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

>Osa05LNT0316300.2

GCTGGTCGTGGTGCCTTCTCTCTTCACAAATGGTCCCTTGTGAGCTGCTATGAATAATTCCATCTATACTTATGTCTGGAAACACCGTGCTTTGGACCAAAGAAAAAGTTCTCTTTTTTTTTCATTTTTGTGATTACAATGAAATCGCTGGCCAGCAGGTCCAGGACAACATCAGGGGGCTCCATTAAAGCAACCTGGAGATTCCTCATGAGCTAGGGTTAGAACCCAACATGGACATGGCAATGGCATGAACCACTTGGTTACAGTTACACACTTGCACCGACAATAGAAAACACGAGAACTACTGTAAACTGAAGAACATATTCAGCACCTTTTGAATACGAACAGGGCGTCGTTAAGCTGAGATATCAAAAGAATCCCCTTCAGTCGCATTCTTCAGGATCACAGAATTGGGTTCAACTAACAATATTCTAACGCCCAGATTCGTCGCTGTTTCCGAACCCTTGATACAGGATATCAACCAGATTACAACTCAAACGTGATCACGGATCATAAAACAAACTCAAGATGCTGAAAGGAAGACACGCCATCAAGATTTATTGTGAGAATACCCTGACCCGGCAACTGCCATCTTGTCCCCATCTCGTTAACTTTCTAATTCTCCACCCTGAACGCTTTAACATACTATCTGCTCGACTTCTGGTAGCATTCGCCAACAAACCAATTCATTTGCGGTTTTGTTCACTTCCCCTTCTCTGATGCTCAATGGATATACAATAAAAGCAATAGTAGAGTTTGTGCTTCTGTTCACTTCCCTTTCTCTGATGCACAACAAATACAATAAAAGCAAGGATATAGTTTTTGTCATCCAAGCACACTGATCCAGGACCAAATCACCACGTGACAGTGGATTGAAATTACTCAACCAACATACATGTATCATGTATGGTCCAATATGAGTGAGCATGCAGAGGGCAGGTAGGGTTTGCATTCTGCCAAGGTCTATTTGCGATGCACCGACCCAACAGCAGAAGACTGCAAACACTGCATGGTCTACATCCTTCAGAAAGAGGGTTTATGATTAATCAGCATGGCTCAAACGGCCATGTTTATGGTTCACGTCAAACACTTTGTAAGCTAGAACTGTAGTTATGTTATTCTGAATCACAAGAGGAAAAAACCCTGGTCACTTCCATCATTAAGTGAAGTTAGTGAATCACCAACACCCTCGTTGCAGTATTTTTCTGAATGTGTTACTTGCCCATCAATATTTGCAGCATGTTTCTGGATATATTACTAGCCCATGAATATACACGTGAACTAGAAACACATCATGCAGCCCTGTTTGAACAACTCGAATCACATCTCCTCTAAGTGAAGGTAAGATCCAAAGAACTGAAAGATCTCCAAGATATCTCTCCAACCCCTCTAACCAACCAAGCTAATATCATGAAGGAATAATAAACAACGGATCATCAAGTTATGGCTTCAATGCGCACCCAAGAACCTACCCAAGAACCTACACAAACTGACCCCCATTCTGCCCTGTCATCAACAAGATGAAAATCATGAAACATAACCTCATCGTACTCTTTTCCCTTCCTCGTCACTTATTTTTCACGCCTGTGCTTGGGCTTTGTATCAGTACTGCTATCTTTGAGAAGTAATATATTCAGGTGGACCATCGCGGTCTTCAATTTACTAAATAAAGACTGGGGATCAGCATCAACTCCACTGGAATCTCGAGAGCAACATCTCTCAGAGCACAGAATTAGTAGCCAAAGGGAACTGATTTACTGAACACTTGATAATCATCTTGGTGCAAACAAGTACCATGTTTCGTGCCTTCATTAAGAATTATTGGAAGCAGATGCAGTCAGCAAGATGCCATCTTACTCTAGTAATTATCGAGCAATTCAGCAGTGCTCATTAGGGCAAATGTTCCACTCATAGCATAACCAGATCAAACATATAATCCATGGTGCCTTTTAGGGAGATCAAGAAAACAATATTATCATTGATGACAGCTTGTTAGTGCCGATGAGCTCCATGTAGACTATGTTGTGTACTTACTCAAAACATCTAGCACAGCAACAAAACGCATTGGTAGGCCAGCAGGCTCAAACCCCATCTCTTCAATGTTGTAGCTCATAATTAGAAGCCTGGATCTCATGATGTGCGATAACGATCAACATATGCCTTCACAAGTTTTTCTATCTTTGGTGCAGAGGCTGTTATATAAGTAGTTATCGCCTTCTCAGTCTCTGGCATCTGATTTGGCTCAAGTGAAGCAAAAATCTTATCAACAGATTTTTTCACAATCAGTTTATGAGCCTCTTTACTCAAATTGCCTTCCTTCCAGATTGGTTTCACCAGCTCCTTTACATGCTCCACCAAATGAAAACGAAAGTCTGATTTCTCATTGTTAAGTGATGCATCATTTTTCCTTTCACAGGTTTTCACCCTATTATCACCATCCAGGCTAGAGCTGTGTCCCCTATCATATGAAATCAAACCAAAATCATTTGATCCTTTAGCAGATACATTCCTTGCCAACTTGTCAGCAAAAGTCAATGGTTTTTCAAGACTTCCCCCTCTTATAACATTCGTATCTACATGTTGGCTTGAAATGCTGCAGGATATGTTTGAGGTCTTCAGATTATTTAAACTTTCAACTTTGGGAGGGTCGATACTGTCGACAAGTGGGTCATACTGACTTTTTGAAGGTGATGTACTGCCAGGAAAATCAGGAAAATTAAAAGAAGGTACAAAAGGCACTGAAGTTATCCAAACCTCATCCTTGATTGGGGAAAGTTTCCCAGCCGATGCTACCACAGGTTGAGATGAACTGCTCACATGTAATGTAGACCTAGAGGTACCACCCTTGTCAAAATCAGCACCTTTATGGTGACTGGCATCCTTATCAGGTGTTAATTGATGAAGAGGCAGGGTTCCATGGTGAGAAGTTGCTCGGAGAGACTGATTAACCAAGAAAAAATCAGAGCTGTCATGACCTTGCTTTCTGAATCCTGTATAACTATTCAAACTGTATGAGACATGGCTTGAACTTTTTTCTTCCTGATGTTTGTGAGGAAGATTCTCTGTTGCTCCACCATAAGCTGACAACTTCTTGCTATATTGGTGAGGATCTAATGAAATAGTTGAGTCAAACGGTTGATACCGATAATCAGGCTTTAAGGGGTTCTTTTCAAGGTAAGATCTTGATAGATGTGAATCCCTTGGACTGTCACCCTTGGCCACTTCAAACTGCAGCTTTCCTCCATCTAGGCGCAATCTAGAATAGGCACCCATGTCATTCAAACAGTTGTTAGTGCCCAAACTAATTTGATGTCCCATGAAATAAGGTTCATGATTCTTCTCTTGAACTACTGGAAGCTGAACCACCTCATTAGTAGGATTTGCAGTCAATGAACCACCAATTTTGAAACCATGCGAAGCCTTTAGCATGTGACAACTATGTTTAACAACGGGATGTGTCAACCCCCTATTATCTTCACCATATGCATGAACAAGGGTCCTATATATCTCATGTTGGGATGACCCCGCTGAATTTTTGAACTGGTGCTCTTTTGAGCTGGATGGATGTTGTATTTCAGATCCTTCTCCAGTGCCTCCATGATTTCCATAAACCTGGTTATCAGAACCAGATACCTCCCCTTCATGAAGAAAAGTGCAACTCTTCCCATTCTTGCATCGCCCTTGAGCATAAAAGGTACAGGTACGCTTTCTGGTTTTGTTCTTCATATCTCCACCAGGAGATGAACTCCCAAATCGTTGCGAACTCAAAGCATTAGAATCAGGTGGGCTTTGTGATACATGACCACCATGCAAATGAAGACCTCCAGTTTTGGATGTATCATCAATGGTAGGAGGTACAGGATCATTCCCAGCTTTCTTCTGATATTTTTCATCGCCATGAAGCTGCAGTGCTGGTTTCTTCTCAGCAGCAATCACTCCAACAAAACCGTTGGGATCCTTGGAGTTGGGCGACGGGTCCCTGGCCCTCTTCGTCGTCCC

Coding Potentia
Explanation CPC Score
noncoding -1.08628
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0316300.2 5 24454562 T C
Osa05LNT0316300.2 5 24454774 G A
Osa05LNT0316300.2 5 24454807 C T
Osa05LNT0316300.2 5 24456010 T C
Osa05LNT0316300.2 5 24456843 C A
Osa05LNT0316300.2 5 24457660 T C
Osa05LNT0316300.2 5 24458478 A T
Osa05LNT0316300.2 5 24458527 A G
Osa05LNT0316300.2 5 24458531 A C
Osa05LNT0316300.2 5 24463693 A G
Osa05LNT0316300.2 5 24464061 T C
Osa05LNT0316300.2 5 24466751 A G
Osa05LNT0316300.2 5 24466970 T G
Osa05LNT0316300.2 5 24469216 G 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
Osa05LNT0316300.2 osa-miR393a Translation 5.0 23.9 1 21
Osa05LNT0316300.2 osa-miR393b-5p Translation 5.0 23.9 1 22
Osa05LNT0316300.2 osa-miR437 Cleavage 5.0 17.14 1 21
Osa05LNT0316300.2 osa-miR1850.1 Translation 4.5 11.842 1 21
Osa05LNT0316300.2 osa-miR1852 Cleavage 5.0 14.898 1 21
Osa05LNT0316300.2 osa-miR1871 Cleavage 5.0 17.672 1 24
Osa05LNT0316300.2 osa-miR2096-3p Cleavage 4.5 19.085 1 21
Osa05LNT0316300.2 osa-miR2101-3p Cleavage 4.5 19.071 1 22
Osa05LNT0316300.2 osa-miR5339 Cleavage 4.5 18.283 1 21
Osa05LNT0316300.2 osa-miR5498 Cleavage 3.0 11.727 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0316300.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0316300.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0316300.2 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0316300.2 5 qRFC-5 Physiological trait Eating quality RG470 RG474
Osa05LNT0316300.2 5 qRGR-5 Physiological trait Germination/dormancy RM421 RM480
Osa05LNT0316300.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0316300.2 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0316300.2 5 APAGE1 Physiological trait Eating quality nan nan
Osa05LNT0316300.2 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0316300.2 5 QFla5 Morphological trait Culm/leaf RG470 RG346
Osa05LNT0316300.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
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