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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACATAGTAAGCTTGCACGGATACGCCTTATCTCCCTTTGGCAACCTCCTCTTCTACGACTACATGGAAAATGGCTCTCTTTGGGATCTTCTCCATGgtttgctattcttcttctcttggaccagttacgttcttttcagccagttttctacttttggaagacttaaacgtagtgattgtatgatgcag

Basic information

species Arabidopsis thaliana
transcript AT5G07180.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G07180.1 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: GRMZM2G082855_T02 (Zea mays), 5'ss of exon 23
AGAAACATAGTAAGCTTGCACGGATACGCCTTATCTCCCTTTGGCAACCTCCTCTTCTACGACTACATGGAAAATGGCTCTCTTTGGGATCTTCTCCATGgtttgct---attcttcttctcttggaccagttacgttctt--ttcagccagttttctacttttggaagacttaaacgtagtgattgtatgatgcag
|| ||| | || ||| | ||||| | | |  | || ||    || ||||| || ||||||||||||||||| || ||||| || ||||||||||||||||||  |      ||| |   ||||    |   ||   |||||  ||||    | ||  | |||  |  | ||  |   |    |    |     |   
AGGAACCTCGTCAGCCTCCACGGCTTCTCGCTCTCCCCTCACGGGAACCTGCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgata-acccacgggccacggccattcccag---

upper sequence: AT5G07180.1 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: GLYMA16G32830.1 (Glycine max), 5'ss of exon 25
AGAAACATAGTAAGCTTGCACGGATACGCCTTATCTCCCTTTGGCAACCTCCTCTTCTACGACTACATGGAAAATGGCTCTCTTTGGGATCTTCTCCATGgtttgctattcttctt--------ctcttggaccagttacgttcttttcagccagttttctacttttggaagacttaaacgtagtgattgtatgatgcag
|| ||  | || |  ||||| || || ||  || ||||   ||| || || || ||||| ||||| ||||| ||||||||||| ||||||||||| |||||| |  | |    | |        ||| |     | || |  | | ||  |  |  |         |  || ||||  |  | |||   | |   || | 
AGGAATCTTGTCACTTTGCATGGTTATGCTCTAACTCCTAATGGAAATCTTCTTTTCTATGACTATATGGAGAATGGCTCTCTGTGGGATCTTCTTCATGgtatattctctaaccttgaaacaactccttataaattttcactgtgttatgaaatctcatcttcaataaaaaacttgtatttggtgcacggaaattggaa

upper sequence: AT5G07180.1 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: GLYMA09G27950.1 (Glycine max), 5'ss of exon 24
AGAAACATAGTAAGCTTGCACGGATACGCCTTATCTCCCTTTGGCAACCTCCTCTTCTACGACTACATGGAAAATGGCTCTCTTTGGGATCTTCTCCATGgtttgctattcttcttctcttggaccagttacgt----tcttttcagccagttt----tctacttttggaagacttaaacgtagtgattgtatgatgcag----
|| ||  | || |  ||||| || || ||  || ||||   ||| || || || ||||| ||||| ||||| ||||||||||| ||||||||||| ||||||    |||||  ||   |||| |  |  | | |    | |||| |     | |    |||  | ||  |  |   |||   | |  | | | | ||||     
AGGAATCTTGTCACTTTGCATGGTTATGCTCTAACTCCTAATGGAAATCTTCTTTTCTATGACTATATGGAGAATGGCTCTCTGTGGGATCTTCTTCATGgt--aatattca-ctcaccttgaaataactccttggaattttttaatgtgatatgaaatcttgtcttcaataataaaaaaaaaattgtagaa-ggtgcatcgaa

upper sequence: AT5G07180.1 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 5'ss of exon 24
AGAAACATAGTAAGCTTGCACGGATACGCCTTATCTCCCTTTGGCAACCTCCTCTTCTACGACTACATGGAAAATGGCTCTCTTTGGGATCTTCTCCATGgtttgctattcttcttctcttggaccagttacgtt---cttttcagcc---agttt-tctacttttggaagacttaaacgtagtgattgtatgatgcag--
|||||| | || |||||||| || ||| |  |||| |||   || ||||| |||||||| || |||||||||||||| ||||| ||||||||||| || |||| | || || | |||  | | |     || | |    | |     |   ||||  || | || |       | | || |  | |   |||  || |   
AGAAACCTTGTTAGCTTGCATGGTTACTCACTATCACCCAAAGGAAACCTGCTCTTCTATGATTACATGGAAAATGGTTCTCTATGGGATCTTCTTCACGgttagttaatcattttccttggaaatgtatatgataaattatctgatctaaagttgatccaattattttgagttgatacctgttcaa-atattttgaaagt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACATAGTAAGCTTGCACGGATACGCCTTATCTCCCTTTGGCAACCTCCTCTTCTACGACTACATGGAAAATGGCTCTCTTTGGGATCTTCTCCATGgtttgctattcttcttctcttggaccagttacgttcttttcagccagttttctacttttggaagacttaaacgtagtgattgtatgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA