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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGGGACGACTTGTAATTTGAGTATGAATTGGCATTATTCTTACAGTACTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatgatcaattttactaattcttagttttgatcatctcaatcttgtgaatcaatggaaagacaagatttttcttgcgaatcacaaatttctgttc...

Basic information

species Arabidopsis thaliana
transcript AT1G04970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04970.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA14G05590.1 (Glycine max), 5'ss of exon 1
TTCAGGGACGACTTGTAATTTGAGTATGAATTGGCATTATTCTTACAGTACTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatgatcaattttactaattcttagttttgatcatctcaatcttgtgaatcaatggaaagacaagatt-tttcttgcgaatcacaaatttctgttc
||| |||   |||||||||||||||||||||||| |||| ||||| ||||| ||||||   ||| || | || |||||    ||||  |||   |||||||||   |   |    |||| |   | |  || |  |       ||  ||       |||| ||   |||  || |||    |    | | ||||   | | 
TTCTGGGGTTACTTGTAATTTGAGTATGAATTGGTATTACTCTTATAGTACATGGCTTGTGCCTGTTAAGATCTCTGACAGAGGTAGAGCAGAAGTTCAGgtatgaaatttttcctttattttgtttgtgtatataaagagagaagatttaattagaatgcaatttcaaagttattttacactgtcctccaattaaagat-

upper sequence: AT1G04970.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv12s0059g01680.t01 (Vitis vinifera), 5'ss of exon 1
TTCAGGGACGACTTGTAATTTGAGTATGAATTGGCATTATTCTTACAGTACTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatgatcaatttta---ctaattcttagttttgatcatctcaatcttgtgaatcaatggaaagacaagatttttcttgcgaatcacaaatttctgttc
 ||||| || |||||||||||||| |||||||||||||||||||| | ||||||| |    ||  | ||||| || |||   || |  ||    |||||||||    |||  ||||||     |     | | |||||   || ||  | ||||    |  ||  |      |  |||  ||  |  |     ||        
CTCAGGCACCACTTGTAATTTGAGCATGAATTGGCATTATTCTTATAATACTTGGTTCGTGCCCGTCGAAATTTCGGATAGTGGGACCGCCCAAGTTCAGgtataagtgagtaattttgaagttgggattgaattttgtcaatttcgttgttgttttgctttgtgatttgttgggtttgtttttgttttgggcatacgca---
















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|86050999|gb|DR346754.1|DR346754
EST:     CTTGGSTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAG                         GTTCAAGGCATGGAAATCGGGCTCTCTCT
genomic: CTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatga ... tctcggtaagGTTCAAGGCATGGAAATCGGGCTCTCTCT
EST: gi|86050998|gb|DR346753.1|DR346753
EST:     CTTGGCTTCCTCCTATTGAA-TATCTGATCAGGGTATTGCATCTGTTCAG                         GTTCAAGGCATGGAA-TCGGGCTCTCTCTAGGCTTGAAAAGTGATGA
genomic: CTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatga ... tctcggtaagGTTCAAGGCATGGAAATCGGGCTCTCTCTAGGCTTGAAAAGTGATGA
EST: gi|19876266|gb|AU237097.1|AU237097
EST:     CTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAG                         GTTCAAGGCATGGAAATCGGGCTCTCTCTAGGCTTGAAAAGTGATGAAGGA
genomic: CTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatga ... tctcggtaagGTTCAAGGCATGGAAATCGGGCTCTCTCTAGGCTTGAAAAGTGATGAAGGA
EST: gi|125295537|gb|EL309622.1|EL309622
EST:     TATTGCATCTGTTCAG                         GTTCAAGGCATGGAAATCGGGCTCTCTCTAGGCTTGAAAAGTGATGAAGGA
genomic: TATTGCATCTGTTCAGgtaattatga ... tctcggtaagGTTCAAGGCATGGAAATCGGGCTCTCTCTAGGCTTGAAAAGTGATGAAGGA
EST: gi|86050997|gb|DR346752.1|DR346752
EST:     CTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAG                         GTTCAAGGCATGGAAATCGGGCTCTCTCT
genomic: CTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatga ... tctcggtaagGTTCAAGGCATGGAAATCGGGCTCTCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGGGACGACTTGTAATTTGAGTATGAATTGGCATTATTCTTACAGTACTTGGCTTCCTCCTATTGAAATATCTGATCAGGGTATTGCATCTGTTCAGgtaattatgatcaattttactaattcttagttttgatcatctcaatcttgtgaatcaatggaaagacaagatttttcttgcgaatcacaaatttctgttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcacaaa