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

>Osa02LNT0174700.1

ACAAGTAGCATTCATCGTCTCCTTCCATAACTATGGTAGAAACCACCAGCAATGTGGTGCCGCTGCCGACCTCCTCTGATCGAACCATCCCAAATGCCCCGTCCACCTGATCTGATACTGCTGCCGGTGTTGCTTCCTCCTTGACCCCAATTTCCCATCTGTGACGATCCACCATTCATTTCTTCTTCCTCCCTTTCATTGTATTCCAGGATCCTGCGCTTAATACTCTGCTTCTCCTCAAGCTCAGCAGCCTCTTGCTGCTTTGTGCTTTGCACAAGTGAGCAGTCACCAGGAACGAACATCTGTTTTGTTTGCTGCTTGTGCCCTTTCTTCATTAGCACCTTAACACGCACCTTGCTGCCACCCCCAGCACTACCACCCTCTTCATCCACAGTTTCTTCTCCACTCTCGGACTCGACAGCCCTTGGGTCCTTAGAACCCTCAAGGACATTCATTGGTACCATCATGTTCAAAGTGGCCCTGGGCCGTACCTCTGATTTACGTGACTCCAAGCTCTCCTGAAGAAGGGCTTTCAGCTCCCGATCAAAGTCTTCTAGCTCCTTAGGATCAACTTGCACGACTTTATGTCTAACCTCAACACCTTCATCTTCATCAGAACCAGCAGGAATGCCATCATCCTCATCATCACCTTCATTCTCAGATGCGTCATTTGATTTATCCTCGAACATAAGATCTTCCTCGTCTTCATGACCATCAATGCTGCCACTATCTGAATAACTTTCACTGTCAGCTCCTTCATGATCCTTGCCATTTTCCTCGGCTCCATTTGCTGAGCTCCTGCCGTTAGCAGAAAAGGCAGTATCATGTGGCTGCACCTTCTGAGATTCGCTGTCTGAGAGCTTTTCATTTTCAGGCTTCTCAACTGAGGCTGCACGCTCACTTTCTTCGAGCTCAAGTAATGCAGCATCCAGTTCTTCTACTGATGAATACCTAGCCATGTTGGGTCTTAGCTCAGCAAACAAATCCTGAACGTCAAATTCTATGTCAAGTGGTAAGGGCCCTTTACTAATAATATATCTTTGAAAATGCAGCAAGAACTTGTCAAGCTTTCTTTTTGAAGAGCCTCTGTTGAAATAGTGGCCACAAGTCTGCAGAAGTGTAATGATTAACCTGATCCTGAAGCAATCTTCTGGTGGATCCAACACATCTTGCTCAGGAGTTCCATGACCAAATACGATGATAAGGTACAGAGTCTCGAATACAACTGATGAATCAATATGCTTGTAGCTGTATAGCTCTCCAAGGAATCTCATGTGGGCGAGACGCCTTTGTTGCATTCCATAGTCATTCAGCTCCAGCCCTACCCTTGTCTCCTCTAAAACCTCATCTACCACTGAAACAGCAAAGTCATCATGATGGCGACTAAGACCAGCAGTTAGAAGGGCAATCAGATGAACATGGCTGTATTTTCCCTTGTGAACCTTTAGAAAACACTTTATAAGGTATTGTTGGCACTCCACCCAAGGTAGCTTGCGTAATTGGCGAAGAACATGTTCAACACTTGATTTATCAAGATCGGAGAAAAGCAATTTCCGTATGTATTGATGCAGAGGTGGCCGAACTTTTGAAACTCGAGCAGATCTTTCAGGTGGTTTACAAAGGTAATAGGCATTTTCTACAAGTGTACTGTGGCGGGGATCCAAATTCTTCACATTTTTCAATCGCATCAGTATCTCCAACATGTTAGCCATACGAATAGTAGTTTCAGGTGAACGATACAAAAAACGTCCACAAGTCTCGAGTAGATTGCAGGCCACATCAATGTTATGATGACTGAAATCATCTAGGCAGGACTTCAAGCAGCTAAAAACAAGAGCTGCAGGTGCAATTTTGAATTTGCACAACTCCCCAATAAACCTAATGTTTTTTATTTTTGTTTCAATGTTGATCTGATCCTTCTTATTTATTAAGAAGTTGAACTCCTCTTCAAGCATAGAAAGAAGCATACTTGGAACATCTTTCATACATGTTGAAAGTGTAGCCACCAACCGAGAATAGTAAGGCAAAAGTTCCAGTGAAGTCCTTGGAACATTGAATAACGTCCGCACGAGTTTCTTTCGACTTGCTTTAGAATTTAGGTAGCAAAACTCAACCGTCAATTGGTCAATAAGATCACGGCTAACACATCCTGGCAGCCTCTGAAGGAGGTTGTCTAAACTTGCACCATCCACAGCTCTTATTTTCTCCTTCTCTCTTTCAGTTTTTCTGTCAAAATCCTTCTCTTTAGATTTTTCCTTGTCTACACCTTTTCCCTTATCTTTATCTTTTTCTTCACTATCCTTCACTCCATCATCTGCCTTTCCTTCCAGATGATATTCAGTGATGGAAGAAGTTTGAGGATTGTCATGTACGTCAGTATCTTGTTCTGCGACGGGTTCAGATTGTTCACGACCCTTCTCATTCAACTTTGGTTCAGCCTCTCCCAATAACACAGCGGGCACAAATGCTCTGAGATCAGGTAAAGATTCATAAAAAGCTTTTGTATCCTCATCATCCCAAATAGGTTCCAGTGCAGACGGTTCTTTTGCAGTAGACGGGGCTACATCACTTCCTGTAGTAACTCTAGTTGTGTTTCCATCATCTGGCATCACGGGGGGCTGCATGTCAAGAGCTTCAGCTAACGAGGATACACCACGTTGTAAATGATCAAAAGACTTCCGGAGTTTTTCATACGAAGCAGTGTTCTCGTCGCTTAGTTCACCTTTGGCAGTTAAAACTTTTGCATTCTCTGCCTCCATCAGACGAAGAGACGCATGTTCTGATTGGAGTAGTTCAGCTACAGCATCATAATAAGTGTTCAAGGCTTTCTTGAAGAACTTTTTCTGATCAGCCGTAACATTTAGATCCTTAAATAACTCATCATAAGCTTCTTGACCATGAGACTGTAACCCTATGAAAAATCTCCCTTGACGAGCAAAGGCAGAAAGAAGAGACAAATTTGCCTGAGTTGTTTCCCGGTCCTTCAAGTGTTCTAATGATGTAAGATCTTTTATAATGTTTACAAATATACTAGCATCTTCAACAATCCCAACAAAATACAGTTCAATTAGAAGTTTCAGTGTGCTTCTCTTCTTCATAGCTCTTGAGTTTTTGTCTGCGTCCAAATCTTCTCCAGATTTCCCAGGAAAGAATACCTTTAGTAGCCCTTGTGTAAGACAAGGAGAGAAATCCTTGTATCTTTGATGAAGTAAGGAGCAAACCTGAACAGCAGCTTGTATATCAGCAGAACGAAGTTTGGCCTCACAAATATAAGAAACTGCCTCGCTGACAAATTTGCTCAAGTTCACACTTTTCAACTCATCCATCAATCCATCCTTCTGTTCATCATTTATTGTTTTGAGTTTCTTTATAACTGTTGTATTTCGCTTAATACTGGAGTCAAGAGTCCTCAAGTAATTTGCATCAGGCCTTTCAGAGTTTAGGTTGCTCCGGCGGAGGGCAGTCTTTTGATCAACAAGTTTTTTGTATTCTTCAAGACGAGCCTCCTCATCATCTTGCTTGTTTTGGCGGGTCTCGTCATCTTGCTTGGCTTCCTTGCTGTTCTCATTCTGAGTGTTCTCCATTTTATTTTACAAAAAGTAGAAACCAGATATACACAGTGGAAAGCTGCAAAACTGCAGGAGAGGGCGCGGCGGTCGCCGGAGACGAGCGCGTGGCTGGGGAGACGCCGCGCTTTCTCGGTCGGAGGCCGGCACGAAGGGGGAGGTTGCGGGCGAGGAGGAGAGGGGTGTGGACTCCCGGTGGGAGGGCGCAGGGGAAGAAAGG

Coding Potentia
Explanation CPC Score
noncoding -1.05176
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0174700.1 2 25281023 C T
Osa02LNT0174700.1 2 25276363 T C
Osa02LNT0174700.1 2 25276368 A G
Osa02LNT0174700.1 2 25279911 A C
Osa02LNT0174700.1 2 25274032 G A
Osa02LNT0174700.1 2 25274446 A G
Osa02LNT0174700.1 2 25275054 G A
Osa02LNT0174700.1 2 25275093 T C
Osa02LNT0174700.1 2 25275198 G A
Osa02LNT0174700.1 2 25275510 T A
Osa02LNT0174700.1 2 25275767 A T
Osa02LNT0174700.1 2 25275769 C T
Osa02LNT0174700.1 2 25275772 C G
Osa02LNT0174700.1 2 25276090 G T
Osa02LNT0174700.1 2 25276425 G C
Osa02LNT0174700.1 2 25276556 T C
Osa02LNT0174700.1 2 25276944 A G
Osa02LNT0174700.1 2 25278909 C T
Osa02LNT0174700.1 2 25279846 A G
Osa02LNT0174700.1 2 25279926 T C
Osa02LNT0174700.1 2 25279945 T C
Osa02LNT0174700.1 2 25280282 A G
Osa02LNT0174700.1 2 25280489 T C
Osa02LNT0174700.1 2 25281056 C T
Osa02LNT0174700.1 2 25281558 G A
Osa02LNT0174700.1 2 25281589 C T
Osa02LNT0174700.1 2 25282618 A G
Osa02LNT0174700.1 2 25282693 T C
Osa02LNT0174700.1 2 25282892 T C
Osa02LNT0174700.1 2 25283128 T C
Osa02LNT0174700.1 2 25283226 G C
Osa02LNT0174700.1 2 25283523 G A
Osa02LNT0174700.1 2 25283196 T C
Osa02LNT0174700.1 2 25283849 C G
Osa02LNT0174700.1 2 25277231 A G
Osa02LNT0174700.1 2 25277243 C T
Osa02LNT0174700.1 2 25278310 A G
Osa02LNT0174700.1 2 25278768 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
Osa02LNT0174700.1 osa-miR5534a Translation 5.0 19.583 1 21
Osa02LNT0174700.1 osa-miR5539a Cleavage 5.0 20.363 1 22
Osa02LNT0174700.1 osa-miR6248 Cleavage 3.5 10.793 1 21
Osa02LNT0174700.1 osa-miR6248 Translation 5.0 17.895 1 21
Osa02LNT0174700.1 osa-miR6249a Cleavage 5.0 20.262 1 21
Osa02LNT0174700.1 osa-miR5539b Cleavage 5.0 20.363 1 22
Osa02LNT0174700.1 osa-miR6249b Cleavage 5.0 20.262 1 21
Osa02LNT0174700.1 osa-miR160f-3p Cleavage 5.0 21.726 1 21
Osa02LNT0174700.1 osa-miR171c-5p Cleavage 3.0 9.576 1 21
Osa02LNT0174700.1 osa-miR171f-5p Cleavage 5.0 7.304 1 21
Osa02LNT0174700.1 osa-miR1858a Translation 4.0 4.844 1 21
Osa02LNT0174700.1 osa-miR1858a Translation 5.0 4.643 1 21
Osa02LNT0174700.1 osa-miR1858b Translation 4.0 4.844 1 21
Osa02LNT0174700.1 osa-miR1858b Translation 5.0 4.643 1 21
Osa02LNT0174700.1 osa-miR1861g Translation 5.0 11.867 1 22
Osa02LNT0174700.1 osa-miR1866-5p Cleavage 4.5 12.31 1 24
Osa02LNT0174700.1 osa-miR1873 Translation 5.0 9.462 1 24
Osa02LNT0174700.1 osa-miR1873 Cleavage 4.5 15.208 1 24
Osa02LNT0174700.1 osa-miR2104 Cleavage 4.5 21.202 1 22
Osa02LNT0174700.1 osa-miR5504 Cleavage 4.5 19.741 1 21
Osa02LNT0174700.1 osa-miR5506 Cleavage 4.5 19.853 1 21
Osa02LNT0174700.1 osa-miR399a Translation 5.0 16.261 1 21
Osa02LNT0174700.1 osa-miR399b Translation 5.0 16.261 1 21
Osa02LNT0174700.1 osa-miR399c Translation 5.0 16.261 1 21
Osa02LNT0174700.1 osa-miR5157a-3p Cleavage 4.0 19.326 1 24
Osa02LNT0174700.1 osa-miR5157b-3p Cleavage 4.0 19.326 1 24
Osa02LNT0174700.1 osa-miR399i Translation 5.0 16.261 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0174700.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0174700.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0174700.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0174700.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0174700.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0174700.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0174700.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0174700.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0174700.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0174700.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0174700.1 2 Hbd2 Physiological trait Lethality nan nan
Osa02LNT0174700.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0174700.1 2 nan Others Others C424 G45
Osa02LNT0174700.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0174700.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0174700.1 2 Sn2a Morphological trait Dwarf 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