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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggatgaatgaacagaaaatcttggttttgtcactcatagattctgttttgtttccacattgatggttgaatctttctcgtttcatcttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAGAGCCATAAGTTTTGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATG

Basic information

species Arabidopsis thaliana
transcript AT4G05450.1
intron # 3
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|116443730|gb|EG486322.1|EG486322
EST:     ACGGGACAAAGAATCTACACCGGTCTTATGGCCACTACTTGCAGTCTTTG                         CCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
genomic: ACGGGACAAAGAATCTACACCGGTCTTATGGCCACTACTTGCAGTCTTTGgttagtctga ... ttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
EST: gi|164197334|gb|ES002066.1|ES002066
EST:     GAATCTACACCGGTCTTATGGCCACTACTTGCCGTCTTTG                         CCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
genomic: GAATCTACACCGGTCTTATGGCCACTACTTGCAGTCTTTGgttagtctga ... ttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
EST: gi|116443734|gb|EG486326.1|EG486326
EST:     ACGGGACAAAGAATCTACGCCGGTCTTATGGCCACTACTTGCAGTCTTTG                         CCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
genomic: ACGGGACAAAGAATCTACACCGGTCTTATGGCCACTACTTGCAGTCTTTGgttagtctga ... ttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
EST: gi|116443712|gb|EG486304.1|EG486304
EST:     ACGGGACAAAGAATCTACACCGGTCTTATGGCCACTACTTGCAGTCTTTG                         CCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG
genomic: ACGGGACAAAGAATCTACACCGGTCTTATGGCCACTACTTGCAGTCTTTGgttagtctga ... ttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttgtttccacattgatggttgaatctttctcgtttcatcttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAGAGCCATAAGTTTTGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATG
               cattgat  putative branch site (score: 4)
                             tctttctcgtttcatc  putative PPT
     tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggatgaatgaacagaaaatcttggttttgtcactcatagattctgttttgtttccacattgatggttgaatctttctcgtttcatcttttcgatagCCAGTGGTACCAAGGCAAGCTAGGACTTCTCAGGAAGCCTGGTTTTTGAAGAGCCATAAGTTTTGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATG

- - - - - - - acagaaa
- - - - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - -actcata
- - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacatt