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

>Osa01LNT0033200.3

GTGAGTATGTCACTATCAAGAATTCAGCGGTGTCCTTTTTTCAACTGATAATGTGACATTGTGGAGCCTGTACAGGTACATGTGAAAAGCATCCAAACAAAAAAAGAATAGTATAAAGGACAACTGGGCATAATTGCCTAATCATCCAAGAAAAGAGAAAGATAAACAGGGAAGTAGGTTTTTTACATCTCCAACCACTGTTGTTTTACTAAGATACAGAAAAGAAGTTGTTATTCGTAGGGCCAAAACCTATGGCATGACACACTGCCATGACGGTTCACGAAGTTCATCCAATAATTTGAACCACCAATTTTTTTATTTTGAATCTACTATTCCCCCTGTTCCAAAATATAGCAACTTAGTAATCGATTAGACATGTTGCTATATTTTAGGACGGGGTGACGGGGGGAGTATATAAGAAGAACAGCATGTTTGATACATCAAGGCCCTTGTTTTTTTCTTATATCTGTAGATGAAATATCCATGCGAAACTTCTCCTCTGGTATAGAGATAAACATTTCCCTTAACTCGACTGGAATGTCCAAATCTTCAAGGACCTTGAAAACTCCTTCAATATTTCGACCACCAACAAGAAATGTTGTACCTGTGTTTTTACATTCGAGAAGTATCTCTAGCATTCTATTGTAATCACCTCCATAATACTTAGGATTAACAAGCCTAGCTGCAGTGTCTGCACCGATTACAAATGCACTGCCTGGAAATAGCTCCGCTTTCTTGTAAAAGTATGGTTGGTTAGATATTATCACATTCTTCCCTACTTTTCTAAATTGCTCAACCCGGCGCTTGATTTCTGCGATAGATAGTGGAGGTTTGTCGGCATTGATTGCTGATATCTCAAAGCATGGAAGACCATCATCACACATGCTTGATGCAACTTCTAACAGCCTAAGGTGTCCATCATGCAGGGGATTGAATGAACCAGGTAGAATTATTTTCCTGTTGAAGTTTTTATCCATTGAATCAGAAAAGTGATACACTTTCATGCAGACTTGCCCATCAATAACTTGCTGGAGTTCTTGGTCTTCATCAAATTGTTCCACGCTTTCTTTTGGAAGTTCAGGTTCTTGAACATCTGACTGAATGGTTGCAGGAACTTTGCAGCCGTCTGCAATTGCCTTGAGCAGAAAGTAGCTTGAAACTTTATCTTCTTCCTCTCTGCTCCGTAAACCCTTTGACAATGTAACATGTGATGTCCTGAGGCAATTTTGTGTTCGTGTTGACACATAGAACCATGTTTTGGACGTGAGCTAGCCAGTGACCCAGTGAAGCCAACACCCATTACTTGTAGACCTGGTCCAGAAAGCTTGAGGGCGCGGTTGAACGCGGCCAATGCCATGTCCTCTGCGGCCTGCTTGCTGGTGAACTGCAAGGGCATCTTGCCGAGCAGCTGCGCCATGGAGGCCATGGAGTAGGGCACGACGACCTCGAGGACGGTGCCGGACGCGCCGGGCACGGACAGCAGCCACCCGAGCGCCTGCGAGGCGCCGCCGGCGAGGTAGATGACGGCCTGGGCGCGAGATGAGTGGATAGCCTCCACCACCGCGCGGACCCAGCTCTCCATCGCGCAGCCGCGAGAAGAAGCTACCAGA

Coding Potentia
Explanation CPC Score
noncoding -1.22643
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0033200.3 1 28542729 A C
Osa01LNT0033200.3 1 28541705 T C
Osa01LNT0033200.3 1 28541777 A T
Osa01LNT0033200.3 1 28542078 T A
Osa01LNT0033200.3 1 28543024 A G
Osa01LNT0033200.3 1 28543179 T G
Osa01LNT0033200.3 1 28543643 C G
Osa01LNT0033200.3 1 28544378 A G
Osa01LNT0033200.3 1 28544871 T C
Osa01LNT0033200.3 1 28545190 A T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0033200.3 osa-miR396e-5p Cleavage 4.5 20.473 1 21
Osa01LNT0033200.3 osa-miR444a-3p.2 Translation 5.0 23.817 1 21
Osa01LNT0033200.3 osa-miR444a-3p.1 Cleavage 5.0 24.161 1 21
Osa01LNT0033200.3 osa-miR444d.2 Translation 5.0 23.817 1 21
Osa01LNT0033200.3 osa-miR444d.1 Cleavage 5.0 24.161 1 21
Osa01LNT0033200.3 osa-miR444e Translation 5.0 23.817 1 21
Osa01LNT0033200.3 osa-miR1862d Cleavage 4.0 16.53 1 24
Osa01LNT0033200.3 osa-miR1862e Cleavage 5.0 17.603 1 24
Osa01LNT0033200.3 osa-miR396g Cleavage 4.5 20.473 1 21
Osa01LNT0033200.3 osa-miR396h Cleavage 4.5 20.473 1 21
Osa01LNT0033200.3 osa-miR396d Cleavage 4.5 20.473 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0033200.3 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0033200.3 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0033200.3 1 yld1.1 Physiological trait Source activity RM5 RG462
Osa01LNT0033200.3 1 nan Morphological trait Seed CDO118 CDO455
Osa01LNT0033200.3 1 nan Morphological trait Root RM3475 RM3494
Osa01LNT0033200.3 1 QPh1b Resistance or Tolerance Submergency tolerance RZ527 RZ154
Osa01LNT0033200.3 1 nan Physiological trait Source activity RG532 RM472
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