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

>Osa02LNT0172500.1

GAGTATTACTACATCGACCAAAATCTTCAGTAATCCAGAGTACAATGATAAAGGTGCGTTAAACGAATCCAAGTGACTCTCAGGCACAAATGTAACGGACTGTCTCCTATGCTAATGGACTGATGGCATCATACTACGTACTTAGTGGCATCCCATCAACGTCGCCTTGGACAAAAATAGGACTCTCTGGACCTTCTTTTCCTGATCTAACCCCAAAACTCCCTGCAGCTAGCTAAGATCCTTGCAAGAACTAAGGTGCACTAAATTGGAGGGCCAGTGATTAGTCATTGTCATTGTTGATGTCAAGTTTTTCATCACCGCCCTCGGGGTTGTGTTGATGTTCATCCCTGGCACTGGCAACTTCATCGGGGTCCTCCTCAATGGGCTTGAACTTAACCAGTATGGCAGTCGCGTTGTCATTTGAGTGCAAGCAATGACCAACAAGCTTCTCACAAGTCTCGCGTAGATTTTCCTCCCCCGGACGTAATTCCTGACGCACAAACTGAACAACATTGTTATTTCTCATGCCATCCCAGACACCATCACTTGCTATGACAAGAAATTCAGTATCATCAGTTATGTTTTCGACGCGAATGTCAGGAACACATGTCACCATTTGCTGTGAAGGAGGCATATTTCTGTTCTGCTTATATGCAAAATCACCAATCGCTCTGGACGTGGCTAACATTCCTAGAATTCTTTGCAAAAATACATGTCCTCCTGCTCTTTGAATTCTTTCGCGTTCAGCTTCATGGTGTGGTTTGTGATCAAAGGATAAACTAATTGCCTGACCATTCTTTGAAAGCACGCAACGAGAATCACCAACATTCCCAACAATGATCTGATTTCCTCTAATGATTACCACACATGCTGTGCTACCTTCATATGACGGCGGAACGTAATCCTCTGTGAAATGGTGGAGATTAGCACAAATGTTAGTGAGACAATTGCGATTAGCACAGGGATTAAGTGACTCCCTCCATTCATTTGATCGTTGCAAATCATCATCAAGTCTGAAGCATACAGACGTAATTGCATTGGGCAGATTGTTGATATAGTCTACATCCTCAAGAAGCATAGTATGAAATCGTTTTGCACAGTACATTGCTACTTCAGCTCCTCCATGGCCATCATAAACACCAAAGAATGACGTGGTCGCATCTAGATCTAGTTCAACTGCAAGTGCATCTTCCATGTGCGGGCGAAATCCTTGCGTAGTATATGAGGCATACTTAACTCTGTGATTCTCTCCTTCACTAGATGATGGTGATTGTTCTAGTGGACGGCTGGGAGATGCACCCATGGCAGAAGCCTCTTTCCTCTCCGCGATTCCGCTGCGCTTGTGACTTGTGAAAATTGTTGTGGTTGCGAAGCAAAAGTGGGTGAGAGGAGCCAAAGCCTTGCATGCAAGAGGAGGTGGGGCACAAAAAGTAGTAAAACCAACCCAAAGCTTCCGTCTTCGGCCCGAGCGGGCGCATCTCGTCCGTTGGATTGGCCCAACGTGGCTGCTGCGCCTGATCCGACGGCCCAGGTGCGCCCCTCGTGCTGCCCGTGCACCTGGGCCCACTCGCGCGCTGCCTTGTGGCCTTCGAGGAGGGATTCCTCCTCCTCCTCCTCCGCCGCCGCCGTAGCCGGGGTATTGGTCGGCGCCGCCGAGCCGCTCGGGAGTACAGGCGGAGGAGCCCCGAGGAGCTGCATTGAGGCCCACGCGCCGCCGGGCTCGCCGTCGTCGGCCGCTTAGCTCCACCCCCTTCGTCTTCTGCTCCGGCCGCCGCACAATCACAGCCTCACCCCTCCCCTCCGGGGTCCAGGCTAGCGCCTCCTCGCGCTCGCGGGCTCGCCGCCCGAGCTGTGCGCCACGCCACGAGAGCATCGGAGCACGCGGCAGCGGCGGAAGAAGGAATCCGGGTCGGCCATGTCGGCGAGGGCGACGGTGGCCGATGCGGGAGGTGGAGCGGCGGCGGCGGCGGTTGCAAGGCAGCACGCGGTGTGCGACGGCGCGTGGAGCAGGAGCAGGAGCAGGAGACATTGGCGTAGACGGAGGGAGCCCCGGCCATGGCGGCGCCGGCAGCGCGGCGCGGCAGGCGGCGGCCGGACGTGGACGACGTGTGGGGAGGTGGAGCAGCGGCGGTGGGATG

Coding Potentia
Explanation CPC Score
noncoding -1.28867
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0172500.1 2 23776405 T G
Osa02LNT0172500.1 2 23776873 A T
Osa02LNT0172500.1 2 23776948 T G
Osa02LNT0172500.1 2 23777010 C T
Osa02LNT0172500.1 2 23777070 G A
Osa02LNT0172500.1 2 23777220 A G
Osa02LNT0172500.1 2 23777302 A G
Osa02LNT0172500.1 2 23777547 T C
Osa02LNT0172500.1 2 23778183 G A
Osa02LNT0172500.1 2 23778326 G A
Osa02LNT0172500.1 2 23778576 A G
Osa02LNT0172500.1 2 23778617 C T
Osa02LNT0172500.1 2 23778861 A T
Osa02LNT0172500.1 2 23778899 G A
Osa02LNT0172500.1 2 23779158 T C
Osa02LNT0172500.1 2 23779486 A G
Osa02LNT0172500.1 2 23780371 A T
Osa02LNT0172500.1 2 23781578 G C
Osa02LNT0172500.1 2 23781814 T C
Osa02LNT0172500.1 2 23781935 C T
Osa02LNT0172500.1 2 23781969 C T
Osa02LNT0172500.1 2 23782087 A C
Osa02LNT0172500.1 2 23782147 T G
Osa02LNT0172500.1 2 23781398 A G
Osa02LNT0172500.1 2 23779259 T C
Osa02LNT0172500.1 2 23780405 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
Osa02LNT0172500.1 osa-miR5807 Cleavage 3.0 14.035 1 24
Osa02LNT0172500.1 osa-miR5835 Cleavage 5.0 21.198 1 24
Osa02LNT0172500.1 osa-miR166h-5p Cleavage 4.5 16.165 1 21
Osa02LNT0172500.1 osa-miR1851 Cleavage 5.0 12.287 1 21
Osa02LNT0172500.1 osa-miR2092-3p Cleavage 5.0 16.583 1 22
Osa02LNT0172500.1 osa-miR5487 Translation 4.5 18.386 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0172500.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0172500.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0172500.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0172500.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0172500.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0172500.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0172500.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0172500.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0172500.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0172500.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172500.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0172500.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0172500.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172500.1 2 nan Others Others C424 G45
Osa02LNT0172500.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0172500.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
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