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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacgatttgtctcaattgttttttcactgatcctggtatggtgtgtatatcatctcttattccaatgtgcttctgaatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTCCTCCTAATGCGACGCTCGAGATCAATTTGGAGTTAGTTTCGTGGAAAAC

Basic information

species Arabidopsis thaliana
transcript AT3G25230.1
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|164207439|gb|ES085740.1|ES085740
EST:     AAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGACGACGGT
genomic: AAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGG-CG-CGGT
EST: gi|116475203|gb|EG517795.1|EG517795
EST:     GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
genomic: GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
EST: gi|116434999|gb|EG477591.1|EG477591
EST:     GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
genomic: GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
EST: gi|116475202|gb|EG517794.1|EG517794
EST:     GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTT
genomic: GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGG-AGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTT
EST: gi|116435001|gb|EG477593.1|EG477593
EST:     GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
genomic: GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
EST: gi|47828402|gb|CK118086.1|CK118086
EST:     GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGAGAAGG-CTAAGACAGCCTCTGCTGGTGAAGGCGCGGTT
genomic: GAAAACTATGAAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGGAGAAGGGC-AAGCCAGCCTCTGCTGGTGAAGGCGCGGTT
EST: gi|164208663|gb|ES093802.1|ES093802
EST:     AAAAAGGGTGAAAAGG-CCTTCTGACAGTTAAACCACAAT                         ATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC
genomic: AAAAAGGGTGAAAAGGTCCTTCTGACAGTTAAACCACAATgtaagacgat ... aatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctggtatggtgtgtatatcatctcttattccaatgtgcttctgaatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTCCTCCTAATGCGACGCTCGAGATCAATTTGGAGTTAGTTTCGTGGAAAAC
               tatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacgatttgtctcaattgttttttcactgatcctggtatggtgtgtatatcatctcttattccaatgtgcttctgaatgagacagATGGTTTTGGGGAGAAGGGCAAGCCAGCCTCTGCTGGTGAAGGCGCGGTTCCTCCTAATGCGACGCTCGAGATCAATTTGGAGTTAGTTTCGTGGAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG