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

>Osa11LNT0101200.1

GTAGATAATATATTAGACTCAATTAAACAGGGGCTATTTACAAGGAGGTGGCAGCTTAGTGCTGAGAGAGAGGAAGTGCAGGGTGGGAGGGCTGAGCTTACTTTTCTACGCATACCAACATTTATATGGTAGGACTGGCGGCTGACAACTTACCTCACCAAAATAGAAAACCAAAACTGCAGCAAATAAGAGTGCAACTTGACCACCAAGGACAAGCACCATCTACAAATAGGGTACTTTGAGCTTATCCAATACATCAAAGGGGGAAAAAAAGCATTAACTCCACTACGAAATGCATTTTCTTATAACGATGCATCGCGTTCTTGTCTCCCATGTTACTTCAAAAGACGTTACCAGATGGGAAAGCATTAGCAGTTCTCAGAATTAAGAGACGAGGTTGACAAGCAGCCTCGCATTTCTCTGCCGACTGAGCCCCTTTCCATTGAATTAGCATGACTATCTTCTGATCTTGAGTTCAGGGTTCCCGGATTCATCCGCTGAACCTCTTCTCTTGTGTAGATGAAGATCTTGTGAACCATGTCGCAGAATTCAATCCAGGGATCATCCCCAACTAGCATCATGTCACCTTCGTTGTCAGTGTAGACAACCATCCACTCCTTCTTAGGACCCTTCAGTTCACCATTGAAATCAAACATGTCATCCAGCTCAGCAATCAACTCTTCATAGCCATTAAACTTTGTAAGGTCCACAGACCTGCCAAGTGCAATGCCTTGCTTGTGGACCTTCTTGCAGCTTCTAGTTGATACACCTTGTGATTTGCACGACATGTTTCGTGAAGCTTGCTGAGAAGAAGGCTTCTCAGGAACAGAGTCTGGTTGCGGAGTATCAAGTGGCTTCATGGCCTTAGAAGGATCAGAACATTTCTCTACTTCAGTTACATCTGGTCGGCGCCATTCAGTAGCACCTGGTGTTTGTGGCGTCCCATCATATACAACACTTGATGGAGATTTCAAAGGTTCAGATTTCGCTGGGCTGTCAAGGTGAATTCCAAATAGTTTGCATGAAGCACCTTTAGCTTTCTGAACATCACCATGGGCAACAACCAGAGGTTTAGGCTTGATCAGGCGTGGCTGTGTATCATCCATGTGGGAATTTGGCATCATATGGCCAAACCAACCCCCTGAGTATTGCTCAGTACCTCGGCCTGGCAGTGCAGCATAAACTCCATTCCCAAACTTTGTATTTCCAGGCCTTTGAGACAACACACCAGCTTCCTGAATCATTGAATAGTTCTGTTTGTTTAATCCAAGGCGAGTATTTGGAGGCATGAAGGACCATGAGCTGGGGAACATATTGTGATTGCTCTGTTGATCTTGATACTGAGCATTTACTGTGTGCCAGAAGTTAGAATGGCCTGCAGTAATCTGCTCAGGTAAAGAACAGAAACCCTGTGGGATTTGTACATCTTTAGGTGGCTGAAATCCAGATAGCATCTCACTGTAACTCTCAGGCTTGCTCATCTGCATCCGACCATCTGAACCTAGCTTCCACTGTATGGGAGTGTTATTTTTCTCACGATCAAATCCAGATGGACGCATGATTGATTTCTGAGCACTTTCTAACTCGCTGCTATTGCCGAAACCACTTTTTGGGGTTGCATTCTCTTGTGTCTGGAAGGTCCTTTGCGTACCATTTGGTTCAGACTCGACCACAACTTTCGTAGCAGCTTCTTTTGCTATAGCAGAAGAGTCAGCCGGCAAAGCGGTAGCATTCGGACGAAGCCTCTTGGTTCTTGGAACTGGTAGTGGGTTGACAGGAGGAGGGCTTACAGCAGGTTCTATTTGCCAGGGAGAAACTCTTTCAGGGCGAGGTATGGAAGAAGCTTCATCCCATCTCACCTTAAGGGAGCGCCATTTTGATTCAGGCCAGCCAGCTGGATCAGAATCCCCCATTCCGACAATAGTCCCAGTGAATCTTTGCTCTGGAGCCTCTTCACCTTCAAACCTCATCTTAAATCTCATCCCAATGGAGTAATTTTGTTTCAGTGATTCCATATAGCGATCGTAAGGGACCACAAACTCGGCTGGACTTGTCCTAGGCTTGTAGTAGACAGTGAACATGGTCCCTGTGTTAACAGCATGCCATGCTGTGGCAAGAACCCCAAGATGCATGCTGTGGCTTGATATCACTGAAGATGGAACATTAGTTTGCTGCCTCATTGCACGCCTGACTCCAACACGCAGTTCCCCGTTCTCACCTCTGAGAAAGATAAAGGCATCCCCAGCAACAAGCCGTTTGGCACTAACAAACACACTCCAGCCACTCTGCAAAAGGTGTCTTCGTGGTTGACCTCTGAATATGTGACGAAAGCGCCATTCCACACCGTGCAGATCCTTGGCCACCAGCTCTTGTGTTGGAGGCTGACGGCTCATATCCAGTGGTGGGAGGCATTCGTCCGCGTGGCGTCGCAGCACCGAGAAGCCGCCATGTGTGCTCGTGTCCGAGGCGGTCAATGTCTTGCAGAATGAGTGCACCCGTGGCCTAACATGCCCAGCTGCTGGAGCAGAAGGCACCTCCTCCTCAGTAGAGCCGTTATCTTCTTGTTGCTTCGATTCAGGAAGCAGAGTGAGCTGAGCATAAACCTCGTCGGTGTCTGGCTCGGCCTTCAGCTCAACGTTCATAACCTCACACAGGATCTTCCATGGGAGATTGTACAACTGCATCCGCTGCTCGCCTACCTGGTTGGTCGAGGCCTCCACCTGCTCGATGTGCCCCTGCGGGAAGTAGAACACCTTCTCCCCAACCCTCGGCACCGTCACCAGCGGCCCCGCGCACGCGCTCCACAGCTCCGTGAACAGCGCGTCCTCCCCTCCTCCTCCTCCTCCTCCGCCGCCGCCGCCTGCTCGCGCCACCGCCGCGGCAGCAGCATCCCCCTCACCGCCGCCGCCGCCGACCTCCGCCGTCGCCATCACCCCACCAGATCTTCACATCCCCCGCGGCCACGCCCGAATCGCGCGAATTCCCCCGCCGGATTCGCGCCCCCCGCCCCCTCGAATTCCCCTCCGATTCGCAGCAGCAGCACAAGCAGCTTCTCCTCCTCCTCCTCCACCACCTCCTCTTCTTCCTCTCCTCTCCTCTCTTTTGTTTTAAATTTTTTTTTTACTGGGTGAATTTAAGCGAGAAAAAAGAAGAAAAAAAAAACAGTATTGGCACAGCAATTGTGTGAGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.596424
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0101200.1 11 18935820 T C
Osa11LNT0101200.1 11 18936094 T C
Osa11LNT0101200.1 11 18936331 G A
Osa11LNT0101200.1 11 18936346 A G
Osa11LNT0101200.1 11 18936734 A G
Osa11LNT0101200.1 11 18936847 A G
Osa11LNT0101200.1 11 18937213 G A
Osa11LNT0101200.1 11 18938614 A T
Osa11LNT0101200.1 11 18939186 G A
Osa11LNT0101200.1 11 18939235 A C
Osa11LNT0101200.1 11 18939382 A G
Osa11LNT0101200.1 11 18939504 T C
Osa11LNT0101200.1 11 18939506 A T
Osa11LNT0101200.1 11 18939965 C T
Osa11LNT0101200.1 11 18939966 T G
Osa11LNT0101200.1 11 18940078 A G
Osa11LNT0101200.1 11 18940102 A G
Osa11LNT0101200.1 11 18940397 A G
Osa11LNT0101200.1 11 18940758 G C
Osa11LNT0101200.1 11 18940773 T C
Osa11LNT0101200.1 11 18941272 G T
Osa11LNT0101200.1 11 18940764 A 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
Osa11LNT0101200.1 osa-miR5512b Cleavage 4.0 12.352 1 21
Osa11LNT0101200.1 osa-miR319a-3p.2-3p Cleavage 4.5 12.94 1 20
Osa11LNT0101200.1 osa-miR319b Cleavage 4.5 12.94 1 20
Osa11LNT0101200.1 osa-miR408-3p Cleavage 4.5 24.055 1 21
Osa11LNT0101200.1 osa-miR1425-3p Translation 5.0 22.956 1 21
Osa11LNT0101200.1 osa-miR2096-3p Cleavage 5.0 22.414 1 21
Osa11LNT0101200.1 osa-miR2872 Translation 5.0 16.818 1 21
Osa11LNT0101200.1 osa-miR5503 Cleavage 4.5 14.949 1 22
Osa11LNT0101200.1 osa-miR5512a Cleavage 4.0 12.352 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0101200.1 11 gpl11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0101200.1 11 gw11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0101200.1 11 yld11.1 Resistance or Tolerance Drought tolerance RZ537 RZ900
Osa11LNT0101200.1 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0101200.1 11 hbd3 Physiological trait Lethality nan nan
Osa11LNT0101200.1 11 Hbd3 Physiological trait Lethality nan nan
Osa11LNT0101200.1 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0101200.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
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