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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatctattgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT

Basic information

species Arabidopsis thaliana
transcript AT1G32380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 3
---------------------gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatctattgatgtttt--cagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
                      | |||| |||   | ||  |  ||| |    |||  |||      |  | || || ||| | || ||      |   ||||| ||||| |||||||| |||||||| ||| | || || |||||||| ||| |||| || |||||  | ||||| |||||||| ||||||||||| || |
tattgaatttttttaccttcaattggtt-tttgcattttgcttgatgatgtcaacaa-atgggtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT

upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 3
---------------------gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatcta--ttgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
                     || |||| |   | | ||  |||||| |     || | ||     ||  |  | || ||| |  |    |  | | |  |||| |||||||||||||| ||||| || ||| | || || |||||||| ||| |||| || |||||  | ||||| |||||||| ||||||||||| || |
tattgaatttttttacctttagttggttttgcat-ttttgctcaatgatgtgagcaat-tggattttacatggaactaatggagtttgcctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT

upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaattt-catctgatgtatct--attgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
                  | |   |||   |   ||||  | |||  | || |   |  || |||| || |||||  |  ||||  |||  | | ||||||| |||||||||||||| ||||| || ||| | || |||||  |||| ||  |||| ||||| ||  | ||||| ||||||||||||||||| || || |
actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT

upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 2
gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatctattgatgtttt-cagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
                        | ||   |    |    |   |  |||||    |    ||   ||||||||| ||||| ||||| |||||||| ||||| || ||  | |||||||| ||| | ||||||||||||||  |  | ||||| || || ||  | || || || ||  
-----------------------gtagtcactgtgatccagctttttctttcaatctacacgtcgtgtgatgtttttcagACTCAAGGACGTGAATCGATTGCAGCAAAGCTTGTAGCAAATCTTTTGACAGAAGCCGGTGCGAACCGTGTTCTTGCATGCGACTTACACTCGGGGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtagatacagtatgtcaagtaatttcatctgatgtatctattgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
                                        tattgat  putative branch site (score: 3)
                                              tgttttc  CT-rich tract
                  aagtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatctattgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT