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

>Osa03LNT0212100.2

GGAATACCAAAAATTTTCAGTTTCTGTAGAATAAATATGGTCAGTACACCCCACATGGTCAGGAAGGCCTCTTGTGTGTATAACACTATAACTGGGGAACAAGAGCTTCTGCTGCCCCTGAAAAATTGACAGGGGAGGAAGAAAAACTGGTAGTGACACGAGCACACTACCAAGAACTGAACAGAGGTTCCATATCTCTGTTGAATTCAGTGCATCCATCGTATACATCCTCACAATCTTAGCGAGATAACTGTGTGAGCAGAATCAAAACAGGAAGACTCCTCTTTCCAAGAAATACAGATCTCAAGCTGCTTGATGGCATTAATGGAGAATTACTTCTGGTTCACCAAATCAGCACCACTGACATACCTAGCAACGAATGAAATCAACCGGAATGGAGCACCGACGATTGGAGCATCAGAAAATGGAACCTCCTCTGCCTCATCATCGGCTACCGGTGGTTGTGGGTCTTCCTCATGAATCTGTATATCATCTAATGCAACTGGCAGAATTTCTTCGCTTGTTCTTGGTTCATCAAAATCTTGCTTTGACCTTTGATGTGCATTCATGTCAATGAGGCCCTCGGAAGAAACATCATTGATTGTTGTTTCTGGAAGTTGCATTGGAGCTTCTTCTAGATGATTACTAACATAGGCGTTGCTAGGACTGCTGTTGATTGGACTATAGTTATCCACAGAAGTAATTGCTGCAGAACTGTTTACACTTCTATCAACAATCAGTTCATTACCCTGCAAGCAGAAAACAATTACGCTGTATACAAGTATATATGAATTCTGGCGGTTTCCAGACATTTGATATTCTGTCACACTGCATGCGGAGACTCGTACTTCTTACCAAAACCAACAGTCTGCTCATTGAGAACTGTGCTGGTCAAATCCGTTTAATCCATCACATTATTTTCAAAGACCTCAATTATCATGTCTCTATCTTATGCACTAGAATCTGGAAGGACAAGTGTTTTATGCACAAGAGAGAAGAGACTACTGATATCAAGTGGTATTTCTCCCCAGGCAGATCCACTGGAGTGTATAGCGTCTACCAAATTGGACACAGGTGACAAAAAGGAATGTTCTGCATAACATTTACCTTTTTAGTCACGGAGGCTTCAGTAAGAGCAGACTTTGCTTCAAAGACTCCTAATCTTGATGCCAGTTCATCAAAACCTTTTACCAACCTCTGGCTTTCCTCAACAGTATTGTTTGAAGCTTCCTCCAGCACCTTCACCTGCCAGACTGTACAAGCAGTACTTTATTTGTCTCCTCCAGTCCACTTAATCTCTCTTTAAGAGACGTCTCCTGATGAGTTAAGGCATCATTGATGACCTCTATGGACCTGACTTTGTTATCCAAAGCTACCTCCTTCTTAATCAGCACATCATACCCATTCTGTAAATTATTGAGCTTTTCCTCCAAACGGACCTCATTCTGTGCATGATAATCCACTTTGTTATGCAACTTTTCAACCTCAATCTCCATGGAGCTCATTTTTTGATGCCACAAACTCTTCTCATCTTCCAACTTCTTTATCGTATCATGTAATTTATCAAGCTTTGCTTCATATAGTCTGTGCATGTCAAGCTCCACGGTGGAATCTGACATCTCAACACTCCTCTGATCAGCATGGGCTGTACTACTGACTTTGTGATTTTCATGTGTCATGGCAGGGTCAAGGTTCTGAAATGGAATCCCCTCTCCAACAGAGGACATGACATCATCAGTGTTTGTGCTATCATGATTTGCCTGTCGATCTGGCTCATGATTCTGGTACTGAGGAGCTTCCTCTCCAACAGTGGACATTGCATCATCAGCATCAGTGCCATTATGATGGTCATTAGGGGCTGTCTCATGATTGTGGGACCGAATGGCAGCCTCTGCAGTGCTGGACGTTACATCACCAGTGTTCTTCCCTTGGTTCCCCTTCTTCTTCTTGTTCCTCTTCTTTTTAGCATCCATCTCCGGTTGCAAACCCAAGCCCTTACAATACTTTATCTACCTACGAGAAATGCCGGCGGAGCGAGAGCTAACCCTAGAACAGCCGCAGGCCGCAGCCTCCGCCACGAATCTGGGAGGCTGGGGATTTGTTGGGTGGAGGAGGGGGGGGAAAGCTCTCACGAGAAGACTTTTTGGGGGAAGCGAGGCGAGCGCGGGGTGGAGATCTGCGTCTCTTGGGAAGGAGGAGCGCGGAGGCGTAACTGCCGGTGGCTTTGTCGC

Coding Potentia
Explanation CPC Score
noncoding -1.11434
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0212100.2 3 12291961 C A
Osa03LNT0212100.2 3 12293580 C T
Osa03LNT0212100.2 3 12293842 T C
Osa03LNT0212100.2 3 12295901 A C
Osa03LNT0212100.2 3 12296682 T C
Osa03LNT0212100.2 3 12295737 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0212100.2 osa-miR5788 Translation 4.5 24.446 1 21
Osa03LNT0212100.2 osa-miR7693-3p Translation 4.0 23.105 1 22
Osa03LNT0212100.2 osa-miR396a-3p Translation 4.0 23.814 1 20
Osa03LNT0212100.2 osa-miR396b-3p Translation 4.0 23.814 1 20
Osa03LNT0212100.2 osa-miR2096-5p Cleavage 5.0 22.219 1 21
Osa03LNT0212100.2 osa-miR5073 Cleavage 4.5 15.658 1 23
Osa03LNT0212100.2 osa-miR5073 Cleavage 5.0 12.44 1 23
Osa03LNT0212100.2 osa-miR5157a-3p Cleavage 5.0 11.846 1 24
Osa03LNT0212100.2 osa-miR5157b-3p Cleavage 5.0 11.846 1 24
Osa03LNT0212100.2 osa-miR5337a Cleavage 3.5 15.975 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0212100.2 3 qLVG3 Resistance or Tolerance Cold tolerance RM251 RM282
Osa03LNT0212100.2 3 ccs3 Physiological trait Source activity RM282 RM251
Osa03LNT0212100.2 3 dcf3 Physiological trait Source activity RM282 RM251
Osa03LNT0212100.2 3 qLEI3 Resistance or Tolerance Submergency tolerance RM7249 RM3803
Osa03LNT0212100.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0212100.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0212100.2 3 qLEI3 Resistance or Tolerance Submergency tolerance nan nan
Osa03LNT0212100.2 3 qGL3-1 Physiological trait Eating quality nan nan
Osa03LNT0212100.2 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0212100.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0212100.2 3 nan Physiological trait Eating quality RZ574 RZ284
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