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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacgatgctgtcctcgatggactcttacagttgttgcaaattacctagtgtcttgtgtacttattgctataacattgttataaatttatcctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGGATCTGGGCAAAGCGTCAAAACCATACTTACCGCCCCAATCGTCCCCTAT

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 13
ttacgatgctgtcctcgatggactcttacagttgttgcaaattacctagtgtcttgtgta-cttattgctataacattgttataaatttatcctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGGATCTGGGCAAAGCGTCAAAACCATACTTACCGCCCCAATCGTCCCCTAT
                                                || | | |   | |    |||| |   | | || | | |||   ||  | ||||| || ||  |||| |||||    || || ||  |    ||  |||| ||| | ||||| ||||||||||||||||||||||| || |   | ||  |  
------------------------------------------------gtctgtagcccaacgctctgctgtccgaattttttgactttgagct--tttagGAGGAAGTTTCCAAGGAGTTCAACGTTCCCGTAAATTGCCAAAGGTTTTGGCTATGGGCTAAGCGTCAAAACCATACTTACCGTCCGAGCAGACCATTGA

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 13
ttacgatgctgtcctcgatggactcttacagttgttgcaaattacctagtgtcttgtgta-cttattgctataacattgttataaatttatcctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGGATCTGGGCAAAGCGTCAAAACCATACTTACCGCCCCAATCGTCCCCTAT
                                                || | | |   | |    |||| |   |   || | | |||   ||  | ||||| || ||  |||| |||||    || || ||  |    ||  |||| ||| | ||||| ||||||||||||||||||||||| || |   | ||  |  
------------------------------------------------gtctgtagcccaacgctctgctgtccgaagtttttgactttgcgct--tttagGAGGAAGTTTCCAAGGAGTTCAACGTTCCCGTAAATTGCCAAAGGTTTTGGCTATGGGCTAAGCGTCAAAACCATACTTACCGTCCGAGCAGACCATTGA
















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|125261735|gb|EL275820.1|EL275820
EST:     GAGTTTTCGTAATCCAGAAACAGACCCCCTTTCAACAATTTAAG                         GAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGG
genomic: GAGTTTTCG-AATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgctt ... cctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGG
EST: gi|124919850|gb|EH993588.1|EH993588
EST:     AAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAG                         GAAGAGGTAGCCAAAGAGTTTGGTGTCCC
genomic: AAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgctt ... cctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagtgtcttgtgtacttattgctataacattgttataaatttatcctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGGATCTGGGCAAAGCGTCAAAACCATACTTACCGCCCCAATCGTCCCCTAT
                      ctataac  putative branch site (score: 3)
                                        tttatcctc  putative PPT
                ttattgctataacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacgatgctgtcctcgatggactcttacagttgttgcaaattacctagtgtcttgtgtacttattgctataacattgttataaatttatcctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGGATCTGGGCAAAGCGTCAAAACCATACTTACCGCCCCAATCGTCCCCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tataaca