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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatcaaacttcaaaagtttaccataaaaaaaacactctttttgtccgctgaatcctccattcttgcttctgcataaaattttatcagGAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGCGCAACGTTGATAGAAACATTCATGGAAAAACTAGGCTGATCCGTAAACT

Basic information

species Arabidopsis thaliana
transcript AT3G54860.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54860.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA10G35210.1 (Glycine max), 3'ss of exon 22
-----gtatatatcaaacttcaaaagtttaccataaaaaaaacactctttttgtccgctgaatcctccattcttgcttctgcataaaatt---ttatcagGAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGCGCAACGTTGATAGAAACATTCATGGAAAAACTAGGCTGATCCGTAAACT
        ||||||   ||| |     ||  |     |  |  | |   | |    | |   | ||    || |  ||||  ||    ||   ||  ||||| |||||||| |||||||||||| |||| ||||||||||| ||||| |||  ||| ||| | ||||| || |||||||| ||||| ||||   | |   
ttcttccttatatcctgctttatccaattgactgggcattaggaataaatcttcttgtttggttcttatctcctaattcttgatgtggtttactttgcagGAGGGAATGGCATATGATTTGATTATTGCAACAACAAAAATAGTCAATGGCCAAACCTTGGTTGAAACGTTTATGGAAAAGCTAGGTTGATTAATGAGTG

upper sequence: AT3G54860.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv13s0019g04720.t01 (Vitis vinifera), 3'ss of exon 21
--------gtatatatcaaacttcaaaagtttaccataaaaaaa-acactctttttgtccg--ctgaatcctccattcttgcttctgcataaaattttatcagGAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGCGCAACGTTGATAGAAACATTCATGGAAAAACTAGGCTGATCCGTAAACT
             | |||||    ||||  |||| ||||      |   |||  |||| |   || |   | ||| | |    ||||    | || ||  ||||||||||||||||| || ||||||||||  ||||||||||| ||    ||     | |||| |||||||||||| || |   | || |||   | | || 
gcactgttaatcttgtcaaaa--aaaaaagttacaataaggttgcattttctccttgttcatactcaccaccccaatttcttatctgatctacatcttg-cagGAAGGAATGGCTTACGACTTGATTGTTGGGACAACAAAAATTGTGGGTGGTCATTCATTGACAGAAACATTCATCGAGAGCTTGGGTTGACTTGCATACA
















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|125214782|gb|EL229088.1|EL229088
EST:     CGGTATCTCGCCTCTAAG                         GAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGC
genomic: CGGTATCTCGCCTCTAAGgtatatatca ... attttatcagGAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGC
EST: gi|125107474|gb|EL160767.1|EL160767
EST:     GAGGTGTAACATTTGCTGAAATCTCTGCTTTACGGTATCTCGCCTCTAAG                         GAAGGAATGGCTTATGATTTGA
genomic: GAGGTGTAACATTTGCTGAAATCTCTGCTTTACGGTATCTCGCCTCTAAGgtatatatca ... attttatcagGAAGGAATGGCTTATGATTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactctttttgtccgctgaatcctccattcttgcttctgcataaaattttatcagGAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGCGCAACGTTGATAGAAACATTCATGGAAAAACTAGGCTGATCCGTAAACT
                                              ttttatc  CT-rich tract
                                        ataaaattttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatcaaacttcaaaagtttaccataaaaaaaacactctttttgtccgctgaatcctccattcttgcttctgcataaaattttatcagGAAGGAATGGCTTATGATTTGATTGTTGCCACAACAAAAATCGTCAACGGCGCAACGTTGATAGAAACATTCATGGAAAAACTAGGCTGATCCGTAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT