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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttatcaagacataaagctcatagtttggacattcaatgcatcaaaatttgatgtcttattaagattagattgattcataggtactgtttggaaactaccaattattctcatgtagttttgcaattctaaaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCAAAGCTATTGTTTGAAGGCAAGGTCCCAATTGGTATAGGCGAGAACACAA

Basic information

species Oryza sativa
transcript LOC_Os01g44220.1
intron # 14
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116875182|gb|EC365690.1|EC365690
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|88559223|gb|CI489782.1|CI489782
EST:     TTAGCATCCGGTNTGAACTCAAG                         GATACCATGATGAT-GGTGCCAGATCAATATGAAACTGAAGAAGAAACTTC
genomic: TTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTG-CAGATCAATATGAAACTGAAGAAGAAACTTC
EST: gi|15850643|gb|BI798919.1|BI798919
EST:     CATTGGGAATCTCTTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTCCAGATCAATATGAAACCTGAAGAAGAAACTTC
genomic: CATT-GGAATCTC-TTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAA-CTGAAGAAGAAACTTC
EST: gi|13420391|gb|AU174481.1|AU174481
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|29680979|gb|CB677254.1|CB677254
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|116875001|gb|EC365509.1|EC365509
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|15847934|gb|BI796210.1|BI796210
EST:     TGGAATCTCTTCACGC-TTACCATCGGGGTGTGAACTCAAGG                         GATACCATGATGATGGGT-CACGATCAATATGAAACTGAAGAAGAAACTT
genomic: TGGAATCTCTTCACGCGTTAGCATC-GGGTGTGAACTCAA-Ggtactttatc ... aaattcacagGATACCATGATGATGGGTGCA-GATCAATATGAAACTGAAGAAGAAACTT
EST: gi|66915625|gb|CX102473.1|CX102473
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|29668852|gb|CB665127.1|CB665127
EST:     ATTCTGTCATTGGAATTTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|116875027|gb|EC365535.1|EC365535
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAGCTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|7134800|gb|AU082679.1|AU082679
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|15851101|gb|BI799377.1|BI799377
EST:     CATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTCCAGATCCAATATGAAACTGAAGAAGAAACTTC
genomic: CATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGAT-CAATATGAAACTGAAGAAGAAACTTC
EST: gi|15850562|gb|BI798838.1|BI798838
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTCCAGATC-ATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|88693552|gb|CI737127.1|CI737127
EST:     ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
EST: gi|86604151|gb|CI114925.1|CI114925
EST:     ATTCTGTCATTGG-ATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAG                         GATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA
genomic: ATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAACTCAAGgtactttatc ... aaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttggaaactaccaattattctcatgtagttttgcaattctaaaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCAAAGCTATTGTTTGAAGGCAAGGTCCCAATTGGTATAGGCGAGAACACAA
                                        ttctaaa  putative branch site (score: 2)
                                      aattctaaaattca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttatcaagacataaagctcatagtttggacattcaatgcatcaaaatttgatgtcttattaagattagattgattcataggtactgtttggaaactaccaattattctcatgtagttttgcaattctaaaattcacagGATACCATGATGATGGGTGCAGATCAATATGAAACTGAAGAAGAAACTTCAAAGCTATTGTTTGAAGGCAAGGTCCCAATTGGTATAGGCGAGAACACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG