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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaattcgagacatggttgtcattgatttcattgttgatgtcaaaaaaaaaaattccttgtttttgtgatatatctctcattttgacttcatttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTCAACCTG

Basic information

species Arabidopsis thaliana
transcript AT5G64400.1
intron # 1
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|47829059|gb|CK118743.1|CK118743
EST:     TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
genomic: TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
EST: gi|124859165|gb|EH943602.1|EH943602
EST:     CTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
genomic: CTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
EST: gi|125205714|gb|EL220668.1|EL220668
EST:     CTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGACACGCAGCCCAGCTCCT
genomic: CTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTG-CACGCAGCCCAGCTCCT
EST: gi|116462329|gb|EG504921.1|EG504921
EST:     TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATTTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
genomic: TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
EST: gi|124715146|gb|EH806548.1|EH806548
EST:     TCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
genomic: TCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
EST: gi|164006218|gb|ES124348.1|ES124348
EST:     TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCAC
genomic: TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCAC
EST: gi|301502466|gb|HO208006.1|HO208006
EST:     CCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
genomic: CCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
EST: gi|124980086|gb|EL053066.1|EL053066
EST:     ATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACG
genomic: ATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACG
EST: gi|152035094|gb|BP844446.2|BP844446
EST:     TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAG                         GAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC
genomic: TTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGgtaaagtttc ... atttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaattccttgtttttgtgatatatctctcattttgacttcatttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTCAACCTG
                                   ttttgac  putative branch site (score: 3)
                                         cttcattt  CT-rich tract
               tttttgtgatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaattcgagacatggttgtcattgatttcattgttgatgtcaaaaaaaaaaattccttgtttttgtgatatatctctcattttgacttcatttgtgcagGAAGATCTGCCCCTCGCCCTCGTCCTGCTGCTGCACGCAGCCCAGCTCCTCAACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctca