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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagacaatggcatacatatgtacctatcaggtagctacagttaaaatcttgctgtcagcacctatacaattcgtttgatttttgcattatgtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATCAGAGATGGCTGTGAGTCCATCATCTGCAATGTCAAGCAATCATGTTTCT

Basic information

species Oryza sativa
transcript LOC_Os05g12170.2
intron # 6
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|32948032|gb|BP184604.1|BP184604
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
EST: gi|29637797|gb|CB642806.1|CB642806
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
EST: gi|86595095|gb|CI260334.1|CI260334
EST:     TGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: TGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
EST: gi|29662992|gb|CB659267.1|CB659267
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
EST: gi|29637418|gb|CB642427.1|CB642427
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
EST: gi|29671008|gb|CB667283.1|CB667283
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCANGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCA
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCA
EST: gi|29664499|gb|CB660774.1|CB660774
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
EST: gi|29671009|gb|CB667284.1|CB667284
EST:     ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGG                         CATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC
genomic: ATTCCTGCACCAGGTGGTTATAATCCGATTCGCATGAGCTCAGGAAATGGgtaaagaata ... gtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgctgtcagcacctatacaattcgtttgatttttgcattatgtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATCAGAGATGGCTGTGAGTCCATCATCTGCAATGTCAAGCAATCATGTTTCT
                           gtttgat  putative branch site (score: 5)
                                            tgtttct  putative PPT
                            tttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagacaatggcatacatatgtacctatcaggtagctacagttaaaatcttgctgtcagcacctatacaattcgtttgatttttgcattatgtttctgaagCATGACAGAGAATGAAGTTCCTGGAACTGCACATGCTGGAGCCATGTCATCAGAGATGGCTGTGAGTCCATCATCTGCAATGTCAAGCAATCATGTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA