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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtctttcataccagtttttttttttttatctgtctattatgatgttatgtttctagagttttaactgtggttctccatacctgcagCTTCCAAAATCCAATAGAAAACGGACAGCATATGAATTCAACTGCGGAGGATGTAAAAATTATGAACCAGAGGTCACACATTCTGTATGAGCAATTGAAA

Basic information

species Arabidopsis thaliana
transcript AT1G08600.4
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08600.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA20G37100.1 (Glycine max), 3'ss of exon 22
gcaagtctttcataccagtttttttttttttatctgtctattatgatgttatgtttctagagttttaactgtggttctccatacctgcagCTTCCAAAATCCAATAGAAAACGGACAGCATATGAATTCAACTGCGGAGGATGTAAAAATTATGAACCAGAGGTCACACATTCTGTATGAGCAATTGAAA
                 ||  |  |||||       | |||||  |||| | || ||||  |    || | |  || |  ||   ||||||||||||||||||||||| || |||||||| |  |||||||||  |   |||                                                
-----------------gtactgatttttactgtaatttatta-aatgtaa-gTCTCTAACG----AAATATTTTTATTTATG--TGCAGCTTCCAAAATCCAATAGAGAATGGACAGCACACCAATTCAACTCTGATCGAT------------------------------------------------

upper sequence: AT1G08600.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv14s0036g01460.t01 (Vitis vinifera), 3'ss of exon 17
gcaagtctttcataccagtttttttttttttatctgtctattatgatgttatgtttctagagttttaactgtggttctccatacctgcagCTTCCAAAATCCAATAGAAAACGGACAGCATATGAATTCAACTGCGGAGGATGTAAAAATTATGAACCAGAGGTCACACATTCTGTATGAGCAATTGAAA
| ||| |||    |    | || || |  ||| |||| |    |  | ||   || |  |  | || |   || ||  |  | | ||||||||||||||||| ||||| || ||||| |||||||| || ||  | || ||||||||||| ||||| |||||||| || || || ||||| ||| | |||
gtaagacttcttcaatgctattattctaatta-ctgtattcccttttctttacttccatgtctcttgatcatgctttcctttccatgcagCTTCCAAAATCCTATAGAGAATGGACAACATATGAACTCCACATCAGATGATGTAAAAATAATGAATCAGAGGTCTCATATCCTCTATGAACAACTAAAA
















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|125187681|gb|EL202635.1|EL202635
EST:     GATTTTGTGAGAGAAGGATTCTTGGGAAGTAGCCCTGAGTTTAGAAACCG                         CTTCCAAAATCCAATAGAAAACGGACAGCATATGAATTCAACTGCGGAGGA
genomic: GATTTTGTGAGAGAAGGATTCTTGGGAAGTAGCCCTGAGTTTAGAAACCGgcaagtcttt ... atacctgcagCTTCCAAAATCCAATAGAAAACGGACAGCATATGAATTCAACTGCGGAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctattatgatgttatgtttctagagttttaactgtggttctccatacctgcagCTTCCAAAATCCAATAGAAAACGGACAGCATATGAATTCAACTGCGGAGGATGTAAAAATTATGAACCAGAGGTCACACATTCTGTATGAGCAATTGAAA
                           ttttaac  putative branch site (score: 2)
                                       ttctccat  putative PPT
             ttatgttt  TA-rich tract