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

>Osa01LNT0010300.1

CATTGAATGCTGACAATATTTCATAAATATGAGTGGTAAACATTTGATGAATTCCACGCTTCACGCAAAATCTGACCAATTCCAGCGATCAGTCGAGGAGACTCTATCTGATGAAGCTGCACGTGCACTCCATACCGGATGGCAAATCCCAAAACCGACGGTAAGGGGTAATCACTAATCAGCTACAAGTGTCTCAAAATCTTGAAAGGTTCCACATACTGGAACAAGCTATACATGGGCCAAATGTGCTGTCAGCCATGATACCATAAACAAGCTGCCAGCATTTTGCCCCTGTCTACAAAAGATGGCCTACAATTCCTAAAGCAAATATAAGAACCTGAAAGTTTGCCCTGCCATGCAGTTTTTGGTGCTAGTAGTTTAAATATAGATACTGTCAACAGCACCATTTGATCCAGTTCAGTAAGTTCAAATTACTGAACGGGTAAGCTAGCACCGCCAGCAGATCTTCTCAAGACCGCACCTTGCAGAAGATAAGAAGCCTTGTTCCGAACCTTTGAGGCATATAATCTCCAGTCTGTGCATCCTATTTGGGTTGAACAATTCCGCAGATAATTACGCCAAGAATTAATGATCGCATGCTTATCTCTAAAGGCATCACTTGAGAAGAGTAAGTTATCCATCAAAACTAGGTATACGTACAGACTGAAAAAGTTGCAATCTTTATCCTTCACATTTATGGACATGACTGACTTCAAGATCTTCTCAACATTTGCCACCTTAAGGCCAAAGCTAACTTTGAGGAATTGTAGGGCCAGCTGGCTCCTTAAGAATTTGCTACGGTAATCAGTCCCAGTGATACAGTCAACAATCCTTAAACAATTCAGGTCCATTGTGACTCTCTGGGAAATGGACTGAGCCACTATTAGACAGCTACTTTCCCATTCACTTGAATTGAAGTACAAGATAAGTGAACTCAGACAGTCTCCCAAAATAAGCAGCAGGCCCTCAAGTTGTCGGTCCAAAAATAAGGAAATAACAATAACAAGGAGTTCTTCTGCCTCGGAAGATGAGAATATGGAATGCACATTTCTGATTTTGCAGCAAGCAGATGTAATTTTTAACCATTCAATGATGTTTTGAGGTGGGCCATCATCTGCAATCACACTTTCAGAGGTGGAAACTTCAGTGCAATTATCAAATATATATCCATAGTTGAGTATGGCACTCTTTAGAACAGAGTAGCTTGGAAAGTGTCCAATGTCAACTGAGAGTTTGTCAGCCTCATTTAGGGAAAGAACACTGTCCCAAAAGTCAGATGCAGCAACTCGAAACTTCTTATTACACGAGTACAACACTGGTAGCTAGTGGTGTTAAGCATACAGTACAGTTTAATCAAACAATAATAACTGGAAAAACACACATATATCAATTCTTACATTTGGTTAGTGCCCAAGATGCTATAGAATCTTCAACAGAGCCATGCAAGAGGACCAACTTCAAAAGCCATCCATCCACCAACAAGCCTTCTAGAAACCCTTCTCCTTGTTCAATGTTTAGATCAAAACCTAAATGCTCATTTGCACAGAATGATTTCAGAAGTTGACAATTTTCAACTCCTGTGACAGTAAGAACAGAAGGGGATTTCTGGCAACCAAAAACTCTCTGACCCCATTGGGGCACATCATCACCAGCATCCAACTCTTTCGACTGCTCCTCATACTCCTCAACAAATTTGCGAAACTTAATCTCCTTCTCCTTCACTTTCTTGTCTTCATCATCTGAATTATATCCTTTGGATCCATGCTTGGACTCAATACCATAAGCTTTAAGGTCATCCTTACCACTTGCAAAGAAATCCTCTAAAAGATCGTCCAACCCAATAACCTTCTTCCTCTTGGCGGGGCGCGCCTTAGGGAGGAGCGGATCCTCCTTCTCGAAGTCGAGGGGCTCGTCCAGCAGCATCTCTCCCCCCGGCGAGCTCGCGCGAAGGCGGGGAGGATTTGTGGCTCCGGGGTGCCTCGCAGTCGCAGCAAACCTTGGCGACGCCGGCCGAGAGGTGGAAAAGGATGAAGC

Coding Potentia
Explanation CPC Score
noncoding -1.21108
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0010300.1 1 7807191 G A
Osa01LNT0010300.1 1 7807594 A G
Osa01LNT0010300.1 1 7808570 C T
Osa01LNT0010300.1 1 7809043 C 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
Osa01LNT0010300.1 osa-miR5538 Translation 5.0 20.181 1 22
Osa01LNT0010300.1 osa-miR426 Cleavage 4.5 9.085 1 21
Osa01LNT0010300.1 osa-miR2876-5p Cleavage 4.5 18.682 1 21
Osa01LNT0010300.1 osa-miR3980a-3p Translation 4.0 23.512 1 21
Osa01LNT0010300.1 osa-miR3980b-3p Translation 4.0 23.512 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0010300.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0010300.1 1 An9 Morphological trait Panicle/flower nan nan
Osa01LNT0010300.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0010300.1 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0010300.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0010300.1 1 Rf Physiological trait Sterility nan nan
Osa01LNT0010300.1 1 ppp1.1 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0010300.1 1 prg1.2 Physiological trait Source activity RG140 RM243
Osa01LNT0010300.1 1 spp1.2 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0010300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0010300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0010300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
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