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

>Osa01LNT0028000.2

AAAAGGCTTGGGGGTTACCAGCTTAAAAGAAAGCTACTAAGAGATCTCCACCTATACCCAAAAGCTTAAACATTAAGCCAACACAATCCTATCCAACAGACTGAAACCTTAGATCACTCTGATCATATGCTAGCTAACATTCCTTACATAGCTTCCACTTTTTCAGCTACAGAACAAAAGGCCACACTTATCCCTGTCCACCCGTCAAGCAGAACAATGCTCCAGGACTGCAAGAGAATGAATTTATAAAGTATCAAATCAGACTTGTAGGGAATTTCTTAACTACCAAATAGACCAAATACAGAAAATACAAACAATACCAAGGGTTGGCAAGGCTTTTGAATCTTTGACAATAAAAAAAATTCTCAAATGCTTGGTTTTCTATACAACCAATATAGCTTACATGATAGTTGTGGGATGAGGTGGCAATATCATCAAGCTTCTTTCCATGAAAATTACAGCATTTAGGCAACATATATTCTATCCTTTTGTTCTGATAGTGTTAGAAACAAATTATGACAGGATGCCAGATCAAGCAACCAGAATAACATCTAAGCACATAAACATGTCCTTTTCAACTCTTGCAAGACAACTTCTGTAATCAGCAATTTGCAGAATTGTATCGCAAATATAGATAACATCATATTGCAGTTATACACAGAAATAACCAGCAAAGTTTCTAATCATAGATAGACCAGCATTTTCAATGTTGTAACAAAAATTTTGTGATCAGAAAACTAATAGATGTATACAGACAAATTTTGTGATCAGAAAACCGATAGAGCCATATAGGCTGTACATGCTTTGTATTATCTCAAATTAGAAAGGCAACCAGGATTGTAGATGTAGGACCCCAAGGAATGCATGTAAGAATTAAACGATGCGAACACCTCTAGCAAATAGTGAACCCATGGCCCGCTGTTTAAATCATTTAAAATTTAACAGCAAATCCAGCTCGTTAAGCACCTTAATCTAATCAAACTAACTAAAAAAAGGAAAATAAAATGAACAAAGATGGCATTTCTGCCGCTGGCTTTTTTCTCGAGCACGCAAGAGAGTTGTTCTGCCCGTGGCTTTGTGCCATCACCAATGTGTAATCTCCTTCCCACCTGAATGGTGCATTCAAATGTGAAATACATGAGAGGTTTTTTAGAGTGTCTTTCAGCTGTGACAGAATCATTTGCACAGTATTCCCCACCTAATGTTAGTATTTTCCTTGAAAACTCAATCAGGAATCACAAGAACCATACAGATTTATGAATCACAGGGACAAGCAATGACTGATTATAATTGGAGAAGTTTGTTAGCTATTTAGGTAGTCACATAAATATTCTAGCAAAAGAAGCAGTTATCAGCAATCATTATCTATATGAAATGCATGCATCTACAGAGCTAACTACAAATGAATATTTTCAATGATGCATTTCATTAGATATTTTAACTGCTAACATTAAGGTAGGTTCAAATGTTTAGGGCAAATTAAGTGGAAGCTAGGATCCAAATCTAAAGCCCAACAAACCATTCAGGCTTACACACTAACAGGTCATGTAAGATTGCCACATTCCCATGCTTGTAGGGAAAACAACGAACACCTTGTAGGCAGGACACCACACAAAACAAACACCTCAAATTTTTGTGGGGAATACAAACGAAAATCAGATACCAATGGAAGATGGCTTGCTGCATCCAGAGAACGGCAAAAATCAGATACTAATGGGAGATGGCTTGCTGCATCCAGAGAACGGCTAGGCGATGGGAGACAACTCCTCCTCCATCTGGTGGCCAGAAAAAAATAGGAGCTTTGCCACTGCTTATGGAGCACCCACATCACTCGAAAATCAAGCCATGCACCGCCAGACATATACCTCGCCACCTCACCTTGGAGAACTCCATGCCAACGCCATTTCTAGCAAGCTCGAGGCATTGTCCACCTGAACCAGTGAACCACCACCACACCGGGGACGTTGCCAGCTACACACTTCAGGCCCGCTCCGCCATGCGCTCCTCCTCTCTTCGCCAGATCTGGCCGCTGCAAGGTAGATGCCACCAGATCTGATTGAAAGCCAGATCGACCTACTCGCTAGCTCGAGCCCAGCGGCATCGGCAGCAAGAAGAGAGAGGAAGTGGAGGACATGCGGCGAAGCATGTGGCGGTGTCGGGGCGAGGTTAGGTGCTGGAGGATGGAGCGGCGGCGCAACTGCGCAGGGTGTCGGTGTGGCGGGGAGAGGCGGCGCGAGGAGGGGGAAGCGACGCACCGTCACGGGAGTGGTGGCGGCTAGGGTTTC

Coding Potentia
Explanation CPC Score
noncoding -1.15649
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0028000.2 1 25019369 A G
Osa01LNT0028000.2 1 25020472 T C
Osa01LNT0028000.2 1 25021030 A G
Osa01LNT0028000.2 1 25021194 T C
Osa01LNT0028000.2 1 25021327 C T
Osa01LNT0028000.2 1 25021462 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
Osa01LNT0028000.2 osa-miR5836 Translation 4.0 13.028 1 21
Osa01LNT0028000.2 osa-miR172a Cleavage 3.0 16.773 1 21
Osa01LNT0028000.2 osa-miR172b Cleavage 3.5 16.773 1 21
Osa01LNT0028000.2 osa-miR172c Cleavage 4.0 16.773 1 21
Osa01LNT0028000.2 osa-miR166h-5p Cleavage 5.0 12.472 1 21
Osa01LNT0028000.2 osa-miR172d-3p Cleavage 3.0 16.773 1 21
Osa01LNT0028000.2 osa-miR529a Cleavage 4.5 20.59 1 20
Osa01LNT0028000.2 osa-miR444d.3 Cleavage 4.5 16.1 1 21
Osa01LNT0028000.2 osa-miR1871 Cleavage 4.5 12.958 1 24
Osa01LNT0028000.2 osa-miR2097-3p Cleavage 4.0 19.743 1 22
Osa01LNT0028000.2 osa-miR2097-3p Translation 5.0 19.168 1 22
Osa01LNT0028000.2 osa-miR2873b Translation 4.5 13.833 1 21
Osa01LNT0028000.2 osa-miR5077 Translation 4.5 12.091 1 19
Osa01LNT0028000.2 osa-miR5148a Cleavage 5.0 22.984 1 24
Osa01LNT0028000.2 osa-miR5148b Cleavage 5.0 22.984 1 24
Osa01LNT0028000.2 osa-miR5148c Cleavage 5.0 22.984 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0028000.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0028000.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0028000.2 1 nan Resistance or Tolerance Drought tolerance RM129 RM5
Osa01LNT0028000.2 1 nan Morphological trait Root RM23 RM306
Osa01LNT0028000.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0028000.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0028000.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0028000.2 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
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