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

>Osa01LNT0047100.1

CGTCAGAAATGTTAGATTGCTAAGAGGAGCTAATGGCCTTTAATTTGATATTTGTGTCATCTGTCACCGGCATGCTAGGAGTACAAGTTTGTTATGTGCATCAGACTGTACAGAGAAATTCGTGAGACCTTATCTTCCTAATAAAGAGGACTCATACATTGTCAACCTGTCCCTGCAAGTTACTAGAAGATGTCAATGTTTTAAATGTGACTACCCTGATTTTCCATACTTCCATGTGCAAGCCTTCCATACTAACTACTCGAGAAGCTGTCGCATGTGTCTGTTTGGGAACCAATAGTGAACGGGTGGACTAAATTCCATACACGATTGACAACTCCATCTGACATAAAGGAAAACGCATCTTTTGCGGCTCTTTGACATGCTTCCAGAGCTCTAGAATCACCAAGCAGTTGTTTTAGTGCTTCCAAAAGTTCATATTCTCCTTTGACCTGCTTGACAGCTAAAGGATTTATTTGCCACATTTCGACCAGCATATGATAGAAGTGCCCAACACTAGGACCAGTCATAACAGCGCAACCAACTGCAGCAGCCTCAGAAATATTATGTCCAGCTAAGCCGGGCAAAAAAGAACCCCCAATAACAGCTATTGGAGTAACCCTGTAGAGCATTCTTAATTCACCTAACGTATCAACCACATATATACTGGTGTTTGAAGACACCACTTCTCTTGTTGACCTCAGCACAAAATTCACTTTCTGTTTCTTCAGGGTTTGAGAAACATTCTTGCTGTCCTCAGGATGCCTTGGGACGAGAATTAAAAGTAGAGTAGGATACGCCCTGGTTAACTCATCATGAACACGGAGAATGATTTCATCTTCCCCTTTGTGGATAGAAGCTGCCATCCAGATGGGCCTATTGCTGAACTGCTGCTGAAGATCTTCTATTGCAGCTACCTCTTTCTCCCCAGCAGCAATGTCACCAACAGCGTATTTTAAATCGCCAGCAAAATGGATGATCTGTGGTGGTGCATGAAGTAATTGAAAACGAACAGCTTGAATAGTACTCAATGGGATAACAAGTGATAGTTTGGAGAGCATCAAAGAGACTAACTGCAACCCTAGAGGCAAGGACCAACGGTTGAAAGACTTCAATGACATGCGCGCATTTAAAAGAACCACTGCAATCTGAAAAATAGGAAGGTCATTCACAGCAGATAATTAAATAGTGAAAGAATGTACTATGGACCGAAAATATAGCTAATCTGCCATTGCACATGGAAAAAACAAGGGTAACAAAGGGAAGCCTAACCACTTAGTAGAAAATAGTCATTATGAGAAAAAAAAAACTTACCCCTTTCTCTGCTGCAGACAAAATGAGGTTTGGCCAGAGTTCACTTTCCATAAGAAGTATCAAATTTGGTTTCCAGTATCCAATGAAACTTTCTATTGCATCAGGACAGTCAAGGGGTGCAAACTACACACATATGTATTTCAGTTATGTAAAACAACAATAAGCTACCGTAGATGTATATAGGGCATATCAAACATTTAAACTATCCTTCTGTTAGCCTATTCGTGATTCCCTTCATCTAAACAAGTTCCATCTGTTCCCAAAACTTTGCTTGATCTGTGTCTGTACTATCGAATATTACCACCTTAAAGGTTTAATATTACGAAACCTTACTATCATAGTTCAACGAGTATAATATGACCTTAGTTTAAGGGATACATATAATGAACAGACAATATCTATCTGCCTTGACACAGTTCGAACCTAAAATGTCCTTTTTTTTCAAGAACAGTCCATCAGTAAAAATTTGTTGTGCATACGCCATTTCTCAGAAAACTAAACCGGCCGTCACGACAGGGATCTGAAAGTACAAGAGCAATTTCCGAGCTCACCTGATATATGACACCATCCGGGAGCAAGTCTTTCATCACTTCGAAGGATGAGAGGGTAGTAGTGGTGAGGAGGATGGGGAGACCAGGGTGGAGGCGGGCGCAGTGGCGTACGACCGGGAGCGCGGCCATCCCCTCGCCGAGGGATACGGCGTGGAACCACACGAGCGGCGAGCCCGGACGAGGCCGCGCCACCGACGGCCTGCCCAGCCGCTCGGGCCAACGCGACGGGTGCTCCAGTCCTCGTAGCCGCCGCCATAGAAGCGCCGCCGGCGCCGCCGCGCGGCTCGCCGCCCTGTACAGCTCGTACAGCGCCCGGCCGCCGCGCGCCGCCGACGCCGGCGTGCGGGC

Coding Potentia
Explanation CPC Score
noncoding -1.03662
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0047100.1 1 37039748 C T
Osa01LNT0047100.1 1 37040042 A G
Osa01LNT0047100.1 1 37040937 T C
Osa01LNT0047100.1 1 37041743 G A
Osa01LNT0047100.1 1 37042637 C T
Osa01LNT0047100.1 1 37042747 T C
Osa01LNT0047100.1 1 37042915 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
Osa01LNT0047100.1 osa-miR5802 Translation 3.5 12.474 1 24
Osa01LNT0047100.1 osa-miR5143b Cleavage 5.0 13.136 1 24
Osa01LNT0047100.1 osa-miR6255 Translation 4.5 9.818 1 22
Osa01LNT0047100.1 osa-miR818f Translation 4.0 16.218 1 21
Osa01LNT0047100.1 osa-miR164c Cleavage 4.5 18.296 1 21
Osa01LNT0047100.1 osa-miR416 Cleavage 4.0 19.008 1 21
Osa01LNT0047100.1 osa-miR1863a Translation 4.0 17.444 1 24
Osa01LNT0047100.1 osa-miR2120 Cleavage 4.5 20.87 1 24
Osa01LNT0047100.1 osa-miR2864.1 Cleavage 3.5 14.966 1 21
Osa01LNT0047100.1 osa-miR2928 Cleavage 4.5 8.43 1 20
Osa01LNT0047100.1 osa-miR3981-5p Cleavage 5.0 18.189 1 21
Osa01LNT0047100.1 osa-miR5143a Cleavage 5.0 13.136 1 24
Osa01LNT0047100.1 osa-miR5502 Cleavage 5.0 13.198 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0047100.1 1 nan Morphological trait Seed RZ730 RZ801
Osa01LNT0047100.1 1 tn1-4 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0047100.1 1 fll1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0047100.1 1 ph1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0047100.1 1 sd1 Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Morphological trait Root RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0047100.1 1 Fh1-2 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0047100.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0047100.1 1 nan Resistance or Tolerance Drought tolerance RZ730 RG810
Osa01LNT0047100.1 1 nan Resistance or Tolerance Drought tolerance RG690 RG810
Osa01LNT0047100.1 1 nan Resistance or Tolerance Drought tolerance RG810 RZ730
Osa01LNT0047100.1 1 qNOP-1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0047100.1 1 qPHT-1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0047100.1 1 qPL-1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0047100.1 1 qSF-1 Physiological trait Source activity RZ730 RZ538
Osa01LNT0047100.1 1 yd1 Morphological trait Seed C2340 C86
Osa01LNT0047100.1 1 yd1b Morphological trait Seed C547 C2340
Osa01LNT0047100.1 1 qNSB1-1 Morphological trait Panicle/flower C86 C2340
Osa01LNT0047100.1 1 qSSBp1-1 Morphological trait Panicle/flower C86 C2340
Osa01LNT0047100.1 1 pl1.1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0047100.1 1 qChll1a Morphological trait Culm/leaf C86 C813
Osa01LNT0047100.1 1 qH2O21 Others Others C86 C813
Osa01LNT0047100.1 1 qPHT1-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0047100.1 1 sd-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0047100.1 1 qLVBTS1-1 Morphological trait Panicle/flower C2340 C86
Osa01LNT0047100.1 1 sf1.1 Physiological trait Sterility RM212 RM315
Osa01LNT0047100.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0047100.1 1 nan Resistance or Tolerance Insect resistance RM543 RM472
Osa01LNT0047100.1 1 nan Physiological trait Eating quality RM8084 RM6827
Osa01LNT0047100.1 1 dth1.1 Physiological trait Flowering RG541 RG109
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0047100.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
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