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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC

Basic information

species Arabidopsis thaliana
transcript AT5G61960.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
---------gtacagtct-catattgct-----gctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
          |||  ||| |||   |||      ||||      ||    || |||  || | |    ||         || || |        ||  ||| | || |||||||| |||||||||||||| || || ||||| |||||| | ||| | |||||| | |||||||||||| ||||||||||||| || ||||
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttt-tttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC

upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
-------------------------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
                                                                          ||     |   |    ||   |||  ||     |  | | |       ||            |||  ||     | | ||  ||| | |||||||| ||||||||||| ||||| || || |||||||||||| | ||| | |||||| | |||||||||||||||||||| ||||| |||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtcct---tttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
                                                                        ||  |  |   |    ||   ||   ||     |   ||       |||  | |   |  |   |     ||    |    ||  |||   |||||||| ||||||||||| ||||| || || |||||||||||| | ||| | |||||  | ||||||||||||||||| || ||||| |||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtccttttggga--gagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
                                                        | | ||  || | |        |||| || ||  |    |   |  |||  ||| | ||   |  ||    ||  | |   |||||||||||| ||||| ||||||||||| |||||||| || |||||||||||| | ||| | |||||||| || ||||| ||||| ||||||||||| |||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacatt--cacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
               | |   | |    | |      |   ||||   |   | | |    ||| ||  | |       ||  ||||| | || |||||||| || ||||| ||||| || ||||||||||||||| ||||  |||| || || |||||||| ||  | || || || || || ||||
---------------gttctctgtgaaaaagagagaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
                         ggctaaa  putative branch site (score: 3)
                                   tcttaaaaaaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC