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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGCGATGGCCGTATTACTGGTAACGATGCGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattttgtgttgaaatttattacgttgcttacttgtggaacctttattaatggccattataatgattgaccaagttcatttggggatggagttgt...

Basic information

species Arabidopsis thaliana
transcript AT3G20290.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20290.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 5'ss of exon 2
ACGGCGATGGCCGTATTACTGGTAACGATGCGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattttgtgttgaaatttattacgttgcttacttgtggaacct-ttattaatggccattataatgattgaccaa-gttcatttggggatggagttgt
|   ||||||||| |||||||| || || || || ||||||||| ||||||| ||||||||||| |||||  | || |||||      ||| || ||   ||| |||  |||     | || ||| || |  |||| |    |||||    |  |  || | | ||   ||  ||| || | 
ATTCCGATGGCCGCATTACTGGAAATGACGCCATAAAGTTCTTCGCTATGTCCAATTTGCCTCGCCCGGATCTCAAACAGgttctctctttttgctgtgtttttttagtttg--ggttggtagaatctgtctttaaagagagttataggcttatatgaatgctaatgccggagtggtgtggg
















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|116430168|gb|EG472760.1|EG472760
EST:     CGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGTAG                         ATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTATCTTGGTTTCAAAGAG
genomic: CGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattt ... ttgttgatagATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTATCTTGGTTTCAAAGAG
EST: gi|124962813|gb|EL037192.1|EL037192
EST:     CGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAG                         ATCTGGGCTNTTGCAGATTCAAAGAGACAAGGGTAT
genomic: CGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattt ... ttgttgatagATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTAT
EST: gi|163974596|gb|EL989899.1|EL989899
EST:     GAATTTGCCTCGTCCGGAATTGAAGCAG                         ATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTATCTTGGTTTCAAAGAG
genomic: GAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattt ... ttgttgatagATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTATCTTGGTTTCAAAGAG
EST: gi|124706297|gb|EH797699.1|EH797699
EST:     ATGTCGAATTTGCCTCGTCCGGAATTGAAGCAG                         ATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTATCTTGGTTTCAAAGAG
genomic: ATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattt ... ttgttgatagATCTGGGCTATTGCAGATTCAAAGAGACAAGGGTATCTTGGTTTCAAAGAG
EST: gi|125304529|gb|EL318614.1|EL318614
EST:     CGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAG                         ATCTGGGCTATTGCAGATTCAAAGAG
genomic: CGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattt ... ttgttgatagATCTGGGCTATTGCAGATTCAAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGCGATGGCCGTATTACTGGTAACGATGCGATCAAGTTCTTCACTATGTCGAATTTGCCTCGTCCGGAATTGAAGCAGgtaaggattttgtgttgaaatttattacgttgcttacttgtggaacctttattaatggccattataatgattgaccaagttcatttggggatggagttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC