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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatttccagtaatagcctacttgaaaccaagtgattatgcttaagcttatttctaaattggctcaacattttgtttacagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC

Basic information

species Arabidopsis thaliana
transcript AT2G42490.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
--------------gtagatttccagtaatagcctacttgaaaccaagtgattat--gcttaagcttatttctaaa--ttggctcaacattttgttt--acagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC
               |   ||||  ||   |        | |    ||  | |||  | | || || | |   |||   |  |     ||||   ||  |||||||||||| |||||||| || ||||| |  ||||||||||| || ||||| || |||||||||||||| |  || || ||  | ||| | || |||||||
gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC

upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
----gtagatttccagtaatagc--ctacttgaaaccaagtgattatgcttaagcttatttctaaattggctcaa----cattttgttt---acagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC
       |  |  |  || |     ||  || ||   || |  |   |    ||  | |    ||| ||  | ||    |||||| | |   ||||||||||||||||||||| ||||| || |  |||||||||||  | ||||| || |||||||||||||| |  || || ||  | ||| | || |||||||
gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC

upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 6
gtagatt-tccagtaatagcctacttgaaaccaagtgattatgcttaagcttatttct-----aaattggctcaacattt-----tgttta-cagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC
||  ||| |   ||||     | ||  |     |     ||  |  ||   ||||||       ||||      || |||     |||| | ||||||||||| |||||||| ||||| || |  || ||||| |||||  |||| || ||||||||||||||||| || || ||  ||||  | || || ||||
gtgcattgttgtgtaaagcttttctctattatgatgagataaacaaaaaaatatttccccctggaattaataacacttttaatgatgttgagcagTGGAACTTCCGTATTGGCTTCACCCCTAAAGAGGGTTTGGTCATCTATTCTGTTGCATATGTTGATGGCAGCCGTGGACGTCGGCCGATAGCTCATAGGC

upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------gtagatttccagtaatagcctact-tgaaaccaagtgattatgcttaagcttatttctaaatt--ggctcaacattttgtttacagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC
                   |  |||      | | | || | | |    || | || ||  |||   ||||||  |  ||    ||    |||||||||||||||||||||||| ||||| || |||||||||||||| || || || ||| | || || ||||  ||||| ||||||||  || |  | || |||||  | |
taatggtaaaaatgcttcgacttttgtgtcgaaaacataatattagtttaactaataatagtta---ttatttaaactttctatctgggaattttgtttacagTGGAACTTTCGAATTGGTTTTACTCCAAGGGAAGGATTGGTTATTCATACCGTCGCCTATGACGATGGGAGTCGAGGAAGACGATCAGTCGCACATCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaagtgattatgcttaagcttatttctaaattggctcaacattttgtttacagTGGAACTTTCGTATTGGATTCACTCCAAGGGAAGGTTTAGTCATACATTCGGTAGCATATGTTGATGGCAGTCGAGGTCGAAGGCCTGTTGCACACAGGC
                         ttctaaa  putative branch site (score: 2)
                                           ttttgttt  putative PPT
                     ttatttctaaatt  TA-rich tract