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

>Osa02LNT0174000.1

AAGCAAAACCATTCAAGGATCTGTTGAGCAAATTCTCTGTTTCCGGCACACCCAATGTTTACAGCACAAGGATATGCCCACCAACAAACCCCTCAGGTAAACAAGGGAAAACAGTCAGCTACATCCTGTTATCTTTGTACAGTGTGATGGTAGTACAAGTTAACGCATAACTCAATGCCTCTGCACACAAGGGGAAAAGGAAACAAAAATAAAAGGAATACATACACACACGAAAAGCCAACTGCTCAATACATGAACGGCATCTGTCTGTTATATACAGATCGAATGAATGAAACCAGCTCATCCAAAGAGATACCCATATGATACACAAAACAATATGATCTAGTGGTTAGCATCAATCGGTGCACCAGACCTTGCCTGTGATATCCTGTTTGCATAGATTGTTACTAGGCGCAGCTGCGTGCTATTAAGCCCCTCTAGATATGGTACAAATGCTTTCCCAAGCATAATGTAGATATCCACCAAGCAGAATACAACAGTCTTGCGAACATCTGGACTCTGGTTATTGAAAGCATCAAAAAGTGCTGGTAAAAATGAAGGCAGTTGAGTCATTAATTCCTCCTCTGATAGGCGTCCAACAAGCTTTGTCAAACAGTTGGTACACACGACAAGCATCTTTTCATCATCACTAACCAACAAAGGTACAATAACAGCAAGGCATCTAAAAGGATCATATTTTGCCAACACGACATTTAAGCACTGGTTTGCTTCATTTGAAACCTTCGCCACGACATCCTTGGTCACATGTAGGAGCTTTTCAAGGACAATCTCAATGGATTCTTCCATAGGATCTTTCTGGTTGTGGAGCATCTCAGCAACTAACGATAGAGAAAGCTCCCTGATAGAAGAATCCGAGTCATCCAACACCTCAAGGATGGTTGTTAAAATTTGATTGAAATACTTAGTCCATATAGAGTTGTCATTATTGGTGGAAGCTGTAACCAACTGTTGTAATGCCTCCCGCTTGTCTAGACTAGTAACTTCACTGACATTGCTTATCTGATGAATAAGTTGTGGGATGCTAGGGCCATTACTGGTGTGTGGGGTAATCTTCACAGAACTAAGCTCCACAAGTGGATTTCCCTCTTGAGCGTCTTCCACAGAAGTTGAAATAACAGCACCACGTCCATCAGAAACAGCAAGACGACCAAACTCCAGACGAGGAGTACCAGTAGAATTTTCATCATCAATGGTAGCATCTGATTTTCCAGGATAGTCTGTCCATGAACGTGCAGCTTCTACAACTGTGCGAGCAATGTTCTTTGATTCCCTACTTGTTGCAAGAACTTCAGCTTCAGGTTTGAAACATTGCTTAACATTATCAATGCTGACATCAGAGGATGTTCGGCCAGTAGAAATATCAAGGAATATTGATCCATGAACCATATTCATCTTCTTCCCTGATGCATTATCAAGGGAACTAGCAGAAAACCGCCCAAATGCATAACTACTCTTTGGTGTCAGTGCATAACCATCTTCAGAAGAATTTCCAAAATCAACTTGGTCATAAGATTTGGGACGTGAACGTTCTTTTTTGCTCTGCAAGTAATTTACCAGATCGACCTCGATACGAGGAGTATATTGCTTCAGTGCTCGCCTCACAAGGTTTTGTTCTTCAATAGACAAATTTAAAATAAAATTTAGAACCGCTGTTGAGTCAAAATGAGAATAAACTGCTATGATTCCAGAAATGGAAGTTTCCTTCAACTTTGCATTCTTTTCATGTATTAAAGGTGCTAGCTTTGAAAGCCATAGCTTAAGAAAGCCACTGTTACTATAACCTTCTGAGTCTACTTTGTACCTGCTGAATGACTTATTAGCAAACTCAAGAACAGCCAGTTTTGCTTTTGGAGACCTTTGTTCATCCAGTGAACGTACTAGAGCAGGTAGCAATGTGTCAATGGGATATGTGCGGCCAACAACTTCCAAGGTTGATGAACATGGTTGCCTAACTAATTCCTTTGGATCAATAAGTCTTGAAAATACATACGGTAAAATTCTTTCAACATAGCTCTCAAATTGCTTCTTGCAAGCTGGAATAATATCTGCAAGTGTAGAGAAAGCTGCCTGTGCAACTTTGTGATGAGGATCATCCAAATAACGGAAAAATAACTTCATGACCTTTTCAAAATTCTGCATAACTTCTTGAATGCCTTTCTGTCCTTGTTGCAGTAGTGTCTGAATAAAATTAAAGGCTGTAACTCTAGCTACCCAGTCTGAACTTGCACTAAGACCCCCAGAGAGTGCATCGCTTATAGAAGTTGGACCATCTGTGTATCGCGACATGTCATTAGATGAGATATGGCCATCATCAAAACTGTGTCTCGAACTTGCAGATGTCCTTGATGCCACTTGCTTCCTAAGAGGCCTCTGGAAGTGTGGAACTTGGTGATTGTGTAAATTTCTGTGGCTGGCATCCCTATAGGTCATATCAAGATAGTGTCTGTCCATCTGCATTTGTGGCATCCGCCTGGTTGACCATGTATCATTACTCTCTTCCATAGTGCTACCATATGGAGACCTCCCAGAAGAGCTTCTCGCATAAGGCAGTGACGATCCTGATATTGATTCAGACGACAGACTACTCAAATATGGTGACCTTGACCTCTCTTTATTGGCCACATGAGGGTTCACTGTATCTACCAAGCGTGAACCACCATTTCTTGTGTTATTAATGCTTGGCAGGGATGAATCCAGCAATATGGAATTCTGCAAAGACAGATGGTCCGAAGCAGTTGCAGCAAGTGGGATAGGAGGATCACGAGAGGATGGAGGATCAACTCCAAGATCCAAGCTTGTTGAGCGCATAGCTGAGAAATTTTGCCGGCCGCTTACACCCTTCAATAAACTTTCAATGGCAGAAACCTTTTGTTTACTTGAACTGAGAACGCTCTCTATGCTTCTTTCAGCAGTTCTACCTATTTTCTTTGACTGCGACAGAAGACTTCTTGACGAAAGAGATGATTCAGAAGAAATAGCTGCACTCTTGTCCATCGCAACAATAGCTGAAGTGCTGTATCCGGCTAAATGTGTACCACTTGCATGAGATGAAGCATGAGAAAGTTGGACACCCTTCTCACGCAATGATGGAGAAGGATACCGTTTCTGCAGGCCCCCGTCTTCATCATTTATTATCCTTTGTACTGCAGGATCAAATGACATAAAAAGCCGACGTGAGCGCTCAGGCCATGTCTTGGTGAACATCCTATAGCAAGATCTTGCAGTTGCACGGACCTCACTCATTGCATCAGCCACACAGCATTTTATTAGATCTTCGTATATATCAGATGCACGCTGTATTTCAGGAGCATCTGCCCAATATTCCAATATTAGGATGGCATACTCACTACATCTAGCACGAAGGATAGCGCTGCGATCATTCTTTGCCGTGTCAGCTATAAGTGGAAGAATACGTGAAACCTTGCAGTTCCGCAGGATAGTTTTTATGCAGTTGTCGGCGGATTCAGCAATAACAAGCACAGTTATCACAACAAGCTTGAAAAGTACCGGAATAAATATTTCAGCACATGCTTCAAAATCACCAAGGAGTTCTTTTGATAGCATATTAAGTAGATGGCATGCCTGTTTTACTATGCTAGACCGTCGGTCAGACAGCTGAGCAGATAAGGGAGGAACTAGCTGCTTCAGGAGCGTAAGAAATGATGGATAATCAATTGCACCTCCATATACCAAGGCTTCAATCCTTTGCATTGCGGCAATACGTATAGACCAGTCCTTTTCTGGATCAAGGGCAGATGCAATCTTCTCCATCTCCCTAAGTAATTCTTTCTCTGAATGTACTCTTATGGGTTCCACTGGTTTTTCGGTAATATCTGAGTCACCTCCAAATAATGTGCTTTCCCTTGTTGAACTTTTTTTCCTTGGACTGCCTCTTTTTGCATTAGCACTTACAGATCTTTCAATAACCTTATATTGCATTCTAGCACCATCAGATGAGCGAGCCTTTGGTTCTATTTTATCCAATCTTGAATTTATGTCCTTCAGCATGTAAGAAGGCAGATTATGGCGCTGCAACTCTTCATGGAATTGAGATCCCATGTTTCTATACATCTCCTCAATACATGAGATTGCAGCGTCTCTAACACTTTGATTCAAATCGTTCAGCAATTGCAGGACAGGTGAAAGCAACACTCGCTGTAGAGGGAGCTCTGTAGAAGCAAAGAGGCCAACAGCTGTTGCAACAGTGCGTACAAATTCTTCCCGCACCCTCCAGCTCTTGTGAGTCCATGCATAACTTCCAGCTCTTTCAACAATGATTGTCGGTGATGAAACCTCCATGAGGGTGACAAGCAGCTGCCTGGCGGCGTCTCGGACGGGCTGCTTGCCGTCGCCCAGCCGCTCGACGGCGGCGGGCACGAGGGCGTTGAGGTGGATCTTGAAGTGGTCGCCGGCGAGCACCGCGGCGGCGGAGAGCGCCTGCAGGCCGCCCTGGGCGACGCGGAAGTTGCCGTCCTTGGTCAGATCCATGCAGGCGTCGACCAGCGACGTCACCTCGGCCGACGTCAGCCCTCGCCTCGCCGCGGCCTCCAGCGCCTCGTGGAGCCGCTCCACCCCGGCCAGCCGCTGCTTCGTGTCCTTGGCGCGCGCCGCCTCCAGCGCCGCCTCCATCTCCGCCCCACCCCCACCCGACAACCAACCGACCGAAGCTTCCTCCTCCTCCTACTCCTCACCGGCGGCGGCGGCGGCGGCGACCAGTAGGCGGTGGTTGGGTCGCGCGCTCGCGATGATTTTTGGGGGAAA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.734985
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0174000.1 2 24489283 T A
Osa02LNT0174000.1 2 24492752 T C
Osa02LNT0174000.1 2 24491127 T C
Osa02LNT0174000.1 2 24501255 G A
Osa02LNT0174000.1 2 24492584 A T
Osa02LNT0174000.1 2 24493856 T C
Osa02LNT0174000.1 2 24495770 C T
Osa02LNT0174000.1 2 24488880 G A
Osa02LNT0174000.1 2 24489074 A C
Osa02LNT0174000.1 2 24489314 C A
Osa02LNT0174000.1 2 24489346 G A
Osa02LNT0174000.1 2 24489508 A G
Osa02LNT0174000.1 2 24489968 A G
Osa02LNT0174000.1 2 24489971 T C
Osa02LNT0174000.1 2 24490105 T G
Osa02LNT0174000.1 2 24490137 A C
Osa02LNT0174000.1 2 24490202 A G
Osa02LNT0174000.1 2 24490293 A G
Osa02LNT0174000.1 2 24490357 G A
Osa02LNT0174000.1 2 24490394 A C
Osa02LNT0174000.1 2 24490641 A G
Osa02LNT0174000.1 2 24490847 C T
Osa02LNT0174000.1 2 24490874 G A
Osa02LNT0174000.1 2 24490885 T G
Osa02LNT0174000.1 2 24490976 T C
Osa02LNT0174000.1 2 24491044 A G
Osa02LNT0174000.1 2 24491187 A G
Osa02LNT0174000.1 2 24491221 C T
Osa02LNT0174000.1 2 24491333 A T
Osa02LNT0174000.1 2 24491387 A G
Osa02LNT0174000.1 2 24491388 C T
Osa02LNT0174000.1 2 24491516 G T
Osa02LNT0174000.1 2 24491554 A G
Osa02LNT0174000.1 2 24491783 C T
Osa02LNT0174000.1 2 24491954 C T
Osa02LNT0174000.1 2 24492002 A T
Osa02LNT0174000.1 2 24492051 T C
Osa02LNT0174000.1 2 24492275 G A
Osa02LNT0174000.1 2 24492289 A G
Osa02LNT0174000.1 2 24492358 A G
Osa02LNT0174000.1 2 24492431 A G
Osa02LNT0174000.1 2 24492493 A G
Osa02LNT0174000.1 2 24492872 C T
Osa02LNT0174000.1 2 24492902 G A
Osa02LNT0174000.1 2 24493199 C T
Osa02LNT0174000.1 2 24493384 A T
Osa02LNT0174000.1 2 24493385 T A
Osa02LNT0174000.1 2 24493409 T C
Osa02LNT0174000.1 2 24493693 C T
Osa02LNT0174000.1 2 24494022 G A
Osa02LNT0174000.1 2 24494316 C T
Osa02LNT0174000.1 2 24494378 A G
Osa02LNT0174000.1 2 24494565 A G
Osa02LNT0174000.1 2 24494645 T C
Osa02LNT0174000.1 2 24494686 G A
Osa02LNT0174000.1 2 24494991 T G
Osa02LNT0174000.1 2 24495070 A C
Osa02LNT0174000.1 2 24495139 T G
Osa02LNT0174000.1 2 24495250 T A
Osa02LNT0174000.1 2 24495292 A G
Osa02LNT0174000.1 2 24495334 A C
Osa02LNT0174000.1 2 24495348 T C
Osa02LNT0174000.1 2 24495369 A G
Osa02LNT0174000.1 2 24495610 T C
Osa02LNT0174000.1 2 24495640 A G
Osa02LNT0174000.1 2 24495712 A G
Osa02LNT0174000.1 2 24495808 T C
Osa02LNT0174000.1 2 24495959 C G
Osa02LNT0174000.1 2 24496268 A C
Osa02LNT0174000.1 2 24496283 A C
Osa02LNT0174000.1 2 24496318 C G
Osa02LNT0174000.1 2 24496324 T C
Osa02LNT0174000.1 2 24496423 A G
Osa02LNT0174000.1 2 24496429 C A
Osa02LNT0174000.1 2 24496588 A G
Osa02LNT0174000.1 2 24496718 T C
Osa02LNT0174000.1 2 24497115 T C
Osa02LNT0174000.1 2 24497166 T G
Osa02LNT0174000.1 2 24497186 C T
Osa02LNT0174000.1 2 24497218 T A
Osa02LNT0174000.1 2 24497466 G A
Osa02LNT0174000.1 2 24497679 T C
Osa02LNT0174000.1 2 24497685 T C
Osa02LNT0174000.1 2 24497732 G A
Osa02LNT0174000.1 2 24497769 A T
Osa02LNT0174000.1 2 24497885 A C
Osa02LNT0174000.1 2 24497894 A G
Osa02LNT0174000.1 2 24498171 T C
Osa02LNT0174000.1 2 24498351 A T
Osa02LNT0174000.1 2 24498636 T A
Osa02LNT0174000.1 2 24498666 C T
Osa02LNT0174000.1 2 24498833 C T
Osa02LNT0174000.1 2 24498932 A C
Osa02LNT0174000.1 2 24499007 A G
Osa02LNT0174000.1 2 24499263 C T
Osa02LNT0174000.1 2 24499489 T A
Osa02LNT0174000.1 2 24499683 A G
Osa02LNT0174000.1 2 24499684 T C
Osa02LNT0174000.1 2 24499735 T C
Osa02LNT0174000.1 2 24500039 T C
Osa02LNT0174000.1 2 24500249 C T
Osa02LNT0174000.1 2 24500289 A G
Osa02LNT0174000.1 2 24500381 T G
Osa02LNT0174000.1 2 24500458 T A
Osa02LNT0174000.1 2 24500484 A C
Osa02LNT0174000.1 2 24500610 A G
Osa02LNT0174000.1 2 24500660 C T
Osa02LNT0174000.1 2 24500712 T C
Osa02LNT0174000.1 2 24500729 A C
Osa02LNT0174000.1 2 24501042 A C
Osa02LNT0174000.1 2 24501126 C G
Osa02LNT0174000.1 2 24497100 G C
Osa02LNT0174000.1 2 24501306 T C
Osa02LNT0174000.1 2 24501402 A C
Osa02LNT0174000.1 2 24501465 C T
Osa02LNT0174000.1 2 24501757 T C
Osa02LNT0174000.1 2 24501924 A G
Osa02LNT0174000.1 2 24491370 C T
Osa02LNT0174000.1 2 24489624 C A
Osa02LNT0174000.1 2 24491196 C T
Osa02LNT0174000.1 2 24493972 A G
Osa02LNT0174000.1 2 24496567 T C
Osa02LNT0174000.1 2 24497013 T C
Osa02LNT0174000.1 2 24498828 T C
Osa02LNT0174000.1 2 24501682 T C
Osa02LNT0174000.1 2 24499585 A G
Osa02LNT0174000.1 2 24500955 A G
Osa02LNT0174000.1 2 24490610 G A
Osa02LNT0174000.1 2 24497486 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
Osa02LNT0174000.1 osa-miR5820 Translation 3.5 17.412 1 21
Osa02LNT0174000.1 osa-miR1319b Cleavage 4.0 15.689 1 24
Osa02LNT0174000.1 osa-miR160f-3p Cleavage 3.5 11.048 1 21
Osa02LNT0174000.1 osa-miR160f-3p Translation 5.0 24.986 1 21
Osa02LNT0174000.1 osa-miR169e Cleavage 5.0 15.502 1 21
Osa02LNT0174000.1 osa-miR169i-5p.2 Cleavage 5.0 18.338 1 22
Osa02LNT0174000.1 osa-miR528-5p Cleavage 4.0 15.33 1 21
Osa02LNT0174000.1 osa-miR1442 Translation 5.0 18.463 1 20
Osa02LNT0174000.1 osa-miR1442 Cleavage 5.0 19.195 1 20
Osa02LNT0174000.1 osa-miR1857-5p Cleavage 4.5 12.207 1 21
Osa02LNT0174000.1 osa-miR1860-5p Translation 5.0 13.719 1 21
Osa02LNT0174000.1 osa-miR1862e Cleavage 4.5 12.407 1 24
Osa02LNT0174000.1 osa-miR2093-5p Cleavage 4.5 20.296 1 20
Osa02LNT0174000.1 osa-miR2871a-3p Cleavage 4.5 15.596 1 21
Osa02LNT0174000.1 osa-miR2871b Cleavage 4.5 15.596 1 21
Osa02LNT0174000.1 osa-miR5144-5p Translation 4.0 18.728 1 21
Osa02LNT0174000.1 osa-miR5155 Translation 5.0 15.689 1 24
Osa02LNT0174000.1 osa-miR5157a-3p Cleavage 4.5 14.676 1 24
Osa02LNT0174000.1 osa-miR5157b-3p Cleavage 4.5 14.676 1 24
Osa02LNT0174000.1 osa-miR5338 Translation 3.5 3.417 1 21
Osa02LNT0174000.1 osa-miR5339 Cleavage 4.0 15.742 1 21
Osa02LNT0174000.1 osa-miR5506 Translation 5.0 12.572 1 21
Osa02LNT0174000.1 osa-miR2093-5p Translation 5.0 11.315 1 20
Osa02LNT0174000.1 osa-miR166k-5p Cleavage 3.5 13.964 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0174000.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0174000.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0174000.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0174000.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0174000.1 2 nan Others Others C424 G45
Osa02LNT0174000.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0174000.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0174000.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0174000.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0174000.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0174000.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0174000.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0174000.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0174000.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0174000.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0174000.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
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