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

>Osa03LNT0229000.2

GATGAAGATCACTACTCTCTCTTGATTTAAGGACAGAAGCAAAATACAAAACGAACAATACATTATACTCTATAATTAATTTAAAGGCACTTACAGATGATAAGGAGAAGAGATTTTGATAATAACGTAAAGATAGGAAGAAGAGAGAAGAATACTCTAGGCTAACTGAATGCTTGAAAAATAATTCCAAACTTAACATCTCAATCTGAAGAAAGAAACGAGAGGCATTTCATTTCGTCAGTAACTTGATCTCTCTCTATCAACAGAGCCTATATGAATAACTCAACGCTGATCATGGGTGCAAGCTCAGCCTTCATCGCTGTCGCCATTGCAGGGCACCGTGTACTGAATCACGACTCGAGCTCCTGACGACAGCCCAGCAATGACAAAGAGTTGGGGAGGGTTAAGAGAGGCCACTAGCACTTAACTTTCTTCGATCTTGACGAGCTTCTCCTCCTTCCTGAAAGAGTCTATCCTGCTGCCCGGTGCTCCTGTGGCGTCAATGAACCTCTTGCTGCCGTCTCCTGATGAAGCAAGGCTGCAGTCTGGTCCGGCCGACGAGCTCCTCCGGCAGTCGGAGATCGGTGACTTCATTGCCTCGCTCTTGGGGTGCAGGAAGGATGACAGTATCGGCGTCCGAGGGAGGCACCTTGCGCGAGATGTGTTGACGGTGTCTTCGTCAGGTCTCGCGCAATCTAGCGTCTCGTTGCTCCTTTCCGCATTGTAGGAAGAAGAACGTTTAAGCGCTGAATATCTGTCAGCGGGTACATCTCTTTGCATCTTAGTTTCGATAAGGCTCCCACTAAAGTATTCCTTGTCTTCCAGACGCATACCCATCAATCTGGGATTCTCTGACAGGTAATCAAGCTCACCCATCATCATGGTACGAGAAATTAACGGTGACGGGAACTTCATGTTTGGGAACCTTGGCTTGTATCCTTCAACAAGTCTGATATTCTCATGATCTTTCACCGAAAGCGAACCACAGGTGATAAGTTGCATTAGTACATTCGCTGGCCTCAGCTTGGGGCAGGTTGGCATAATGATATCATCCTCTTCAAGAATCCGAAAACTATTCAATGCATTGTTATCTGCTCGTATCAAGGACTCTAAACTCTCCGACTTGCCACGGGATGAAGGTATGCTCAGTGGAGTATGACACTGGGACATGGCCTCCCTGGCGATCCCTTGGAGCTCTGCTGACCGGCGTGGTTGGCTTTGCCGGTACTCAGTAATTTCCCGGACTACGGAGTCATGATCAGTGCTCAAACTCTTCTTATGCATCTCGGGCACTTTCCGGACTGACCTTCTGCCGAGGTCATCAGTTTGAGTTGCAGCATCCACACAGCCAGTGGGCTTGTAAACTCTGAATTCTGCAGGACTCGCGGAACCAGCCCTTGACAAGAGAGTTCTTTGAGGCTCCGACTCTGGCGACATGTTCTCCAAGGAGGTAACTCTGCATTGCACTGGTGAGTCATCCTCTTCTAGAGAAGGAACCGAAGGCGAACGCCTCGGCTTGGCTTCTCTAACTATCACACTAGGAGGGGAGGAGGAATAGGAAGCCTCTCTAGGCAAAGGCAGCCGTGCACCCTCTTTCAGCCTGCTCTGTTGCTTTTGGTTTCCATTGGTACCCTGATAAAATTGGCCTGAAGAAGACTGGTCCAAGAGCTCGGAGCCCTTGAGCACATATTCGCCGTCGGTTGCCGGGTGGACGAGATCATCCTCTCCAAGATCATGCCACACGAATCCATTCTTGTAGCTCCTCTTGCAGGACCACGAGTACATAGCGGCCATACCCTTGCCGCGCACCATGTTAAGGTGGCTAATCACATCTCTGAGATAGAGCCCCTCCGGCGAGGAGACAGGCACCTCGACGAAGTGAGGATGCTCAAGGTGGCGACTCCGCGTGAGGTAGTACACCACCGGCACCTTCCTCGCCGCCGGCCTCTGCCTCTCCGGGCTCCGCGGCCGCCTCCCTCGGCTCTCCATCTCAGCCAAGCTCTCCAATTAAACCGCCAAAACTACCGCCAGTTCAGCGTGAGCAGCAGAGAGAAGAAGAAGAAGAAGAAGAAGAAGCGGAGACTGAAGCGCCCAAGAAAAAAAAAAACTGTGAGTCTTCCCTGCTGCTGCTTGTCAGCTGTCACCTCTCCAAGACTTGAGCTCTTGAGAGAAATCAACAGGAGCGTGCCTCCAACATAGAGAATCGATAGGTCAAGAATTCCCAGGTGGGCGGTGGCACCTCGAAGAAAAAATGCAAAGCCCTTTTCGCTCTCAGTGAACCAGCCACATGAGGGGACTGAACTGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATAGACTGACAAGAAGTGTGCTTAGCTAGCGAGCTAGCTTGCTCCAAGAACCGCGAAAGTTTATCTCCTTTTTACGCCCACGCCGCAAGAGTGCAAGGTGAGATGAATGTGGACAAGGAGGAGCAAACGGATACCTCCAAGATTGAAACTTTTGCTACAGCCAGTGACGACGCCGCAACGGACAAGCAGGTGGCTCCAAGGCCCTCGACGAGATATGTTGCCAAAAAGTTTCGGCCAAAACGGGAGCAGGAAGAGTAGGAGGAGGAGCACCGCACGAGAGAGGCACGGCAATGGCTCGCTCTGCTGAGGCGACCAATCGAACTTTGCTTGCGCAACTTTTATCGAGCAGGTAGCGGGCGTGCCGTGCAGTGGGACAGGGACATCCCTCGCCCTGCAGGGGTGCGTGCAGGTGCAGGTGCAGCGCAGCTCCCTGCGCGCCGAGGAGGCCGCCACGCCGGGCATGGTGGTGGTGATGGCGGCGGACATGGTGGGTGCCATTGATTGCTCGCTCGCTCGCGCCGGGGCGGGGAGGCAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.681795
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0229000.2 3 27706562 T C
Osa03LNT0229000.2 3 27709796 A G
Osa03LNT0229000.2 3 27705734 T C
Osa03LNT0229000.2 3 27706391 T C
Osa03LNT0229000.2 3 27708380 A G
Osa03LNT0229000.2 3 27708849 G A
Osa03LNT0229000.2 3 27708992 G T
Osa03LNT0229000.2 3 27708274 C T
Osa03LNT0229000.2 3 27705856 C A
Osa03LNT0229000.2 3 27706753 T 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
Osa03LNT0229000.2 osa-miR5806 Translation 4.0 24.671 1 21
Osa03LNT0229000.2 osa-miR1853-3p Translation 4.5 14.799 1 22
Osa03LNT0229000.2 osa-miR2864.1 Translation 4.0 17.833 1 21
Osa03LNT0229000.2 osa-miR2925 Cleavage 4.5 23.508 1 19
Osa03LNT0229000.2 osa-miR3982-3p Translation 4.0 17.066 1 21
Osa03LNT0229000.2 osa-miR5485 Cleavage 5.0 22.135 1 21
Osa03LNT0229000.2 osa-miR5505 Translation 4.5 18.184 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0229000.2 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0229000.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0229000.2 3 nan Morphological trait Panicle/flower RZ448 RZ403
Osa03LNT0229000.2 3 qSB-3 Resistance or Tolerance Bacterial blight resistance R250 C746
Osa03LNT0229000.2 3 nan Resistance or Tolerance Blast resistance RM16 RM168
Osa03LNT0229000.2 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0229000.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0229000.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0229000.2 3 QFlw3 Morphological trait Culm/leaf RZ474 C746
Osa03LNT0229000.2 3 Yd3-13 Morphological trait Seed RZ403 CDO337
Osa03LNT0229000.2 3 nan Resistance or Tolerance Drought tolerance C136 R1618
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