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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcttggttaattggtcttgattttgttaatgtatcggaaaaagttatgaatatgttaatttcctgaaactattgaacgggcttgtatattggcagGTGAATCTTGTTGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCAGAAGAAGTTGTGGATCCAAGACTTGAACCTAGACCTAGTAAAAGTGCTTTGA

Basic information

species Arabidopsis thaliana
transcript AT2G42960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 5
-------------gtgag-gctt--ggttaattggtcttgattttgttaatgtatcggaaaaagttatgaata-tgttaatttcctgaaactattgaacgggcttgtatattggcagGTGAATCTTGTTGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCAGAAGAAGTTGTGGATCCAAGACTTGAACCTAGACCTAGTAAAAGTGCTTTGA-
              | || ||||   | |   || |  | | ||  ||  | |  |   |||||| || |  | ||||  | |  ||||  |        |  |    |  |||||||||||||||||||||||||| ||||||||||| || ||||| || || || |||||||||||  |||| ||||||   | |||    | | ||||||| | 
tatgaaatacttaatcagtgctttcagctttctgcttctaacttctttgtttt-ccatgaaaagtgatcaccactgtttgtatggtgaa--tgggattttgattatcctcatggcaggTGAATCTTGTTGAATGGCTCAAGATGATGGTGGGGACAAGGAGGGCTGAGGAAGTTGTGGACTCAAGGCTTGAAGTGAAACCATCAATACGTGCTTTAAA

upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G42170.1 (Glycine max), 3'ss of exon 5
--------------gtgag-gctt--ggttaattggtcttgattttgttaatgtatcggaaaaagttatgaatatgttaatttcctg-aaactattgaacgggcttgtatattggcagGTGAATCTTGTTGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCAGAAGAAGTTGTGGATCCAAGACTTGAACCTAGACCTAGTAAAAGTGCTTTGA
               | || ||||   ||| | || |  | | ||||||   | ||  |||    | |    | | |  ||  |  |  |  | ||||     ||  |     | ||||||||||||||||||||||| ||||||||||| || ||||| ||| | || |||||||| ||  |||| ||||||   | |||    | | ||||||| |
gtttgaaatacttaatcagtgcttccagtttactgattctaactttgttttcg-atgagaagtgatcacagctttttctatagcgggtgagattttgattatcctcat-----gacagGTGAATCTTGTTGAATGGCTCAAGATGATGGTGGGGACAAGGAGAACTGAGGAAGTTGTCGACTCAAGGCTTGAAGTGAAACCATCAATACGTGCTTTAA

upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 7
gtgaggcttggttaattggtcttg--attttgttaatgtatcggaaaaagttatgaatatgttaatttcctgaaactattgaacgggcttgtatat-----tggcagGTGAATCTTGTTGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCAGAAGAAGTTGTGGATCCAAGACTTGAACCTAGACCTAGTAAAAGTGCTTTGA
||    ||  ||  | ||   | |  | ||  ||    | |||   |||| ||   |||      | | |   ||    |         |||  ||     |||||||| |||||||| || ||||| ||  ||||||| || ||||||||||| |||||||||||||||||||  ||||||  ||  || |  | | ||||| | |
gtatttctctgtccaatgcattggggacttctttctcctttcgtcgaaaggtaaatatacaggcttgttcaagaagagctatgataagctgttcatgctcatggcagGTTAATCTTGTCGAGTGGCTTAAAGTGATGGTAGGGACAAGAAGAGCTGAAGAAGTTGTGGATCCAAACCTTGAAGTTAAGCCCACAACACGTGCTCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttatgaatatgttaatttcctgaaactattgaacgggcttgtatattggcagGTGAATCTTGTTGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCAGAAGAAGTTGTGGATCCAAGACTTGAACCTAGACCTAGTAAAAGTGCTTTGA
            tgttaat  putative branch site (score: 3)
     atgaatatgttaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcttggttaattggtcttgattttgttaatgtatcggaaaaagttatgaatatgttaatttcctgaaactattgaacgggcttgtatattggcagGTGAATCTTGTTGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCAGAAGAAGTTGTGGATCCAAGACTTGAACCTAGACCTAGTAAAAGTGCTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT