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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtgtacaactctgtggaatattgtgttttttcttaccctgactcttaataataatggtctgctgcttacggtcatcaacagAGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G06580.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 9
---------gtaaagtgtacaactctgtggaatattgtgttttttcttaccctgactcttaataataatg--gtctgctgcttacgg---tcatcaacagAGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG
            |||  ||    |  ||  ||  |  |      |  | |  |  | |||    ||  ||   | |  |  | ||     |  |   ||||||||||| || || ||||| ||||||  ||||||||||| |||||||||    ||   ||| ||  ||||
accattgccaataagcatatccattggtaaaaagtattaacaggtaatgcattatcccttttatatgctgttatttaattttgacacattttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGATGTCGTATCTTCGAATCTAAG
















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|116456853|gb|EG499445.1|EG499445
EST:     GCCACGCATTTCAAATTGCATCAG                         AGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGAC
genomic: GCCACGCATTTCAAATTGCATCAGgtaaagtgta ... tcatcaacagAGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGAC
EST: gi|116456852|gb|EG499444.1|EG499444
EST:     GCCACGCATTTCAAATTGCATCAG                         AGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGAC
genomic: GCCACGCATTTCAAATTGCATCAGgtaaagtgta ... tcatcaacagAGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGAC
EST: gi|125123097|gb|EL169546.1|EL169546
EST:     CATTTCAAATTGCATCAG                         AGAGCTGCACACGTTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGA
genomic: CATTTCAAATTGCATCAGgtaaagtgta ... tcatcaacagAGAGCTGCACACG-TTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttaccctgactcttaataataatggtctgctgcttacggtcatcaacagAGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG
                                    tgcttac  putative branch site (score: 2)
              actcttaataataat  TA-rich tract