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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacaagtcatcatttgactttctttcaggtgaaagaagcctcttgcatattgttcttccagctaatctatctttgttattatgaaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTACAACAAATATCATCCTTACACCTCTTGGATTCCAATAAC

Basic information

species Arabidopsis thaliana
transcript AT3G06550.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06550.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 10
gtattacaagtcatcatttgactttctttcaggtgaaagaagcctcttgcatattgttcttccagctaatctatctttgttattatgaaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTACAACAAATATCATCCTTACACCTCTTGGATTCCAATAAC
|||||| |  |  | || | |       |||  | |    | | |  |   | || || |   | |      || |  ||||       | || |||||||| ||||| ||||  ||| ||||||||||| |||||||| | || ||||| ||||| |||||||| ||||| |||||||| |||||
gtattatactttttaatgtca-------tcatattagtataccttgctttgttttattttatgaccctgatcatttgagtta-------atttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGGTCACATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC

upper sequence: AT3G06550.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 10
gtattacaagtcatcatttgactttctttcaggtgaaagaagcctcttgcatattgttcttccagctaatctatctttgttattatgaaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTACAACAAATATCATCCTTACACCTCTTGGATTCCAATAAC
|||||| |     |  |||||  |  ||     | | |  ||  |   |    ||||| |  |   | | |  | ||  || | |   || || |||||||| ||||| ||||  ||| ||||||||||| |||||||| |  | ||||| ||||| |||||||| ||||| |||||||| |||||
gtattata-----ttttttgatgtcatt----atcatattagtataccgtgctttgttttatcttatgaccc-tgttcatt-tgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC

upper sequence: AT3G06550.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 10
gtattacaagtcatcatttgactttctttcaggtgaaagaagcctcttgcatattgttcttccagctaatctatctttgttattatgaaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTACAACAAATATCATCCTTACACCTCTTGGATTCCAATAAC
               |||  |  ||| ||  |  |    |    |||   |     |||      || ||  |       | |||||||| |   ||||||||||| | |||| |||| ||||||||||| |||||||| | || ||||| || || ||||| || ||||| ||||||||||||| 
-------------gtattataaattccttaggacgttcaacttttctcaaa----attcccatgtctgatgcaaacagccttttatgaaattcacagGTGGGATATCTGTGGTTCGAGCATATATACAAGCTGGACAAGCTTACATACAATAAGTACCATCCATATACCTCATGGATTCCAATAAG

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|125314532|gb|EL328617.1|EL328617
EST:     TGAAATTCAGGGTGGCTATCAAAACATCTGTGGCACTGATAGCACTAACG                         GTGGGATTATTTTTGGTACGAGTATATATACAAGATGGACAAG
genomic: TGAAATTCAGGGTGGCTATCAAAACATCTGTGGCACTGATAGCACTAACGgtattacaag ... aaacttttagGTGGGAT-ATTTTTGGTACGAGTATATATACAAGATGGACAAG
EST: gi|124720155|gb|EH811557.1|EH811557
EST:     TGAAATTCAGGGTGGCTATCAAAACATCTGTGGCACTGATAGCACTAACG                         GTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAG
genomic: TGAAATTCAGGGTGGCTATCAAAACATCTGTGGCACTGATAGCACTAACGgtattacaag ... aaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAG
EST: gi|164050720|gb|ES005737.1|ES005737
EST:     GGCTATCAAAACATCTGTGGCACTGATAGCACTAACG                         GTGGGATA-TTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTAC
genomic: GGCTATCAAAACATCTGTGGCACTGATAGCACTAACGgtattacaag ... aaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcttgcatattgttcttccagctaatctatctttgttattatgaaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTACAACAAATATCATCCTTACACCTCTTGGATTCCAATAAC
                     agctaat  putative branch site (score: 3)
                                                ctttt  putative PPT
                                 tttgttattatgaaac  TA-rich tract