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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatctacaacttttgtatgattatacttaagctacggatgaagagatcgttaattttgcggcaattatatatttatatttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAGAATTACATATGTCTCTCCATCAGCTGCGGAATTGCCTAGCAAAATATTG

Basic information

species Arabidopsis thaliana
transcript AT5G39930.1
intron # 8
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|116463899|gb|EG506491.1|EG506491
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463918|gb|EG506510.1|EG506510
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463874|gb|EG506466.1|EG506466
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463877|gb|EG506469.1|EG506469
EST:     AAAGTTCTTGCTATCCCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTG
EST: gi|116463913|gb|EG506505.1|EG506505
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463891|gb|EG506483.1|EG506483
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463879|gb|EG506471.1|EG506471
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463884|gb|EG506476.1|EG506476
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATGTTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
EST: gi|116463901|gb|EG506493.1|EG506493
EST:     AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAG                         CATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG
genomic: AAAGTTCTTGCTATCTCATACGCCATAAAACCTGATCAGATCATCTCAAGgtaatatcta ... ttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggatgaagagatcgttaattttgcggcaattatatatttatatttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAGAATTACATATGTCTCTCCATCAGCTGCGGAATTGCCTAGCAAAATATTG
              cgttaat  putative branch site (score: 4)
                                          tattttttt  putative PPT
                ttaattttgcggcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatctacaacttttgtatgattatacttaagctacggatgaagagatcgttaattttgcggcaattatatatttatatttttttgtagCATTGTTGCTGGATTTGTGTGTATCAAAAATGTTGATATTAGTGAAGAGAGAATTACATATGTCTCTCCATCAGCTGCGGAATTGCCTAGCAAAATATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC