTCCTTTCCGCAGATGAATAAGGCGAATGCCTGCGGTGAGAATGCTTGCTATGTGGAGACCGCGAAACTCGTCTGTTCCTAGATTTTGGGGGTGAGGGGGACATGCTGCTTTTACATGAATGAAGTTTTCTCCTTTTCGAATTATCAGAAGGCTCATCACTTGAGACACTCTCTCGATGTGAAGAACTCTCCTTCTTGGTCCGACTTCTCGCACTTGGTGATCTTGACCTTCTACTGCTATGACTACTTGAGCCCTTTGTAGTTTGCCTCGACCTATCCTCCTTTTCATGTTTCCCTTTCTCTCTTCTATCTGCAGAATCCCTGCTTTTCTCTCTTACGTCCTTTTGATAATCTTTTCTCTCTCCTTTTGCATCATCCTGCTTAGAGTTTCCTCTGGAACGGGGTTCCCTTGTATCAGCTCCATGTCTCACACTCCTGTCAGATCCTTTTTCCTCCTTGAAGCTACCCTTTTTATCAATATTTCCATACATGCTAGATTTATCATCATCATTATATCTTTTGGAAGAAGATTCGGATTCTTTTCTTCGAACAGCCTTTGGCTCCTTTACAAAATCTTCCTCATTGCTGCTCTTCCCTAAATGCCCTTGACTGCTCTCCATATTGCTAAAATTTTCAACATTATTGCCTGAAGGTGGAACTTTTCCATTTTGGGAATATCCATGTGCCTTCTCATCCAGGGTAGGAGCCACATCCTTCGGCTGACTTGATATTTTGGCATCTGAAGGAAATTCCCTACTATGTGTGTCATGAACACGTAGCTCTTGTTTAAGTTCTGCACTTGAGTTCCTATGAGACATTTCATCATTAAATTTACGATCTTCGCCTAATGAAGCATTTTGGACCACAGAATTTCTTTCATTATGATTTCCATGCTGTTCACCATCAGTGGCTTTTTCACCTTCTCCTGGACGAGCTGCGCCAGCTTTAGTTTCAGACGATAAGTTTGAAACTGGAACCTTATCCTCATTATCACCCTCATCGTCCTCATCATCTGAATCATAACTAGCAAGGCCAAGAAGAGCGCCTTTAGGGGAACTTAACCCAGTACCATCAGAATGATCAGCTGAGCTAACATTAGTTGGCTTAGCAGGGACAACAACTTTAGCTGAGACCTTTGGTTTTGATTCTCCCAGACCAGGCCCCTTCACACTAGAAACTCTAGTGGGCTCATTTGGTTCAGCTGATGGATCATCTTCATTCAATACTTTTGTCGCGATCTCATCAAAAAGATCATCAGTAACCTTTAAGAGAACTTCAGTTAATACACGCTTAATTTCCTGGTTCATTGCTGCCATCCGGGCTGCTTCAATTTCGTCCTCATCTTCTTCATCATCATCAGTAGATTTAGCTGAATCTACGCTTCTGCTGTCAGCCTGATCAGAACTTTTAAGTGTTTTTTCAGCATCTTCAGATCCCTTGGAGTGGAACTCTGTTGAGTGTTGCACCGAAGCACTCACTGATGTAGATTTCTTCTTCAAAAGTTCTTCGCGAAGCCAGTTAGGCACTGGAGGTTTCTTTGATCTTTCTGTGACATTAAAAGGAGTGTTTGCATCCACAGGGAATGCTTCTGTCACATTACCAACTCCAAATGCTGCAGGTGGAATATAGCTTGAACCAGAAACTGCTCCAAAGAGTGGTGCAGCATGAACTGAAGGGTCCATCTGTGCTGCTTGTGGTGGTACTGAAGCTTGAGGAAAAAGTACTGTAGTAGATGGAATCCATGATTGCGCTGGTGCTGAATGTGCATCATGATCAGATGCTGCTATTGGAGCTGCTGGAATATTAGAATTGAAATTTGCTGTTCTGTGCACTGCCATATCAGGAGCTTTCCTACTATTAAATTCTAAAGGTTGATCACTGGGATCAACTGCAATCTTGGAAGACTGCCCATCATGCCCAAAATGAGGTTGTTCCAGTGAGGGAGCAATATGCATACTGGAAGGCGCTTGTGGAAATCCGTCTTGCATTGCTGAGGCAGTTGGAGGTAGCTGAGTCTGCGAGCTTGGATATTGAATCATAGCATTCCCAACACCTGTTATTACATTGCATAGTCAGCATTAAGCCTGGATAAAAAATGCAGGTTACCCCATCCAAACACTGAGTTATATACATTGAGCACAGCCAGCCAGTAATTAGCTTTTCTAAAATGTGATTTCCATCTAATTTCCAGGACTGGCAGCAAGAGAAATGAAGATTTTCAGTGCTTCAAAGTAAAAAGGGCTCAACCAAACATTCAATTACATTCATGATATATCAGAGGTAATTATTGAATCCATGATAAAATGGCATAGTCACTGAGAAAGTGATTCTGAGTAGATATCTGCGTATTCCTCCTTTTGAAGGTGGTGAAACCCACCAAGCAATCGCCTCAAATATAGGAAGAGTGGAGCATACACAAACAATAACGCTAGCTCAAATGTTTTTAGAAGGTAACGTGTGTCATATGCTCTTTTTTCTTAAATAAATAGCTCTGTAGACTTGCAAGTCTTTCCATATTTGAATCTGAAGGTATTACCAGGAGGGACCAGCCTTAATATGATTCAGGCTACACAGTAAGTTATATTGCCAAGCAAGCATACCTGGAGTAGAAGGATAATTATAAGATACCTCCTGCTCATAGGCGGATGGAAATGAACCAAAGTTCTTTGCTGGTGGCGCCAATGGACCTCCATCTGCAATATTATCTTCAGCTCCACTCTGGAACTGACATATCCATATATAACATATATTGAGCAATAGTAATAAGATATGGTACCTGGCAGATAGTTTGTTTCCCTGTGCTGTCCTGTCATTTGAAATGGCAACTGGTCATTACTTGACTGAGGGATTGGCGGGCGTAAAGGTTCTGCGGGCAGACCAGCTGGTTGCTGATACTGATCCTGGTAACCGTAATTATGAACTTCTGGCCTATTTGCGGATATGGCATGCTGTTGAATATGATGGTTTTCTGTAACAGATTTAGCAGCAGCCCATGCCTTCGCCTTTGTAGCCCAATCTTCCTCATTTCCATGCCCTGCGTATCCATGACTTTGAGCCCACGAATGATTGGCCCAGCCCTGGCCCGGAGGCGGCGGCGGGTAGCTGGGCGGCGGTGGCTGGGCAGCGGCGTGGTGAGGAGGCCAGGGATTCCCCGCCGCAGGAGGCGGCGGCTGCATCGGCATCGGAGGGAGGGAGGGATGGTACCCATACGGCGGCGGCTGCTGCGGCAGCGGCGGCGGAGGGTGGGGTGGTCCCCACTGGTGGTGCTGGGGAGGGAAAGGGTGGTTGGCGTGGGGAGGGTACGGCGGTGGGGACGGCCCGGGGTACCAGTGCGGGCTCGCGTGGGAGGGAGGTGGAGGCTGCGGCTGCGGCGGCGGCGGCGGCGGGGGGGCGTCGCCGGAGACGGCGAAGCGGCGGTGGTGGGGGTAGGCGTCCATGGAGGCGGAGGGACGGGAGGGGAGGCGGAGGAGAGTCAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.99955
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0285600.2 4 33767872 G A
Osa04LNT0285600.2 4 33767876 C A
Osa04LNT0285600.2 4 33769445 A C
Osa04LNT0285600.2 4 33770900 G A
Osa04LNT0285600.2 4 33771922 C T
Osa04LNT0285600.2 4 33767129 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
Osa04LNT0285600.2 osa-miR812v Translation 5.0 19.14 1 24
Osa04LNT0285600.2 osa-miR1319b Cleavage 4.5 10.579 1 24
Osa04LNT0285600.2 osa-miR166a-5p Translation 5.0 23.811 1 21
Osa04LNT0285600.2 osa-miR166e-5p Translation 5.0 23.811 1 21
Osa04LNT0285600.2 osa-miR395c Translation 5.0 9.676 1 21
Osa04LNT0285600.2 osa-miR156k Cleavage 5.0 6.331 1 21
Osa04LNT0285600.2 osa-miR162b Cleavage 5.0 21.807 1 21
Osa04LNT0285600.2 osa-miR418 Cleavage 4.0 10.808 1 21
Osa04LNT0285600.2 osa-miR435 Translation 5.0 18.367 1 20
Osa04LNT0285600.2 osa-miR435 Translation 5.0 20.799 1 20
Osa04LNT0285600.2 osa-miR444a-3p.2 Cleavage 4.0 23.581 1 21
Osa04LNT0285600.2 osa-miR395o Translation 4.5 9.676 1 21
Osa04LNT0285600.2 osa-miR816 Cleavage 4.5 13.985 1 20
Osa04LNT0285600.2 osa-miR444d.2 Cleavage 4.0 23.581 1 21
Osa04LNT0285600.2 osa-miR444e Cleavage 4.0 23.581 1 21
Osa04LNT0285600.2 osa-miR444f Cleavage 4.5 23.581 1 21
Osa04LNT0285600.2 osa-miR1850.1 Translation 4.0 11.598 1 21
Osa04LNT0285600.2 osa-miR2878-3p Cleavage 4.0 14.458 1 24
Osa04LNT0285600.2 osa-miR1862f Cleavage 5.0 19.544 1 20
Osa04LNT0285600.2 osa-miR1862g Cleavage 5.0 19.544 1 20
Osa04LNT0285600.2 osa-miR5488 Cleavage 3.5 14.088 1 21
Osa04LNT0285600.2 osa-miR5499 Translation 3.5 19.564 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0285600.2 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0285600.2 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0285600.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0285600.2 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0285600.2 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0285600.2 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0285600.2 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0285600.2 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0285600.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0285600.2 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0285600.2 4 QGn4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0285600.2 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
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