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

>Osa01LNT0031300.1

GAGGGGAATAGCTTAGTATTTCGAAATGTATAATAGCCTCACAAAAGGATCCTCGATCTGCAAGTTACCGAGTCAAACACAAATTAAATATAGCATCGACTACAGAACAAGTTACCACGTACTCCACCGGAGTACGAATTAAACGGACAAAATGCTTGCGTTACTCTGCCCTCCAGCCTCCAGGTACTCACCCGGTCACCCCTGCTTTTCGTCCCTTTCACGATTCCACTGTTCGATCTTGGCCCTGCGCTCCTCGCTGCTCTCCCTGACTGGACTCCTCGCACGCCTTGGAGGGCTACCACCGTGCCTACGCCTTCCTCCATCATCATGCCTTTCATGTCTGCTGCTTCCACCCCTCCTTCCACCACCACCAGAGTAATCGTCACGTCCTCGATAGTCATCACGATCATGTCGCTCCCTCCTATGGCGTGGGCTTGGGCTTGGGCTGCGGCTCCTGCCTCGTTGTGGCTTTCTGTAATGGCCAAAGAGTTTTTTCCTCAGATCCCTCCCAAGTCCCAATCTGTTTGACATGCGTGAAATTGCAGTATCCACCACGGTTGCAGCTATTCTCCTCATACTGCCTGCAGGTCGCTTCACGGAAGTCGGTCACAGGAGAAAAGTCAACAATTATCGGGCGCCCAGAGTAGAAGCGGCCCTGGAGAGCAGTATGAGCTGCAGCTGCCTGATCTTCCTCCCTGAACTGGACATAAACATTGCCTATCATGTGATCCGCAAGGTTATCGCAGACGTTGAGGTTCTCAATCTCACCAAACTTGCTTAGTTCCTCAAAGATGTCCTCATAGAAATCCTCAAAATGCTCCTGCATCTGGCGGGGATCTATCGGCTGGCCTTGAGCATCAACCCCGGGCGTGATCATATCAGGGCGCTGATACATGTTCGCAAACACAACAGTTGGTGATATGGTGGGCCTGTTATGAAGACAAGAGCACCGATCCCCATGACGGCAAGCCCCAATCTTGAAGTAAAATGGGCAGTTGACCTTATCTTTCTCTGTACCAAATATTGAAGCTAAGTGCTCTGCCATGATTCAAAATCAACGAACCTGACTGAAAGCCTGCAGATAAAATGTTAAGAGGTCAATATCATAAAAAACAAGAACAGGAATGTTCCCATATACTTGAAGCTCATAATCTTTTACAGTAGCATGTGGCACATCAGCTTCAGAAAAACCATACAGACTAAGATAGTTAAGATAAAGTGCTGTGTTTGCACATCCCTGATTTAAAATAAATGGAACACTGACAGGTGATATAACTTAAACCAGTAACTTTGTAAGTGTTCTAAATCTGTCAAGACATTGACAGAGCTGTTTGGTGCATTCTGATGCAACAAAGCTTTTCAGGGCCTAGTGATCAAGCAGAAGAGACAAAATATCCATGGATGGTTATAGTCCCTGTTGTGTCATGCAAAGTACGCTTTTCTGCATCTTTTTTAGGGAAACCTGGACAATGTATTTTACTGAAATTGTAACAACACATGTTCAAGGGCAAATTACAAAATGAAAAACCAGACAACTAAGTCAAACTATGTTCATACATGTTATTTATCTCATAACACTACCAGCAGATTGGTATCCATTAACTTTACTCATTCAATTGAACATTGAGGTTATCCTCCCCAAAAAGGAGCAGCTACTAAAGCCTGCAGTGCAATATATAAAATATTTCATGTTCTTGCAAGAAAACACTAATCCGAACTGCTTTCTTATTTGTCTAGTCTGCACACTGACTCAAAATGTTAATATTAGGACATAGAAAAACATAAAAGAAAATTGCATTGAGGGTTATGACTTGAAGTTTTATCCTATGAAGAGCATTTATCTAATCCCTGTTCCCTCGGTTAACCTAAATCTGCACACTGAATTCAGAGAGTTAACATCAAAGGATAACCCCTGAAAGGCTGAACTGCATAAACAAGATATTGTTCCCCACTAAAGTGTTAGTGTCTCTGTTCCTGCAACTGTAAAACAAACAAAGCAACTTTTCGCCTTGCACAAGAACACTTCCTTCTCAGGTAGGCCTTGTTACATCCGTCCAACAAAGAATTTTATTTCAGCCATTTTAAAACCTAATCTTGCGACGGAGGCCGTCGGCGGATGCGCTCTCCGCTTAGCGAGCAGAGCGCGAAGCTACAGCGAGCGCGCCGGCCAGGGCCCTCCTACCTACGGCAGCGCGAGGAGGGCAAGGGGAGGAGGTTCGGTGGCGAGCGCC

Coding Potentia
Explanation CPC Score
noncoding -1.05594
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0031300.1 1 27318915 C T
Osa01LNT0031300.1 1 27317403 G A
Osa01LNT0031300.1 1 27319081 T C
Osa01LNT0031300.1 1 27320357 C T
Osa01LNT0031300.1 1 27320558 T C
Osa01LNT0031300.1 1 27319721 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0031300.1 osa-miR160d-3p Cleavage 4.0 22.275 1 21
Osa01LNT0031300.1 osa-miR1852 Cleavage 5.0 14.912 1 21
Osa01LNT0031300.1 osa-miR1846a-5p Translation 3.5 12.346 1 21
Osa01LNT0031300.1 osa-miR1846b-5p Translation 3.5 12.346 1 21
Osa01LNT0031300.1 osa-miR1866-3p Translation 5.0 17.773 1 22
Osa01LNT0031300.1 osa-miR1862d Cleavage 4.5 11.904 1 24
Osa01LNT0031300.1 osa-miR1879 Cleavage 3.5 17.858 1 24
Osa01LNT0031300.1 osa-miR1846c-5p Translation 3.5 12.346 1 21
Osa01LNT0031300.1 osa-miR2871a-3p Cleavage 3.0 12.091 1 21
Osa01LNT0031300.1 osa-miR2871b Cleavage 3.0 12.091 1 21
Osa01LNT0031300.1 osa-miR2095-3p Cleavage 4.5 18.641 1 20
Osa01LNT0031300.1 osa-miR1857-5p Cleavage 3.0 12.546 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0031300.1 1 yld1.1 Physiological trait Source activity RM5 RG462
Osa01LNT0031300.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0031300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0031300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0031300.1 1 QPh1b Resistance or Tolerance Submergency tolerance RZ527 RZ154
Osa01LNT0031300.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0031300.1 1 nan Morphological trait Seed CDO118 CDO455
Osa01LNT0031300.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
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