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

>Osa02LNT0172700.1

AGATCTAAAATATGGTGACTAGAGGGTAGCATCCAAATCCAGCCAATCCGTATTTCCACTTCCACAGCAACCAGTTGAAATTTCGGTTGCAATTTACCTGCCGATCTAGAGCGCTGAGCCTAACTATATGAAAGTCCACATCTTTACAGCAAGCTTCCCTGGCAAATCACGGGCCACTGATCAAAGTTTGCTACTCTGCTCAGAGAAGAGATGCACAAAAAATGGCCGCGTCGCTTTTGATTTACACACGACACAGCCATGAAGTAGCTGAGATACTAGAAAGGTTTCGCCTCGACTGAAATGATACGGTATCAATCTCAACAGGCCAAAAAGCTTCCAGACGCATTTCCATCTACTGCCGTCCTTCTTCCTCATCTTCATTGTTTTCATCTGTTTGTGATGCCAGCTTCACAATGTCTTCCACACGGATCTTCCCATCTTTGTCTTTAGAGAGGTTGCTGACAAGCTCTTGGACGCCTTCCTTTCCTATTGTATCCTTCAGATAAGCTGCTGCTGACGCTACCTCCTCAGGAGTCACCTTGCCATCAAGATCCCTATCAAGAATTTGCCATCGGTTTCCAATTTGTGCATCCACGTCATCAATCTCCTTTTCTAATTTCTGGAGCATAGCATCAACCTTCTCAATCAGCGCCGATGAGACCTTTTCTTCTTCATCAACCTCAGCAGCCTTGTCCGACTCTTCTCTAGCAGCCATGTAAGCTTTCTTAGCTTCCTCTTCACCTTCTGTACCCTCCTTTTCAAGCATAGAGTTATACAGTTCAATCTCTTTGTTGACAAGGCTGAGGAACTCTTGACGCTCCTTGCTAACAGACGATGCGGATGCCAGTACAGCCAGTGCTCGACTAAAATTACAGAGCTTTTCCTTATCGTGCTGTTTTGCTTCTCTCAGTTCTTCTTCTTCCCTAGCAGTAGGACCAGTCATTTCCTTCAAAGCCAAATCTTCTTCAGCAGCCTTTGGTTCTTTGAGTTTGGCCTTTTCTTCTTTCTCTTGTTTCGCTTTTTCTTCTTTCTCTTTCTTCTTCTCTTCCTCCTTGATAAGTTCTTCCTGCATCTCAAGGAATTCCAGTTTTCTCCTCCTCTCAGAAACCGAATCTTCAGATGGCAATACGGTCCCAACTGTATCCACAACTTCATCTGGTAGAGAAGATAAGGTTGCTACAACAGCCTCCTCAGGCTTCATTTTCCCAGATACGGTAAAAGCTCTTGAAAGTATGAGAAGAGAGGATGGCACAGCATGATTAAGTGAGAGATCCAACCAATCTCGGAGCTGTTGGCGCATTTCTTCTGTTGACAGCAAACCTAGGTGACCACGTTCACGACAGGCTTGCCGAAGTTCCTCTTCAGAGAGAGACTCAACACCCTCAGCTTGAATCATCTTATCGTCATTCTTAATGTCTTGCAGTTTTTTGCGAAGCATGAACCTCAAGTAGTGGTCAGTACCGAAAGGTCGAATACCCATATATTTGCACATGTTTACCAAGCGTGGTCTGCTCATGTTATCCAAAGTCAGCTCATCATTAAACAGCTTCGCGAAGTTCAAGATTTCATCATTTGAGACATGTTCACCTCTCCTAACCTTGTTCAAAAATTCATCAAGATCTTCGGCTGTTTGTTTTATTTCTCCACTACGTGATGTTTGAACTTCCTTTGCCATTTCTTTTGCAGTATCTTGCAAAAACTTGGCATACTCCATTCTTGCTTTCAGTTTCCTTTTCAACGCTTCCTCTTCTTTCATCTTGTCTTGGAAAGTTGAGGGAAGCATATTTGGAAATAACTTGAGGAACACTGGAAGTAAGAACTCCATGAATGGAACAATGATGAACACAGCAAAAGGTACCAGCCTGAAGATATCTGCTGTTGTACGGGTCAGTTGTTGTCTCTCTCTTCTTGAAAGGTTCTTTCCACCAGCAAGTTTCACCAGTAATCTTGACGAAATCCTCACATCTGCCCAGAGTAGCTTTGTCCCTAACCAGTAATGCTGCAGCGTTGACACAAATTCATCCTTCCAGTGCTTCAGCTTTGCAGCCCAATCAGCTCTGCTCATCGAAGCAACAGCTCGGAGAGCAGGACCAATACCCAGAAGCCTCGCCCAGAATTTTCGTACAATTGATTGGCCAGCCTTTACAGATTCTTGTACCTGCTTAGCTTTGGCTTTAGCTTTTGCACTGCTTAGGCCTTCCACAGCCTGATCACATTCTTCTGGGGATGCCTCCTTTTTCCTTTTGTTCTGTTTCTGATCCTCACTCTGTTCATCTTCAATATCCAACTTAGGTTGCCCAGCTGTTGCAGTTGAGGCTGTGCGGACTGACTGCAGCAAATGTCTAGCACCCATAGGCAACCCAAATTCCTTCCTTCCAATTCCATAAGCAGGTAGAGAAATCCCATGGGCTGGGCGCCGCAGAAGCCCATTACCAAGGGCTAGTAGATCTCCCTTTATCAATTTCACACCATACTGCCCTTGCTCCCATTTGGAATCCCCAGAGCTTTGCTCAAGAAATCGCTGTCCGATTCTTGATTCATCCTCAGAACCAGATCTTCCATGTTGGAAGGTAGAGAAGGGGGACAATGAGAGGGTAGGTGCGTTAACATGATCCAAAAGATACTTCCTTCTTCTGATGACCGCCCTTGAAGCCATACTTAATTGCTTCACACCTTTCCAATTAGAAGGCCAAGGTCATGCCTTTTTCGGACAAAGACCCGCCGGGCGAGAGGCGCGCCGCCGAGCCCGTCGAGCTGCTTGGATCGAGGAGGGGTTAGGGTTTTGGAGAGAGGAGGAGGAGAGAGAGAAGAGGAGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.577762
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0172700.1 2 23867768 A G
Osa02LNT0172700.1 2 23867620 G C
Osa02LNT0172700.1 2 23867975 T G
Osa02LNT0172700.1 2 23868331 T C
Osa02LNT0172700.1 2 23868548 T G
Osa02LNT0172700.1 2 23868939 C T
Osa02LNT0172700.1 2 23869358 T C
Osa02LNT0172700.1 2 23869654 A G
Osa02LNT0172700.1 2 23869934 G A
Osa02LNT0172700.1 2 23870449 T C
Osa02LNT0172700.1 2 23871226 G A
Osa02LNT0172700.1 2 23871474 T C
Osa02LNT0172700.1 2 23871696 G A
Osa02LNT0172700.1 2 23871735 C T
Osa02LNT0172700.1 2 23872551 A G
Osa02LNT0172700.1 2 23872666 A G
Osa02LNT0172700.1 2 23873196 A G
Osa02LNT0172700.1 2 23873294 G A
Osa02LNT0172700.1 2 23873847 T C
Osa02LNT0172700.1 2 23873951 A G
Osa02LNT0172700.1 2 23874700 A G
Osa02LNT0172700.1 2 23867054 T A
Osa02LNT0172700.1 2 23873946 A T
Osa02LNT0172700.1 2 23869317 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
Osa02LNT0172700.1 osa-miR5806 Cleavage 5.0 11.708 1 21
Osa02LNT0172700.1 osa-miR5818 Cleavage 4.5 13.411 1 21
Osa02LNT0172700.1 osa-miR5337b Cleavage 4.5 17.837 1 21
Osa02LNT0172700.1 osa-miR7695-3p Cleavage 4.5 17.689 1 21
Osa02LNT0172700.1 osa-miR167c-3p Translation 4.0 13.979 1 23
Osa02LNT0172700.1 osa-miR156k Translation 4.5 14.504 1 21
Osa02LNT0172700.1 osa-miR167d-3p Cleavage 4.0 13.979 1 22
Osa02LNT0172700.1 osa-miR415 Cleavage 3.5 10.161 1 21
Osa02LNT0172700.1 osa-miR529b Cleavage 2.5 19.676 1 21
Osa02LNT0172700.1 osa-miR1850.2 Cleavage 4.0 15.872 1 21
Osa02LNT0172700.1 osa-miR1854-5p Cleavage 4.0 10.752 1 21
Osa02LNT0172700.1 osa-miR1320-5p Cleavage 5.0 9.37 1 21
Osa02LNT0172700.1 osa-miR2099-3p Cleavage 4.0 16.306 1 20
Osa02LNT0172700.1 osa-miR2100-5p Translation 4.5 19.486 1 22
Osa02LNT0172700.1 osa-miR5071 Cleavage 3.0 15.31 1 21
Osa02LNT0172700.1 osa-miR5160 Cleavage 4.0 8.961 1 22
Osa02LNT0172700.1 osa-miR5338 Cleavage 4.0 13.414 1 21
Osa02LNT0172700.1 osa-miR5338 Translation 4.0 19.147 1 21
Osa02LNT0172700.1 osa-miR5500 Cleavage 4.5 9.617 1 22
Osa02LNT0172700.1 osa-miR5522 Cleavage 2.5 11.887 1 21
Osa02LNT0172700.1 osa-miR5522 Translation 5.0 11.433 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0172700.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0172700.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0172700.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0172700.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0172700.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0172700.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0172700.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0172700.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0172700.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0172700.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0172700.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172700.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0172700.1 2 nan Others Others C424 G45
Osa02LNT0172700.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0172700.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172700.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
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