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

>Osa02LNT0173100.1

GTCAAAATAATAGTATAAGATTCTCTAAGACAATAATAGCCCTCATGTACTCGCCTCAACTTGAGGGCTGAGGCAATCGAGAGTTGGAGCACAACATTGATTACATGAGATAGTCGAGTATTCTCAGCGAACAACTGTAAATTAAACAAACTATGTAATCAAATGAATATTGTAACAAATTACAACAGGGAGTTTTGGTGGTGGTGGGGAGGAGCAATGCAAAAGAATCGTCGTTCAAAAATCAATTTCATGTGAGAAATGTGTCATCCTATATTATACAGATGAGAAGCGACTTCAGCTATTGCCACTTCATGGCAAAGCGGGCAGGGATGCAGCAGCAGCAGCAGCAGCAGCTTCAGTAACTGACGCTTGTATGCTTGTTGGAGATGTAACGGCAACGGCTGATCTCCTCCTTTTGCATCCCCAGCATATCCGGTGTATTTTCCGTTTGCTTCTCAAGTTAAATGGTACCTCTATACAGTTGGTCCAAGGTAACAAATGTGTCATCGGTTTGTGTCTTGAAGCAGAGGTGTCCTGTTGTATCTTCAAAGATTCAAGCCACTCGTTCTCCAATGCTGCAATTGCGAGAGCACGCTGCGTAGGATTCTTTATTTGGTTGCCCAGGTAACCTTGACAATTTTGTGCCCCGCAATAGCATTTAACCTTCTCCCCGAAATGCACAAACCTGTAGTCATAAGTTAAGTGTTCTCCAACTTGGATGGAACGAGAGGCGAAAACACCAACTCTTGTCTCACCATCAACTTGCCATTTTTCTAATTTACAGTTGGGATCACAACTGTGGTTCAGAAAACGTGATGTGTTTCCTTTAAATGTTGCATCTATTGTAAAATCTTTGCTGATTTCACACATGTAGAAATTTTTATCACCTCGCCGTTTCATGTCCCAAAGCCTTTGTTCACATGTTGCATCATTGATGACTTCACCAACATACTCAATTATAAAATCACCTTTTTCCAATGGCTCCAATGAAATAGCACCCCATCCACAACGTTTTGTCTTGACAGCTTTTATTTTTTTATCCTTGCGGAATGGCTTGTTCGTACACATATCTGAGCAGTGGCAATTCTTGGAACAACTCATGTAAAGGCCCCTGCATTCGCAGTCATCTTTGCACGTAGAATCAGCACTGCAGTTTGTGCACCCAGCTTCCGCGCGAGAATCAGGACGTTTTTTCTTGATTAAATATACATTGCGTCTGATAAACGTAAAGTGTGGTGGTTTGCAGACAGCTGCAGTGAAATCCCTGATGGTTGAATCAATCTTGAAGTCTTCATTAACATATGGAACAGGTAGTCGGCAAAATACTTCCTCTATGCTGTTCGTCAAGTCAGCATTCTGCCACCATTAAACAAAGTAGTCCTCATTTTGAAGGAGCCAATCAGAGGGATGCCTCCAACAGATAGCACTTCCTTGGTCATCTTTTAAATGAATTACTGGCCATGGTGCACATTTTGTATGTGCTGCAACCGTACACCGTCCACAACGCCAAAAAAACATCTTTTGCTTACAGACCATACAGCCATGTTGAGGGCATTTGAAGCTTTCAGCAATGAAATTTGTGGTATCTTCTGCTGCACAAGTCAGGTGGAACAATTCTCCACATCTACTAACCGAACACTTTATTTCTTCTCCAGGATGAATAATCTTAGAACATAATCGACATTCAACCGCCTTAGGCGTGCCGGTTAGGAAAGGCAGCTCGCAGCGTCCGGCCGGCACGCCGAGCGCCGCCTTCTTCGCCTTCCACTCCTTAACGTACTCCTCGAACGGCCGACCCGATGGATGAGCCGGCGCGGTCGCCACCGTGGACGAAGGCGACGGCGCGGAGGACGGCTTTTTCCCGCCCCCGCGGCGCGGGGCGGGGCACGCGGGGACAGCGGCCGCGCCCGCGCCCTCGCCAGCGCCCGCGAAGCTGCGAACTCGGCCGCTCCATCGGCATTCCACCGGGAGAACGGGCGCGCCGTCGCCACCGGAGGCGGATTCTGCTTCCCCCGCCGCCTCCGCCTCTGCCGACGCAGACACCGCCGCCGCGGCGGTGGTGACGGCGGCGGCGGCGGGCTGCTCGCCTGCTAGCTCCCCGCCGGCGGCGGCGGCGGTGGAGGGGGGTTGCGGCGAGAGGGGGAGGCAGACGGTGCTCAGATCTGGCATGGCAGCGAGGCGGGAGGGGTTATGGGCTAGGGTTTGGAGGGCATTGGAGGTGGGTGGAGTCGTGCAGAAGGGGGAGAAGGGAATGGGGGGAATGGAGGTC

Coding Potentia
Explanation CPC Score
noncoding -1.02115
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0173100.1 2 24049318 G A
Osa02LNT0173100.1 2 24049543 C T
Osa02LNT0173100.1 2 24049609 A G
Osa02LNT0173100.1 2 24049647 C T
Osa02LNT0173100.1 2 24049778 G A
Osa02LNT0173100.1 2 24049941 A G
Osa02LNT0173100.1 2 24049955 A G
Osa02LNT0173100.1 2 24050223 A C
Osa02LNT0173100.1 2 24050713 G A
Osa02LNT0173100.1 2 24051135 C A
Osa02LNT0173100.1 2 24051090 G A
Osa02LNT0173100.1 2 24051541 G A
Osa02LNT0173100.1 2 24051658 C T
Osa02LNT0173100.1 2 24052376 G A
Osa02LNT0173100.1 2 24053688 G T
Osa02LNT0173100.1 2 24054277 T C
Osa02LNT0173100.1 2 24054395 A G
Osa02LNT0173100.1 2 24054503 T C
Osa02LNT0173100.1 2 24054555 T A
Osa02LNT0173100.1 2 24054840 T C
Osa02LNT0173100.1 2 24055569 T G
Osa02LNT0173100.1 2 24055666 A G
Osa02LNT0173100.1 2 24055832 A G
Osa02LNT0173100.1 2 24055921 G A
Osa02LNT0173100.1 2 24056681 T A
Osa02LNT0173100.1 2 24056797 T C
Osa02LNT0173100.1 2 24056963 A G
Osa02LNT0173100.1 2 24056996 C A
Osa02LNT0173100.1 2 24057042 T C
Osa02LNT0173100.1 2 24049869 G A
Osa02LNT0173100.1 2 24053581 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0173100.1 osa-miR5535 Translation 4.5 11.421 1 22
Osa02LNT0173100.1 osa-miR5812 Cleavage 4.0 12.034 1 24
Osa02LNT0173100.1 osa-miR2873c Cleavage 4.0 14.397 1 21
Osa02LNT0173100.1 osa-miR6255 Cleavage 4.0 20.138 1 22
Osa02LNT0173100.1 osa-miR395u Cleavage 4.5 16.671 1 21
Osa02LNT0173100.1 osa-miR172d-5p Cleavage 5.0 12.916 1 20
Osa02LNT0173100.1 osa-miR1862d Cleavage 5.0 15.077 1 24
Osa02LNT0173100.1 osa-miR1862d Cleavage 5.0 8.094 1 24
Osa02LNT0173100.1 osa-miR1862d Cleavage 5.0 12.755 1 24
Osa02LNT0173100.1 osa-miR2118a Translation 4.5 3.086 1 22
Osa02LNT0173100.1 osa-miR2118o Cleavage 5.0 12.52 1 22
Osa02LNT0173100.1 osa-miR5144-3p Translation 4.5 15.097 1 21
Osa02LNT0173100.1 osa-miR5160 Cleavage 5.0 20.114 1 22
Osa02LNT0173100.1 osa-miR5339 Cleavage 4.5 24.47 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0173100.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0173100.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0173100.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0173100.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0173100.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0173100.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0173100.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0173100.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0173100.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0173100.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0173100.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0173100.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0173100.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173100.1 2 nan Others Others C424 G45
Osa02LNT0173100.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173100.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
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