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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatctggaacttaatatgtcgtgtttcagtatatgtccatcatgctattatgttttttaacatgttatatattattgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAATCCAACTGCTTATTTCTACTTTGATCCCTACTCTCGCCCTTCAGAAAAGA

Basic information

species Arabidopsis thaliana
transcript AT5G10540.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 9
gtaaaatctggaacttaatatgtcgtgtttcagtatatgtccatcatgctattatgttttttaacatgttatatattattgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAATCCAACTGCTTATTTCTACTTTGATCCCTACTCTCGCCCTTCAGAAAAGA
|||||  || ||      | |||   | ||   |   |||       ||   |||  |      | |   | | | |||||   |  |||||||||| |  ||||||||||||| |||||| || ||||||||||| | ||||| ||| ||||| || |||||||| ||   ||| ||| | ||||| |
gtaaa--ctagattcccttctgttcagatttgattcttgtagggggagcatctattataaacttcctaacaca-agtattgttattcagGTCTGGAATAATGATGTTAGGTTCTTCTGTGTTAAGGATTCTTCTGGTAGTCCAATTGCGTATTTTTATTTTGATCCTTATAGTCGTCCTGCTGAAAAAA

upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 9
gtaaaatctggaacttaatatgtcgtgtttcagtatatgtccatcatgctattatgttttttaacatgttatatattattgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAATCCAACTGCTTATTTCTACTTTGATCCCTACTCTCGCCCTTCAGAAAAGA
|||||  || ||      | |||   | |||  |   |||       ||   ||| ||      | |   | | | ||||    |  |||||||||| |  ||||| ||||||| |||||| || ||||||||||| | ||||| ||| ||||| || |||||||| ||   ||| ||| | ||||| |
gtaaa--ctagatacccttctgttaagattcgattcttgtatgaggagcatctattttaaacttcctaacaca-agtattcttattcagGTCTGGAATAATGATGTCAGGTTCTTCTGTGTTAAGGATTCTTCTGGTAGTCCAATTGCGTATTTTTATTTTGATCCTTATAGTCGTCCTGCTGAAAAAA
















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|86060879|gb|DR356636.1|DR356636
EST:     TGTGCCAGCAGACGGTGTAGCGCCG                         GTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGGAAT
genomic: TGTGCCAGCAGACGGTGTAGCGCCGgtaaaatctg ... tgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAAT
EST: gi|116452131|gb|EG494723.1|EG494723
EST:     CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCG                         GTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTG
genomic: CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCGgtaaaatctg ... tgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTG
EST: gi|116476839|gb|EG519431.1|EG519431
EST:     CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCG                         GTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAAT
genomic: CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCGgtaaaatctg ... tgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAAT
EST: gi|86060877|gb|DR356634.1|DR356634
EST:     CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCG                         GTCTGGAACAG-GATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGGAAT
genomic: CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCGgtaaaatctg ... tgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAAT
EST: gi|116452116|gb|EG494708.1|EG494708
EST:     CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCG                         GTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTG
genomic: CTAAGACACTATTTGGAATTGATGTTGTGCCAGCAGACGGTGTAGCGCCGgtaaaatctg ... tgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtccatcatgctattatgttttttaacatgttatatattattgccgtgaagGTCTGGAACAGCGATGTTAGGTTCTACTGTGTCAAAGATTCTTCTGGAAATCCAACTGCTTATTTCTACTTTGATCCCTACTCTCGCCCTTCAGAAAAGA
                        ttttaac  putative branch site (score: 2)
           atgctattatgttttt  TA-rich tract