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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA

Basic information

species Arabidopsis thaliana
transcript AT1G13170.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
-----------------gcaagtcaaccatcaca--tcattctaatgtag-aagttgtattgaaaaatcatgcatgaat--gtgaaaaactttaacacttcattatctttttaaatctatcagac--atatataatagcaacccct-caccttct-ttgccaccataattct---------cttgttc-agGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
                   || |   | ||||    | ||   ||||    ||  | ||  |  ||||   |||  |||     ||||  |||    |||||||||  | ||   |   | |  |  | |||    ||  |    |    ||| |  ||| |   |  ||||         |||| || |||| ||||||||||| |||||||||||||| || |||||||||   || ||||| || |||| ||| || ||| | ||||||||||| ||||| || || |
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA

upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 5
------------------gcaagtcaaccatcaca--tcattctaatg--tagaagttgtattgaaaaatcatgcatgaa---tgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgc-cacca-taattctc--------------ttgttc-agGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
                    || |   | ||||    | ||   ||||  |  ||||| ||  |  ||||   |||  ||       || || |||    ||||||| |    ||   | |||   |  |  | ||  |||     |    |   |||    |   ||||| ||              |||||| |||| ||||||||||| |||||||||||||| || |||||||||   || ||||| || |||| ||| || ||| | ||||||||||| ||||| || || |
gtaactgggtttttccttttaacttttcaatcaaggttaatgggaatgagtcaaagtt-tacaggcaaatgcggcaaaaaatagactaataaatttgttgcttcattcttgccttttgt-tattgaatctgaaaaagggcagtgatttgtgtctattgtatgctgctaattttcatctaacaagaagcttgttccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA

upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctc-ttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
                                                ||| || |      | ||| ||   |    ||| ||     ||   ||||  ||||| |    |||     ||||   || | | | | ||   | ||  ||||| |||||||||| || || ||||||||||||||||| ||||||||   ||| ||||| ||||||| |||||| ||| ||||||| || || ||||| || || |
------------------------------------------------cattcaggttccatagaaatttgggctagacataatgga--tagcactat--gacatttcctgtagt----cctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA

upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaaca-cttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
                                                       | |  |   ||  |  |||  |||  | || | |||  | || |     |  || ||    | |  ||  | |  | |  | || ||  |  ||| | ||||||||||||||||| |||||||| || || ||||| |||||   ||| ||||| |||||||| |||   ||| | ||| | || |||||||| || ||||
-------------------------------------------------------ggagatattaatttgcaacctctttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctt-tgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA

upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
                                                      | ||  |    ||||| |  ||   || || |     |||  ||  | ||| |   ||  | ||   |     | |||      ||  || | |||| ||||| ||||||||||| ||||||||||| |||||||| |||||   ||||||||  |||||||| |||   ||  | ||| | || |||||||| || || |
---------------------------------------------------ctttaaacatttcgaacttcagaac---ataatatgagctaattaatttg-catcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
                  ccctcac  putative branch site (score: 3)
                                          ttctcttgttc  putative PPT
     atataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA