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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcttccgttgtgaacctctttttttcatgttgttgctccacaatactgtgtatcctgatttcaactttttgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTCTCCTGCTAGAGAAGTTTCTCCTGATAAGCGTAGCAATGAGAGGTCTCCA

Basic information

species Arabidopsis thaliana
transcript AT5G64200.2
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|116484584|gb|EG527176.1|EG527176
EST:     GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGCCGTTCCTTGAG                         TGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
genomic: GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAGgtttcttccg ... tgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
EST: gi|86085148|gb|DR380907.1|DR380907
EST:     GTCAGAGSCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAG                         TGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
genomic: GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAGgtttcttccg ... tgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
EST: gi|86077808|gb|DR373565.1|DR373565
EST:     GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAG                         TGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
genomic: GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAGgtttcttccg ... tgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
EST: gi|125206412|gb|EL221366.1|EL221366
EST:     GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAG                         TGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCT
genomic: GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAGgtttcttccg ... tgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCT
EST: gi|86080095|gb|DR375852.1|DR375852
EST:     GTCAGAGSCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAG                         TGCATCTCCTGCTCGCCGYAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
genomic: GTCAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAGgtttcttccg ... tgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC
EST: gi|116476600|gb|EG519192.1|EG519192
EST:     CAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAG                         TGCATCTCCTGCTCGCCGCAGCCCTAGGAGTTCCTCCCCACAGAAAACCTC
genomic: CAGAGGCCGTTATGATAATGAGAGCCGCAGTCACAGTCGTTCCTTGAGgtttcttccg ... tgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgttgttgctccacaatactgtgtatcctgatttcaactttttgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTCTCCTGCTAGAGAAGTTTCTCCTGATAAGCGTAGCAATGAGAGGTCTCCA
                                          ttttgac  putative branch site (score: 3)
                                        cttttt  CT-rich tract
                                      aacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcttccgttgtgaacctctttttttcatgttgttgctccacaatactgtgtatcctgatttcaactttttgacatgcagTGCATCTCCTGCTCGCCGCAGCCCTAGAAGTTCCTCCCCACAGAAAACCTCTCCTGCTAGAGAAGTTTCTCCTGATAAGCGTAGCAATGAGAGGTCTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG