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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcccttttcactttcttacctcttttagcaaaatatcactcaatgtcgttcctatgatttgtactgatgtgtttatgatcccgtttggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAATTACTCCTCTGTATATACCTCGAGAGTTCTTATG

Basic information

species Arabidopsis thaliana
transcript AT1G18470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G18470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 2
gtatgtcccttttcactttcttacctcttttagcaaa-atatcactcaatgtcgttcctatgatttgtactgatgtgtttatgatcccgtttggt-ttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAATTACTCCTCTGTATATACCTCGAGAGTTCTTATG
 | | | |  ||||   |       ||| || | ||   | |    |  ||    |  | |||   |||   ||    |  |||     ||   | | |||||||||||| |||||||| ||||| || ||||| || ||| | ||||||||||| ||||| |||||||| || ||||| |  ||||
ttgttttctctttcttgtctaagtttctattggaaagtgttttttcccctgaaaatgttttgacaagta--aatacaatactgaattgcttcattgtgacagTGGGCTCCATGCCATGCCGTTGTTGCAACACCATTGCTTATTGCATTTGAATTGCTCCTTTGTATATATCTTGAGAGCTTATATG

upper sequence: AT1G18470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G13040.1 (Glycine max), 3'ss of exon 2
--gtatgtcccttttcactttcttacctcttttagcaaaatatcactcaatgtcgttcctatgatttgtactgatgtgtttatgatcccgtttggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAATTACTCCTCTGTATATACCTCGAGAGTTCTTATG
   | | | |  ||  |     |    |  | ||||    | || |   |||  |||   |||| |     |    |  | |    | |  |||  | ||||||||| || |||||||| ||  | || ||||| || ||| | ||||||||||| ||||| ||||||||||| ||||| |  ||||
ccttgttttctcttgtataaattactattatatagcgttttttcccctgatgatgttatgatgaataaatttaccatactgaattgctctattg--tgacagTGGGCACCATGCCATGCCGTCATTGCAACACCATTGCTTATTGCATTTGAATTGCTCCTTTGTATATACCTTGAGAGCTTATATG

upper sequence: AT1G18470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------gtatgtcccttttcactttcttacctcttttagcaaaatatcactcaatgtcgttccta-tgatttgtactgatgtgtttatgatcccgtttggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAATTACTCCTCTGTATATACCTCGAGAGTTCTTATG
                            | |||   |||     ||  |||  |       |||| | | |  ||   ||   | || ||| ||    | ||      ||  |    |||  || ||||||||| || || ||||||||||| || |||||| | ||| | ||||||||| | ||||| |||||||| ||||| ||   |||||
gtatggcatttgcctttcactgtttttggaatgcatcttagtgattctttaggttgacatacaaattttaatccatgatcaaccatagtgacttcgcattattaaaacatctttttttttttttgacagTGGGCACCATGTCATGCTGTTGTTGCAACACCGCTGCTTATTGCATTTGAACTTCTCCTTTGTATATATCTCGAAAGCATTTATG

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|86039339|gb|DR335094.1|DR335094
EST:     CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCAT                         TGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
genomic: CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCATgtatgtccct ... tggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
EST: gi|86039336|gb|DR335091.1|DR335091
EST:     CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCAT                         TGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
genomic: CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCATgtatgtccct ... tggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
EST: gi|116478068|gb|EG520660.1|EG520660
EST:     CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCAT                         TGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
genomic: CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCATgtatgtccct ... tggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
EST: gi|86039335|gb|DR335090.1|DR335090
EST:     CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCAT                         TGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAG
genomic: CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCATgtatgtccct ... tggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAG
EST: gi|86039337|gb|DR335092.1|DR335092
EST:     CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCAT                         TGGGCTCCTTGSSATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
genomic: CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCATgtatgtccct ... tggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
EST: gi|152035998|gb|AU237167.2|AU237167
EST:     CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCAT                         TGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA
genomic: CAAGGGGCAGATTCTCTCTTCCTGCTCCTGTTGCTCCACGTAACCGTCATgtatgtccct ... tggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgtcgttcctatgatttgtactgatgtgtttatgatcccgtttggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAATTACTCCTCTGTATATACCTCGAGAGTTCTTATG
                     tactgat  putative branch site (score: 2)
                                      tcccgttt  putative PPT
            tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcccttttcactttcttacctcttttagcaaaatatcactcaatgtcgttcctatgatttgtactgatgtgtttatgatcccgtttggtttacagTGGGCTCCTTGCCATGCTGTTGTCGCGACACCGTTACTTGTAGCATTTGAATTACTCCTCTGTATATACCTCGAGAGTTCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC