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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttattatatatctccttcaaattctgctcctttgaggatgtttctttgcttggagttataatttgataaacccgaaaatgcagATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGCAGAGCAGGACCAGGGAGCTCGAGATGGTCAATGTACAGCATCCCGGCAA

Basic information

species Arabidopsis thaliana
transcript AT1G54130.1
intron # 5
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|125183671|gb|EL198625.1|EL198625
EST:     GTGGTAACCAAGAAGGACCAGTCTATGTGATTGTAATCGAAAATGAGAAG                         ATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACG
genomic: GTGGTAACCAAGAAGGACCAGTCTATGTGATTGTAATCGAAAATGAGAAGgttagttatt ... gaaaatgcagATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACG
EST: gi|47828974|gb|CK118658.1|CK118658
EST:     GTGGTAACCAAGAAGGACCAGTCTATGTGATTGTAATCGAAAATGAGAAG                         ATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGC
genomic: GTGGTAACCAAGAAGGACCAGTCTATGTGATTGTAATCGAAAATGAGAAGgttagttatt ... gaaaatgcagATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGC
EST: gi|124960271|gb|EL034951.1|EL034951
EST:     ATGTGATTGTAATCGAAAATGAGAAG                         ATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGC
genomic: ATGTGATTGTAATCGAAAATGAGAAGgttagttatt ... gaaaatgcagATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgaggatgtttctttgcttggagttataatttgataaacccgaaaatgcagATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGCAGAGCAGGACCAGGGAGCTCGAGATGGTCAATGTACAGCATCCCGGCAA
                                atttgat  putative branch site (score: 5)
                         agttataatttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttattatatatctccttcaaattctgctcctttgaggatgtttctttgcttggagttataatttgataaacccgaaaatgcagATGACTGTGCAAGAGTTTCCCGAGAATTCTACCGTGTCGGACCTGTTACGCAGAGCAGGACCAGGGAGCTCGAGATGGTCAATGTACAGCATCCCGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG