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

>Osa02LNT0175000.1

CTTTGCCACCTGGCCTTAATTAATCCCTTACAACCATATATTCCTCACAAATAATGATAGTAATATACAACAGGCGTGGGCTATCCATACGTACTGTAACCTAAAATTACACACAGGAAATAAAACAATACAGCATACCCTGTTCAGAACGGAACTACAAAGCATATCAGATATCACTTCACCGTGGTATACCTAATTAGCGTGGCAAACTAATTGAAGATGATAATTCTTGCTCCAGACTGTAGCAACCAGAACCTGGGATTCCTTCAGATGTTAAATCACCAGCATTTGTATAAATATTCTGTGCATAAGAGTTACTAGTATTTGGGCTTAAAAGGTGCTCGATTTCTCCATCATTTCCTGGGAGCAGTTGGAATTTTCTTAGCCTCTTAGTTTTCAGGAACTGCAGCCTCATCTCTACTTCTTTCATAGTAGGTCTATCTACTCCTTTAACTTTCAAGCATGCCATTGTAAGCGAGGCAATTCCATCGATCTCTTCCTTGTTTGCCTCTTCAACAACCTGAGGATCTATTATTTCCATTAGAGAGCCCTCTTGAAGTCCTTCAACGAAGTAATGAGACAAGCTTTGTTTTGCACCTGCCTCATTAATGAAAATTGGTTTCTTTCTTATTAGAAGTTCCACAAGTATCACTCCAAAACTATATACATCACTTTTTTCAGTTAGTTGTCCAGTATGATAATACTCTGGGTCTAGATAACCGAATGTGCCTTGGACAATAGTCACCACATGAGTTTCATCAAGTGAAACAGATCTTGAAGCACCAAAATCAGAGACCTTTGTAGTAAAGCTGCCATCTAAGAGAATATTGGAAGATTTCACGTCTCTATGAAAAATTGGTATTGCAGCAGCTGAATGCAGATAGGAAAGTGCCCCTGCTGCTTCTACAGCAATCCTAATGCGATCATCCCATGACAGCGAGCATCTAACACTAAGATCGGTATGAAGGTGGTCATGCAGTGTGCCATTCGATATGAATTCATAAACCAGCAGTGGCACCTCAGATTCAAGACAACAACCAAAAATCTTTACCACATTGCGGTGGATAATTTGAGATAAGATAACAACCTCGTTGATAAATTGATCTATCTCAGTTTGCTCAACGATTTTTGATTTTTTAATGGCCACCACACGCTGGTCAGATAGAATGCCTTTGTAAACTGTGCCATGTCCTCCACGTCCAAGAACACGAGTTCCATCAAAGTTGTTGGTTGCCTCCTCTAGTTCTTCCAAGGAAAATATCTTCGTTTTGTTTGTGGCGCTTTCATTTGAGATTAGTTGCTCCAAGAGTAGGCCTTGATTTTTCTTGAAATATGCTCTCCGTATTCTCTTTTGGATGCCTTTCCTCCACTTATTGGCAAGTATCATTGCCCCCAACACGATAACTATGGAGCCAAGACCACAACCAATTCCAATTGCAATACCTAAAAGAAGATTGCGTTGCTTTGCTGATGTAACACACTTCTTTTTGATTGGATCAAACTCTTTTCTATGCGGGCAGCTTGTGCATGTATAATTTCCAAGTAAATTTTGACACGTGCCATTGCAATAGTTTGGCAGTAAGCATTCATTGATGTCTGTGCAGCCATCCTCGATGTATGGGTTTCCTTCAAAACCGGGAGAACACTTGCAACGATATCCCATGAACTCTTTCCTGTGGGTGACGTTCAGGCAGTAGCTGTGGCTACTGCGGCATGCGTATGTAGTGTTCTTCTGCACAGCTACTTCACAAGTTAAGTTGGTAACTGCCCATCTTATAACAATGGCGTATTCCATAGAGAGATCAAATCTATCTTCCACAGGGCCTGAGAATGAATAATCACGGCCAGTATCTGTGGTCTGAACAATTATCGCCTCTTTCTCGTAGTTTGTGTCATTCATCATGTTTCCGACAGTTAGAGTCCCATCATCCAAAGACACAGCAGTCACATGATATTGTGCTTCTCCTAATTCGCAAACAGTTAGGTTACCTTCTGTACAATTAAGTCTAAACCTTTCGTTAGCAAAACAACCTTCTTCGACTCCAAAAGGGAAAGGAATCTTCATGTCTCCACAGGATGTTGAACAGTGTTCTTTATATTTGGGGTTGTAATCCGTGCATCCATCTAGAAGGTAAGGATTCCCCTGTTCATAACCAGAGCAGTAACAATGATAACCTCCAGATGACACATTCCGGCAATTGCTGCCAGGGCTACACGCATAACTTGTGTTGTTCATGCGCGCGCGTTCACAGCTTGGTTGATCTATGGTAGCAAAAGAAAGTACTGTGCCTTCAACATTACTTGTGTTTGTCCAACCTAAGAAAAGGTCACTTGTGTTTGATATATAATAGTCCGATGACATGAAAGCCATGATTCCAGGGTGCACTGGATCTGTTTGTGCTACAGGAATGCCATCCGACCGAAGAATTATGGTTGACTGAAAGCCCCGCAAGACCCTTGGTAACTCGATGAAACAGCATCCCATCCCATTACAAGGCCCTCCTATTGGTGCCTTTTCACCATCACATCTACTCATGCAAGAACCTATGAGGTCCTCCGTGCCATACTCGAACAAGGTAGCATCGAAATTACAACCGATAACGTAAAATGTGTTGTAATGATCAATAGTAATACCCTCTGTTGGGGCCACCCAGGATATGTTGTAGGTATCCGTACCTGGTCTCACCGTAATGTTGAAGTATATCTGGGCCAAAACATACCTATAACCCAAGTCTGTGATCTCAGTAGTACCATCACCCAGAAAGAGCTTAGGAGTTTTGGCGGTGTTGCGGCAGATGAGCTCGAAGCCTTCCCGGAAACAGCCCGGCGCTATCCCGAAGGGGTAGTCGATGCCAACATCTCCGCAACGAGAGGGGCAATGAGCCAGGGAATCATTAGAAGGGATAGACAAGAGCCCTCCGCCAACTCCGTAGACTGCAGCCGATGCTGGGGACGTAGCAGCCGAGCACAGCAGCACAAAAGAGACGGCGCAAGCTGCCACTAATAAGCTCGAGCTCATCTTTGCGCCGATCGGCTAGCTTGCCTAGCTTTGTGGGTGCAGATATGTATGCTAACTACGCGTGAGATCGATT

Coding Potentia
Explanation CPC Score
noncoding -1.33695
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0175000.1 2 25351415 T C
Osa02LNT0175000.1 2 25351424 G A
Osa02LNT0175000.1 2 25351439 T C
Osa02LNT0175000.1 2 25348349 A G
Osa02LNT0175000.1 2 25348372 C T
Osa02LNT0175000.1 2 25348377 C T
Osa02LNT0175000.1 2 25348395 G A
Osa02LNT0175000.1 2 25348421 G A
Osa02LNT0175000.1 2 25348619 A G
Osa02LNT0175000.1 2 25349287 A G
Osa02LNT0175000.1 2 25349332 C T
Osa02LNT0175000.1 2 25349801 A G
Osa02LNT0175000.1 2 25349832 T G
Osa02LNT0175000.1 2 25350787 A G
Osa02LNT0175000.1 2 25351114 G A
Osa02LNT0175000.1 2 25351313 A C
Osa02LNT0175000.1 2 25351307 T C
Osa02LNT0175000.1 2 25351416 A G
Osa02LNT0175000.1 2 25350926 C A
Osa02LNT0175000.1 2 25351306 T C
Osa02LNT0175000.1 2 25351288 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0175000.1 osa-miR812q Cleavage 5.0 19.044 1 24
Osa02LNT0175000.1 osa-miR5816 Translation 4.5 17.867 1 24
Osa02LNT0175000.1 osa-miR5828 Cleavage 4.5 18.237 1 21
Osa02LNT0175000.1 osa-miR396a-3p Cleavage 5.0 17.976 1 20
Osa02LNT0175000.1 osa-miR396b-3p Cleavage 5.0 17.976 1 20
Osa02LNT0175000.1 osa-miR171f-5p Cleavage 4.5 18.177 1 21
Osa02LNT0175000.1 osa-miR444a-5p Translation 4.5 12.756 1 21
Osa02LNT0175000.1 osa-miR1860-3p Translation 5.0 18.329 1 22
Osa02LNT0175000.1 osa-miR1861c Cleavage 5.0 19.2 1 22
Osa02LNT0175000.1 osa-miR1861g Cleavage 5.0 19.2 1 22
Osa02LNT0175000.1 osa-miR1861g Translation 5.0 13.543 1 22
Osa02LNT0175000.1 osa-miR1320-5p Cleavage 5.0 12.524 1 21
Osa02LNT0175000.1 osa-miR2863b Cleavage 5.0 16.068 1 21
Osa02LNT0175000.1 osa-miR5078 Translation 4.5 14.747 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0175000.1 2 nan Others Others C424 G45
Osa02LNT0175000.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0175000.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0175000.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0175000.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0175000.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0175000.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0175000.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0175000.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0175000.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0175000.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0175000.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0175000.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0175000.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0175000.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0175000.1 2 Hbd2 Physiological trait Lethality nan nan
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