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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaaaaacagttcatgtttctgtgcaaaatctttagctttatgtataattgacgagcccttgttgttgtttttaatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCTTTGGCAATGTTCTTAGTGCTAATTTGGGTCAAGCTCCTGCTCGTCAAGC

Basic information

species Arabidopsis thaliana
transcript AT5G48230.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 3
gtattaaaaaacagttcatgtttctgtgcaaaatctttagctttatgtataattgacgagcccttgttgttgtt--tttaatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCTTTGGCAATGTTCTTAGTGCTAATTTGGGTCAAGCTCCTGCTCGTCAAGC
       | | ||||   |  |  | |||   || | ||  | |   | |||   |        |    |  |   | |  ||||  ||||||| ||||||| ||||||||||||||||| ||||| ||||| ||  ||||||| |||||  | |||||||||||||| |||||||||||  | |||||
----gtgataccagtatcttctcatatgctgtatgtgtaattgttcttttaacccaaatataactaacatcatcagtgtggtgatc-agCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCTTTGGTAATGTGTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC
















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|116435447|gb|EG478039.1|EG478039
EST:     ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAG                         CTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
genomic: ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAGgtattaaaaa ... aatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
EST: gi|116435458|gb|EG478050.1|EG478050
EST:     ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAG                         CTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
genomic: ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAGgtattaaaaa ... aatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
EST: gi|116466365|gb|EG508957.1|EG508957
EST:     ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAG                         CTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
genomic: ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAGgtattaaaaa ... aatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
EST: gi|116435448|gb|EG478040.1|EG478040
EST:     ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAG                         CTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
genomic: ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAGgtattaaaaa ... aatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
EST: gi|164009146|gb|ES078016.1|ES078016
EST:     ATCCCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAG                         CTGCTTTGAAGAGAGCAAATGT
genomic: ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAGgtattaaaaa ... aatgatttagCTGCTTTGAAGAGAGCAAATGT
EST: gi|116435459|gb|EG478051.1|EG478051
EST:     ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAG                         CTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT
genomic: ATCTCTTTCATCTTTACCTGCCACAAAGCTTGGATCTTTAGCTATTGCAGgtattaaaaa ... aatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttagctttatgtataattgacgagcccttgttgttgtttttaatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCTTTGGCAATGTTCTTAGTGCTAATTTGGGTCAAGCTCCTGCTCGTCAAGC
                                         ttttaat  putative branch site (score: 3)
                                     ttgtttttaatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaaaaaacagttcatgtttctgtgcaaaatctttagctttatgtataattgacgagcccttgttgttgtttttaatgatttagCTGCTTTGAAGAGAGCAAATGTTGATCCAGCTCTTGTTCAAGAAGTTGTCTTTGGCAATGTTCTTAGTGCTAATTTGGGTCAAGCTCCTGCTCGTCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT