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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaatttgaaatctttcagggatttaagtttgattttgtgttgatcttgattctgatgtatgttgtggtttttgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGTGTTATGTGACTGTGAGAGGTGAGAAGGCAATGCAGCTTCTTGAGAGTGG

Basic information

species Arabidopsis thaliana
transcript AT5G45775.1
intron # 2
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|164029018|gb|ES146696.1|ES146696
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTA
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTA
EST: gi|86063997|gb|DR359754.1|DR359754
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|86077797|gb|DR373554.1|DR373554
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|124864628|gb|EH949065.1|EH949065
EST:     GTGTTGGAGCAGCTCAGTGGAACAAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTG
genomic: GTGTTGGAGCAGCTCAGTGGA-CAAA-CCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTG
EST: gi|124885528|gb|EH964430.1|EH964430
EST:     TGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: TGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|47828470|gb|CK118154.1|CK118154
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|47828450|gb|CK118134.1|CK118134
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|86063987|gb|DR359744.1|DR359744
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|125298726|gb|EL312811.1|EL312811
EST:     TTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: TTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|164111227|gb|ES195380.1|ES195380
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATG
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATG
EST: gi|86084150|gb|DR379909.1|DR379909
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTTTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|86063981|gb|DR359738.1|DR359738
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|116451722|gb|EG494314.1|EG494314
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
EST: gi|86064031|gb|DR359788.1|DR359788
EST:     GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG                         CGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT
genomic: GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGGgtatgtgaat ... tgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgattttgtgttgatcttgattctgatgtatgttgtggtttttgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGTGTTATGTGACTGTGAGAGGTGAGAAGGCAATGCAGCTTCTTGAGAGTGG
                       ttctgat  putative branch site (score: 3)
                                         tttttgtt  putative PPT
                                         tttttgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaatttgaaatctttcagggatttaagtttgattttgtgttgatcttgattctgatgtatgttgtggtttttgttatacagCGAGGTACACTGTGAGGTCTTTTGGTATCAGGCGTAATGAGAAGATTGCGTGTTATGTGACTGTGAGAGGTGAGAAGGCAATGCAGCTTCTTGAGAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT