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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtactcatattttatcaaggttattctctaagttcttatgctaatcatttacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC

Basic information

species Arabidopsis thaliana
transcript AT5G18620.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
-------gtatg-tactcatatttt--atcaa--ggttattctctaagttcttatgctaatcatttacc---tcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
        | || ||  |||||| |  ||  |  | | ||  |     | ||| |   | |  | || |   | |   ||| ||||||| || |||||||| ||||||||| | ||||| ||||| |||||||| ||||| ||||||||||| || ||||| |||||||| |||||| | ||||
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
--------------gtatgtactca-tattttatcaaggttattctctaagtt--cttatgctaatcatttac-----ctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
                   | |||| |   | || | | | ||  | |  |    | |       ||||| |       || ||| || ||||||| || |||||||||||||| ||| | ||||| ||||| || || || ||||| || |||||||| || || || || ||||| |||||||| ||||
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 8
----------gtatgtactcatattttatcaaggttattctctaagttcttatgctaatcatttacctcatcttt---gtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
             | |  | |||  | || |  ||  ||    | |  ||  |  ||||  |||    || ||||     ||||||| || |||||||||||| ||||| | || || |||||||| || ||  ||||||| || ||||| || ||||| |||||||| |||||||| ||||
gttgggatataattatcatgataactaattatagtactttaaaatgaactcttaataattgtttcttgcaacttttgcaaagGTTCTTCGCCCATTTCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGTCTACCTCCGAAGAAGGAAACCATACTTAAAGTTGGAATGTCTCAGATGC

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 8
----------gtatgtactcatattttatcaaggttatt--ctctaagtt--cttatgctaatcatttacctcatctttgta------gGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
          | |  | ||  |  ||  |  | ||  ||     |||  |  |  ||  |  |||||| | |  ||| ||||      ||| || ||||||||||| ||||| ||||| || |||||||| |||||||| || || ||||||||||| || || || ||||| |||||||| |||||||
gtaaattacagaaccttcttttgattgttggaagtccttgatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGACCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGATTGCCACCAAAAAAGGAAACTATTCTTAAAGTAGGCATGTCCCAAATGC

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 8
---------gtatgtactcatatttta--tcaaggttattc--tctaagttcttatgctaatcatt-tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
           |  | || || |||||  || |  |||||   ||| | ||  |    |  |   | ||  ||   ||| ||||| || || || || || ||||||||  | || |||||||| ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||| |||
gtaaacccaagacctcctaattttttagctctaccttatttcatctcatttactgaaatggtttctgtatttctgttttttagGTCCTCCGGCCTTTCCTCCTTCGGAGACTGAAGTCAGATGTTGAGAAAGGCTTGCCTCCAAAAAAGGAAACAATACTTAAAGTAGGCATGTCTCAATTGC

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtactcatattttatcaaggttattctctaa-gttcttatgctaatcatt--tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
                       ||  || || |   ||  ||    || |||   || | | | ||   ||||  | || ||||||||  |  |  |  | || || ||||| || | ||| ||||| ||||| ||||||||||| ||||||||||| |||||||| ||||
-----------------------gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtactcatattttatcaaggttattctctaa-gttcttatgctaatcatt--tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
                       ||  || || |   ||  ||    || |||   || | | | ||   ||||  | || ||||||||  |  |  |  | || || ||||| || | ||| || || ||||| ||||||||||| ||||||||||| |||||||| ||||
-----------------------gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTGCCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcaaggttattctctaagttcttatgctaatcatttacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
                            tgctaat  putative branch site (score: 2)
                                     tttacctcatcttt  putative PPT
                               taatcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtactcatattttatcaaggttattctctaagttcttatgctaatcatttacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA