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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgattttgtttgtaaaaatctgacctttacgattatccatcattgatttagtgatttagatttgaattattgtttttggttatttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG

Basic information

species Arabidopsis thaliana
transcript AT5G45775.1
intron # 1
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:     TCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|164096843|gb|ES054880.1|ES054880
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAA
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAA
EST: gi|86063997|gb|DR359754.1|DR359754
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|86077797|gb|DR373554.1|DR373554
EST:     GTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: GTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|124864628|gb|EH949065.1|EH949065
EST:     TTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGAACAAAACCCCTGTCTTCTCTAAGG
genomic: TTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGA-CAAA-CCCCTGTCTTCTCTAAGG
EST: gi|47828470|gb|CK118154.1|CK118154
EST:     CCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: CCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|47828450|gb|CK118134.1|CK118134
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|86063987|gb|DR359744.1|DR359744
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|164111227|gb|ES195380.1|ES195380
EST:     TCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|86084150|gb|DR379909.1|DR379909
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCNTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTTTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|164022554|gb|ES125965.1|ES125965
EST:     TCAACA-TTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAA
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAA
EST: gi|86063981|gb|DR359738.1|DR359738
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|116451722|gb|EG494314.1|EG494314
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
EST: gi|86064031|gb|DR359788.1|DR359788
EST:     TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAG                         GTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
genomic: TCAACATTTCCGTTGGTGAGAGTGGTGATCGTCTCACTCGTGCCTCCAAGgttcgatttt ... tttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcattgatttagtgatttagatttgaattattgtttttggttatttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG
   cattgat  putative branch site (score: 4)
                                          ttatttc  putative PPT
                atttagatttgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgattttgtttgtaaaaatctgacctttacgattatccatcattgatttagtgatttagatttgaattattgtttttggttatttcgtatagGTGTTGGAGCAGCTCAGTGGACAAACCCCTGTCTTCTCTAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA