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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctcttttatttttgtaaatcactttttcttctgtttttgttgttgttgttgttgttgttattgaagttgttgtgtttgattggttgctttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G57040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G57040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G31320.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------gtttgctcttttatttttgtaaatcactttttcttctgtttttgttgttgttgttgttgttgttattgaagttgttgtgtttgattggttgc-tttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTCAAG
                                                               ||| | | || | |||||        |||  || ||           |||  | ||  ||  |||       |||| ||||  |  |||  | |  | |||  || || ||||||||| | || |||||||| ||||||||||||||||| || ||||| ||||| |||||| |||||
gtatggtgtgtttttttttgttagatgcataaaggtgtttttagttttaaaattttaaccaacttgttgtgttgtgtttgtgttcagtgtttatttttggccacagatcagtttctttttctgggattctgag-attgtttttggatttttgtgtctttatagGAGGTGGAGGTGAATCTTGTTATAACAGATTACTGTATGCCTGGCATGACAGGCTATGACTTGCTTAAGAAAATCAAG

upper sequence: AT3G57040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G28570.1 (Glycine max), 3'ss of exon 2
----------------------------------------------gtttgctcttttatttttgtaaatcactttttcttctgtttttgttgttgttgtt-------------gttgttgttattgaagtt-----gttgtgtttgattggttgc-tttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTCAAG
                                               ||||   ||| |   || |||   |||| || |  ||| ||   ||||  | ||             |||  | ||  ||   ||      |||| ||||  |  |||  | |  | |||  || || ||||||||| | || |||||||| ||||||||||||||||| || ||||| ||||| |||||| |||||
gtatagtgtgtttttttggttagaatgcataaaaggtgttttttttttttgtaatttaaaaattttaaccaacttgttgtgttgtgttcagtgtttatttttggccacagatcagtttctttttctgggattctgagattgtttttggctttttgtgtctttatagGAGGTGGAGGTGAATCTTGTTATAACAGATTACTGTATGCCTGGCATGACAGGCTATGACTTGCTTAAGAAAATCAAG

upper sequence: AT3G57040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g05390.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------gtttgctcttttatttttgtaaatcactttttcttctgtttttgttgttgttgttgttgttgttattgaagttgttgtgtttgattggttgctttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTCAAG
                                                  || ||     ||||   || ||      || || | | ||| || || || || ||   |   ||   |    | | ||   || ||   |||  ||||| ||| || ||||||||||||||||| || || ||||||||||| ||||| || |||||||| ||||| ||| |||||
gtatgattcttcttcttttttccattgtcaagggtcaggaatctcaaatctttcttgaggatttccttacattttccctttttttttatttttttttattattctttccgagttttctgaatcttttttcactttgtgaattt--acagGAAGTGGAGGTGAATCTTATAATTACTGACTACTGTATGCCTGGAATGACAGGCTATGATTTACTCAAAAAAATCAAG

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|124720223|gb|EH811625.1|EH811625
EST:     TAACGACCCAAATGCGTTTTCTAAGGCTCCTGTTAATCACCAG                         GTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACT
genomic: TAACGACCCAAATGCGTTTTCTAAGGCTCCTGTTAATCACCAGgtttgctctt ... ctttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttgttgttgttgttattgaagttgttgtgtttgattggttgctttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTCAAG
                                gtttgat  putative branch site (score: 5)
                                          ttgctttc  putative PPT
             ttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctcttttatttttgtaaatcactttttcttctgtttttgttgttgttgttgttgttgttattgaagttgttgtgtttgattggttgctttcaacagGTAGTTGAAGTGAATCTTATAATTACAGATTATTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTCAAG

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