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

>Osa05LNT0320100.2

TACGAACTGAATTCAAAATTTCACTCGTTAAATGGATAGTAACATCCGAACGTATACACCAATCATCCGAAATCTATATGTCAAACTATTACACGTTGATCTATGACATGATGCAACAAAGCTCACATCGTTGCACAAAAAATACACTTGAGTTAATCATCGTACTTCTGTGAGTTTTTCATCTGTAACTGACTGCCCGACCATTTCCTTTCCCACACTGTTTGGAGCACTTACCAAGATTTTAATCCGTCCAGAAAAATACACATTCATTGATGAGCCCCTCTGATGAAGTGCAGGGTGAGCAACTGGTAGGCTATTTTTCAGTTCCAGTTCTTTCTTTGCCTAAAATGTTTTTTCCTAATCATATTTTCTTTAAAGAGCGTAAATGGTGTGAGTACTTTCTGTTCTTCTGCTGGGCCCTCCAGAAGCAAGCCAGCGCCCCAAATGTACAGCTGGCAATCGCAACACCCAGGGCAGCTCCAATTGGGACGCTTGCAGCATTAGAAATCGATGAATCCTCTGAAACTATCTTCTTCTCTTGTTGCTGAAGAGACTCCATGTAGGTCTCCTTGTAGGATGATACAAGCTTCTTTCCATAGTAGTTAACCAAGAATTGATACACTGCATCCTCGTTCCAGTCCACAGCTCCATCGGTGACCTTGCTTGAGCGGTAGCAAGATGGGCAGAGCTGATTTGGAGGCCAGGTAACCTTCGGAAACAAGGGATCACCAGTTCCCATATCCTTTTCTTCTTTCATCAATCTCATATTGACTTTGTTATGTGTGCTCCATAACCAGAGACTGAGCTCACGAGCAGTTCTGAAGGGGGCTGACACGCTTGAACACATTTCATAAAAGTGCTTGCGGCATTCCTCACAGATGAAGAAGTTGTGAATAAAATCACATATTGATGTAAAGGTTGACTGGCTCTCTCCATCCCCAATTCGGACGGTTAGTGAATGCATCAAAACCCATAGACCACAGCTAAATCCTCTTGTTTCACTTTTACTGCCGCGGCAGAACAGCCAATATCCACGTGGCACCTCTTTTCCACAGATCCAGTGGTTCTCTTCCGCAACACTTTCCAACAATTTAGAACCCTCTTGTGAACTTAACGACAGATTCGATGACCAGTGATCATCGAAGTTAATAAGTAGCTCAGCAGATCCCCTTCGGCACCTCTTGGATGGGTGACGAGCCACCAAAATTTGTAAAAATCTGATGAGCGAATCACGATTCTTTGGTTTGATCGTCTTGCGCTCCAAAATTATCTGTAACGCTTGAGCTGTTGCTTCCTCAACATCGTAAATTGCTTGAACAATCTGCTCAGGATCCGAAGCATTCTTTGGAAGCATATTTTCATTCTCGTACTTTTTGTCTTCTAAACTGAAAGAGCTTTTCATCTGATTATTTATCCACTTCAGTAAACGTTCTGCTGTTCTTCCATCATCAATTAACTTTATTTCATTATTCTCTTGCTTGGGATCCCACTTAGCAGAAGCAAATTTTGTTGGTGGACCCCAAAGTAGGAAAGGGTAATGGTCAACTGAGAATCTATTGCAAAGATCGATGTTCACCTGTGCTTTGATGCACAATCAACCCTAGCCATCAGTATTAACCCTGGATGTGCAGCGTCCCGACCATTGAATAGTTTTGCAACCTTCTCATAATGAGGCTTGTAGTTTCTGCAAGCTGGACACCTGAGCAAACACGGTACGTATTTCAATTAGCATCAATTCAACAATAAAACAAATGCCATCTAGGCAGCCTCAAAAGAAAAAAAAAAGAATACCGATATGACCAATAGAAGTTCATTCCAATTAAAATTATCTCGAGTAAGTGAAAACTTGAGGCTCTGGAGAAACTATACGCCACTTCATAGTTCATATCTAATGCATATGGACTAACCTATTCTGAATAGTGACGACTTATAATGATTAACCAATGGAATATAATATCAAAATAACTTGACATGGAATATTTGGAAGACCAGAACATGGACATTAGAGTGAAAAGGATAACAAAAGGATGCTAATCATTCAAGTCCTTGATTCCCCATAAACAGGTCCATGTGTATTAATCAAATCGTCAAGTTCCATTAAATCATGTGAGGTACAGTATCAATGCTCATATAAGTGTATTATTTTTCCTGTTAACATCCAAAAGAAGCATTTAAATATAACTCAATCTCATGAAGCTAAAATTTCAAAAAGAGATGATCTCTGCAAATTAGAATTAAACGGCATGGCATTTATAGCCCAATGTGGGGAACAGTGGAACTTACATAGAGCAAAAATGACCGTACTTATGCTTTTGAGAAAGTTCCGCACACCCCAAATCACACAAGAAATATCGCATCGAAGCAATACTCTGAGTAAGTGGCAACACTGAGAAACTATATAGTGATAAACTTACAACCCAGTCAATTCCTCTTTCATCATTACAGTAAATGCTCCACTGATTTTCCATAATTAACTGCTGGCCTACATCCGATTTAGTCCTACATATAACAAATTTCCAAGCTTCGGGGCTCATTCATGTCTGCACCTTTCTTCTAGCTCACAACTTCACAGGTCACAGTACTACAACACGGACAACACTCCCAGGGTCGCATCCTCACATGACATTTCAAGGTAGTACGAGCGAAGCATTTATTGGTTACTCTCATCGAGTTTTGAACAACACGCATCCTTACTCCTTCTCTATTCAATGAAATTGGCAGCTTGCCGATTCGTTCAAAAAAAAAAAAAACAACACGCATCCATCCCACCAATCAGACCTTGCAACACCTACACAACCCTACATGCTTGAAACCCCAAAAATTGTGGATTATATTGGCATTCACTTGCTCACAGACGACGAAACGAGTAAATCATTTCGATTCTATAAACCATACATCGGGGAAGACGACGAAACCCCGCAGTCGCATCTCACGCCATCGGACTACCACGATTCTCATCCACTTATCGATTCTACCAAGTACTACAACTAACGCCTCAGTCACGAATCGGGGAGAAAAAAACGAGTCAAAGGCGAGAGTCGAACCAGTGGGCGAAGAACTCGACGACGGCCCAGGGCTCCAGCGAGGCCTTGAGGAAGGCGTCGAAGTTGGTGGCGTTGAGGTCGACGGCGGCGTCGGCGTCGACCTCCCCGGGGCCCTCCCTGCCGCCGAGCGAGCGAGCGGCCGCCCCGCGCGGCGCCGCGGCGAGGGAGGCGGCGGCGAGGACGAGCACCAGGACGACGCGGCGCGCCACCGCCGCCGCAGCCATGGATCGGGCCACCGGATCTCTCTCCCGCCGCCGTGATCCGCTTCGGACACCTGCCCCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.789819
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0320100.2 5 27475375 T C
Osa05LNT0320100.2 5 27474180 A G
Osa05LNT0320100.2 5 27475067 T C
Osa05LNT0320100.2 5 27475611 T G
Osa05LNT0320100.2 5 27475963 A G
Osa05LNT0320100.2 5 27477190 G A
Osa05LNT0320100.2 5 27477772 G A
Osa05LNT0320100.2 5 27478071 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
Osa05LNT0320100.2 osa-miR5528 Cleavage 4.5 9.825 1 21
Osa05LNT0320100.2 osa-miR5834 Translation 4.5 11.533 1 21
Osa05LNT0320100.2 osa-miR399e Translation 5.0 24.878 1 21
Osa05LNT0320100.2 osa-miR399f Translation 5.0 24.878 1 21
Osa05LNT0320100.2 osa-miR399g Translation 5.0 24.878 1 21
Osa05LNT0320100.2 osa-miR418 Cleavage 5.0 7.218 1 21
Osa05LNT0320100.2 osa-miR418 Translation 5.0 8.502 1 21
Osa05LNT0320100.2 osa-miR1425-3p Cleavage 4.5 17.167 1 21
Osa05LNT0320100.2 osa-miR1429-5p Translation 5.0 12.59 1 21
Osa05LNT0320100.2 osa-miR2871a-3p Translation 4.5 16.357 1 21
Osa05LNT0320100.2 osa-miR2871b Translation 4.5 16.357 1 21
Osa05LNT0320100.2 osa-miR5144-3p Cleavage 4.0 14.922 1 21
Osa05LNT0320100.2 osa-miR5486 Translation 4.5 14.837 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0320100.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0320100.2 5 QFla5 Morphological trait Culm/leaf RG470 RG346
Osa05LNT0320100.2 5 nan Physiological trait Eating quality C246 C1447
Osa05LNT0320100.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0320100.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0320100.2 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0320100.2 5 qGR5-1 Physiological trait Germination/dormancy C246 RM26
Osa05LNT0320100.2 5 qRA5-1 Morphological trait Shoot/Seedling C246 RM26
Osa05LNT0320100.2 5 qRDW5-1 Morphological trait Shoot/Seedling C246 RM26
Osa05LNT0320100.2 5 qRFC-5 Physiological trait Eating quality RG470 RG474
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