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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaaggtaatcattataaacaattggtctatggttcagttgtttaatgaattgttggatttggtactgatttcgtacttgttctgttttcgtttgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGAGACTACTTGCCTATTGTACGTGAGAAGCCTACCATGGAACTCGTCAAGC

Basic information

species Arabidopsis thaliana
transcript AT3G49010.4
intron # 4
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|86018575|gb|DR314321.1|DR314321
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAG                         GTCAAGGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTT
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGgtcaaggtaa ... tgtgtgttagG-C-----TGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTT
EST: gi|86074609|gb|DR370366.1|DR370366
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt
EST: gi|86076156|gb|DR371913.1|DR371913
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt
EST: gi|47829477|gb|CK119161.1|CK119161
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt
EST: gi|86085358|gb|DR381117.1|DR381117
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt
EST: gi|47831958|gb|CK121642.1|CK121642
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt
EST: gi|86074296|gb|DR370053.1|DR370053
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt
EST: gi|86018573|gb|DR314319.1|DR314319
EST:     TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAG                         GTCAAGGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACC-AAGTT
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGgtcaaggtaa ... tgtgtgttagG-C-----TGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTT
EST: gi|116471273|gb|EG513865.1|EG513865
EST:     TGAAAACCTACAAGACCGAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                    
genomic: TGAAAACCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTG-CC-C---G-CAAGgtcaaggtaa ... tgtgt


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgttggatttggtactgatttcgtacttgttctgttttcgtttgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGAGACTACTTGCCTATTGTACGTGAGAAGCCTACCATGGAACTCGTCAAGC
               tactgat  putative branch site (score: 2)
                                ttctgttttcgttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaggtaatcattataaacaattggtctatggttcagttgtttaatgaattgttggatttggtactgatttcgtacttgttctgttttcgtttgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGAGACTACTTGCCTATTGTACGTGAGAAGCCTACCATGGAACTCGTCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA