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

>Osa02LNT0173300.1

GGCTTATTTCATAAATAAGCGAAACAATGAGGCCATCAGATTCATGACACGCAAGAGCGCGAAATGCAAACAGTACGAATTCCCATATCCTACCTCACAGCCTCAGATGAGAAGATAAGACTGCATTGACAGGTTAAATTGAACCAAACAAATCTCGAATAAATTGTCATGAGATTGGCTGGAAGAATTACATCAGATCTCAACTTTCGACTAAATTATGAACTCAGTTGTACCCAACGCTAACAAGTATGCTTGCCAACACGCAGCAGTACCTGTTACAAGAGGAGTAGCCGCGTAAACCACCATCGAGGTATTGTTACGGTGTTATCAGAGCTAAATCTATAGCTTTTCTTTACTTCATTATCAGTCATCTGACCTTGCAAAAAAATACAGCTCACAAAAAGCTGTTCCTCAACTTCAGTGTTGTAGTTTCTCGAACTGAAAGGGCAAAACCTGCCAACTACCGAGTAACAAATAACCAATGTAACATTCCCAGTTAGGACATCAGTAATAAGGTAGAAGTTGGCCTAGTCAAACTTGCGACAAATATTTATTCCGAGGATAGAAGTTTGCTGCACGCGTCGATCTTAGCAACATGTGAGCCCAAGATAGCCTGACCTGATGGATTTGCTTTCATGATTTTCATCATAGCTTCAAACACTGCAGCACGAAAGAAACTGTCCTCAATTTTCTTTAGAGTATCCTCAACGACTTCTATGCTCAGGCAATGTGACAAGACCAGCCGCCCAATAACTTCACCAAAATGTACTGGAGCTTTTGGAAGGTCAATAGCAAGCTCATCAAGAAGAGAACTGTAAAGCAAGCATCCAGTTTCCAAGTCAGTCGCTTTGAAAACATTCTTGTTGTAGAGATGCTCCAACAGCCTCAAAAGAGGATCGATGGAATTGGTGCCTTTATCAAGAGCAAGATTGATGGCTTCTTTAACAACTTCTGGGTAGTAATCAGGACTCTTCAGCTCCTCAATGCACTGTTGTGCTTCATGTAGAAGAAGTATGTGGAAATACTCCTTAAGAAGAGATATGGTCTTCTTCTGAAGCTCTGTAGAGCTTGGCTTGGGGGCAGCAGCTGGTTGCTCAACTATAGGATCTACAGATGGAGCTGGGATGAGTGATTTTGGTGGTCCTGTAGTTTGAGATGGTGTGACAACCAGACCATGGGATAGTGGGCCACCACTGCCCACAAGTGCACTCGTCTTGCCACTAATTAATGCTGCACTGCCTTGAGGAAGCAGTCTGGAATTATTAGGTGATGGCTTATTGGCCAATGATGGGGTGAGGTTCCGAACTGGATCAGCTCTGGGCTTTGATCTAGAATGCGGAACTTCCCAGTCATCACTACCTAGCCCTGGCATTCCAGGCATCTTTCTCGCTCCAGGCATACCAGGCAACATGCCAACTATACCAGGTTGGTTCATAGAAAAAGCTCCTGGTGAAAGGGGTCCTCCACCTCCAGTACCAGTACGGCCAGTTCTTATGCTTGCAGTCGACCCTGGACGCAATCCAAGATTGTTTTCTGCCTCTCTATGAATTTCACTGATTTTCTTAGCTTTCATCTCTTCACGTCGAGGCACCCATTGGTTTGAACGAAGATCAAGGACATCGCGTGCCATGAACCTCAATCGTGATGCCAACTGAGAATTAGTTGTTAGATCCTTCAGCCGGTTGAAGTATACGTCATTAAATCGTCGAGACTTTGGATTCTCATCCAACTGTTTACCAATTGTGTTGAAGAACTGACAGATGGCCTCCACATTTTCCTCAGCAGGGCATCTGTTGCTTTCAGAACCTAATAGCTCCTGAACAATGTGATGTACTATCTTCTCAGGGACCATTTTTTGCTTAAGTAGCTCACCAACAAGACGAATGTTTCCAAGTGTCCGAAGCTTCACTAGCCTTTCTTTATCACGTCTCTCCATCTCTTGGTCTAGACCAGTCAATTTATTGACCTCAGACCGCAGATTGTCAGCACCTTCAAATGCTTCTTGGCAATTGTTCAACAGCACACGTTTGAACGTGATCTCTTTACCACCAGGTTCTTCAGAAGGGAATGAGGGTAACTTCTCATTGAGATCAAAGCAAAGCTGAGCATACATTGGACAGAAGGTAGGCTCAAGAACAGCCTTCTCAAATATGAGACTAATAACATCCTTCAAAATATCAGCTGTAGTGATCCCTGCTTCAATTAACTGGCCCTTAAGAAGATCAAACTTTTCTGGAGTCAATTTGTTCAGTATACTGTGAAACAAATAACAAATAAATATATGCAAGAAAAAACATAATGTTTGGTTACTCTCTCCAGCCACAAATAAATACCGCTTTGGACATCAGTACAGTCCCAAAAGCAAAACTATGACAACTAATTTCTATTAAAGGACATCAATAAAGCTCGATATAGTGAGTTCTCCACAAGTTTCATGTGTCAAATCAAAATATTTAAAGAAGCATTAGTGCTCAACATTCAAAAGGTTTGGCTGCAGGTATGTCTAAAACAGCACATTAGGGACTAGACGAAAAAGAGTAAATAAATTATATTTCCTAAATATGAAAATATAAAAATGATGAGGAAGGATGATACAAATCAAACAATACCCTTTCACTGTTTTCAGAACTCTTTCTTTGTTGGAGAGATTGCCTCTCTGGATTGACCAAGGGACTTCAGCCTTGACAAGAGCAGGAGCCGGACCAACCTGAGCTTTTGCACTGAACTGGGAGCTCAATTTGTCTTGATTATTAAATTGATCTTGCTTTCCACTTGAAATGTATGATTCTTTTGCTTCACGAAATTTGTCCCAAGATTTCTCTTCACCACCAATAGCAGGAGTTTGCACAGGTTGTTCAATCCGTGAACGCCAATCACGGTTGTCTGTCTCAGCGTAGCGGTTATATGACTGAGTTTGCACACTTGAGTCATTGTTAATCCAGGGTTCATCTTCACCATGGAGTTCTATGTCAATATCTTGCTTAAGCTTCAAGATGTTCTCAGGTATGTCGATAATCTCATGCAGTTCAACAAGTTGATCCCTAGTGTAACGAACCCGCTCGAGAGGTTCAAACCGCAAGTCTCCAAGCTTGGCAGCGAAGCCGGAGGATGCGCCGCCGCGCGGGCGGAGGAAGTCGAGGGAGCCTGTGGAGGCGCCGAAGGGGAAGAGGCGGCCGGCGCGCGGGCCACCGATGCCGCCGCCGCCGCCCGGGCGCAGGCTGATCACCGCCTGATCCGCCTGCGTCATGATCCGCCTATCGAAGAAGAGAGGCGGAGAGACGGAGGCGCGGATTGGGGGCGGGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.807202
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0173300.1 2 24073194 G A
Osa02LNT0173300.1 2 24069962 T C
Osa02LNT0173300.1 2 24069678 A T
Osa02LNT0173300.1 2 24072032 C A
Osa02LNT0173300.1 2 24069738 A G
Osa02LNT0173300.1 2 24069908 T C
Osa02LNT0173300.1 2 24069913 C G
Osa02LNT0173300.1 2 24070244 G A
Osa02LNT0173300.1 2 24070283 C T
Osa02LNT0173300.1 2 24071040 T C
Osa02LNT0173300.1 2 24071053 C T
Osa02LNT0173300.1 2 24071275 T C
Osa02LNT0173300.1 2 24071943 A G
Osa02LNT0173300.1 2 24072143 C T
Osa02LNT0173300.1 2 24072267 G A
Osa02LNT0173300.1 2 24072347 T A
Osa02LNT0173300.1 2 24072606 A G
Osa02LNT0173300.1 2 24072642 G A
Osa02LNT0173300.1 2 24072716 G A
Osa02LNT0173300.1 2 24073062 C A
Osa02LNT0173300.1 2 24073959 T G
Osa02LNT0173300.1 2 24074408 T G
Osa02LNT0173300.1 2 24070404 A G
Osa02LNT0173300.1 2 24068667 T 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
Osa02LNT0173300.1 osa-miR5827 Translation 2.5 16.999 1 21
Osa02LNT0173300.1 osa-miR6248 Translation 4.0 14.507 1 21
Osa02LNT0173300.1 osa-miR6248 Translation 4.0 8.186 1 21
Osa02LNT0173300.1 osa-miR396c-5p Translation 4.5 17.111 1 21
Osa02LNT0173300.1 osa-miR1853-3p Cleavage 3.5 9.26 1 22
Osa02LNT0173300.1 osa-miR1854-5p Cleavage 4.0 10.202 1 21
Osa02LNT0173300.1 osa-miR1428b Translation 5.0 16.473 1 21
Osa02LNT0173300.1 osa-miR1428c Translation 5.0 16.473 1 21
Osa02LNT0173300.1 osa-miR1428d Translation 5.0 16.473 1 21
Osa02LNT0173300.1 osa-miR2866 Cleavage 4.5 21.429 1 20
Osa02LNT0173300.1 osa-miR1863b Translation 3.5 16.142 1 24
Osa02LNT0173300.1 osa-miR2931 Cleavage 3.5 12.788 1 20
Osa02LNT0173300.1 osa-miR1862f Translation 4.5 14.845 1 20
Osa02LNT0173300.1 osa-miR1862f Cleavage 5.0 14.544 1 20
Osa02LNT0173300.1 osa-miR1862g Translation 4.5 14.845 1 20
Osa02LNT0173300.1 osa-miR1862g Cleavage 5.0 14.544 1 20
Osa02LNT0173300.1 osa-miR5155 Translation 4.5 22.361 1 24
Osa02LNT0173300.1 osa-miR5488 Translation 4.0 19.017 1 21
Osa02LNT0173300.1 osa-miR5488 Translation 5.0 15.138 1 21
Osa02LNT0173300.1 osa-miR5495 Translation 4.0 20.617 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0173300.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0173300.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0173300.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0173300.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0173300.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0173300.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0173300.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0173300.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0173300.1 2 nan Others Others C424 G45
Osa02LNT0173300.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173300.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0173300.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0173300.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0173300.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0173300.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
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