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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttagactaaaactatacaaactaattttaacaggaattaatcaagtgctataacccctaacatagtaattacctaatttatagattacatgtttttccttcaaaattttttatgaaaagacaagtaaaatactaaccaactcagatttgtgtaataagattaatttgtgttgtgttcttcttgtaatgatagAAATATAGGTCACATCGGAAACATCTACTAGCGCGTGAAGCAGAAGCTGCCAGCTGGAATCTCCGGAGACATGCCACGGTGGCAGTGCCCGGAGTAGGAG

Basic information

species Arabidopsis thaliana
transcript AT5G44190.1
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|124729842|gb|EH821244.1|EH821244
EST:     TTATGAACGTTAAATCTCTCACTCGTCACAACGTTGCTAGCCATCTTCAG                         AAATATAGGTCACA
genomic: TTATGAACGTTAAATCTCTCACTCGTCACAACGTTGCTAGCCATCTTCAGgtaaatttta ... gtaatgatagAAATATAGGTCACA
EST: gi|124819436|gb|EH904302.1|EH904302
EST:     ACGTTAAATCTCTCACTCGTCACAACGTTGCTAGCCATCTTCAG                         AAATATAGGTCACATCGGAAACATCTACTAGCGCGTGAAGCAGAAGCTG
genomic: ACGTTAAATCTCTCACTCGTCACAACGTTGCTAGCCATCTTCAGgtaaatttta ... gtaatgatagAAATATAGGTCACATCGGAAACATCTACTAGCGCGTGAAGCAGAAGCTG
EST: gi|125038559|gb|EL110828.1|EL110828
EST:     TTATGAACGTTAAATCTCTCACTCGTCACAACGTTGCTAGCCATCTTCAG                         AAATATAGGTC
genomic: TTATGAACGTTAAATCTCTCACTCGTCACAACGTTGCTAGCCATCTTCAGgtaaatttta ... gtaatgatagAAATATAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcagatttgtgtaataagattaatttgtgttgtgttcttcttgtaatgatagAAATATAGGTCACATCGGAAACATCTACTAGCGCGTGAAGCAGAAGCTGCCAGCTGGAATCTCCGGAGACATGCCACGGTGGCAGTGCCCGGAGTAGGAG
                    gattaat  putative branch site (score: 3)
                                     ttcttcttgt  putative PPT
       atttgtgtaataagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattttagactaaaactatacaaactaattttaacaggaattaatcaagtgctataacccctaacatagtaattacctaatttatagattacatgtttttccttcaaaattttttatgaaaagacaagtaaaatactaaccaactcagatttgtgtaataagattaatttgtgttgtgttcttcttgtaatgatagAAATATAGGTCACATCGGAAACATCTACTAGCGCGTGAAGCAGAAGCTGCCAGCTGGAATCTCCGGAGACATGCCACGGTGGCAGTGCCCGGAGTAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA