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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggttattgttctcctctggaagcatctctctagatcttgagtcaatccctctgtctcttgcatgattaactccataaatatattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA

Basic information

species Arabidopsis thaliana
transcript AT3G08930.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 5
gtctggttattgttctcctctggaagcatctctctagatcttgagtcaat-ccctctgtctcttgcatgat-taactccataaatata-ttacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
     | |||  | ||  | | |      |   ||| || |||| | |||   |  |      |  ||| | |   |   |   |||  ||  |||| ||||||||||| |||||||| |||| |||||| ||||||||||||||   ||||||||||||||||||||||||| | ||||| |||||||  || |
---gtgctat-atgcttttatagcgaagacgtactaaatgttgattgaatatgcagtactatatttatggtgtggttggttggttatggttgtagGAAGCAACCGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAGTCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGAAGGAAATTTCGTA

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
gtctggttattgttctcctctggaagcatctctctagatcttgagtcaat-ccctctgtctcttgcatgat-taactccataaatata-ttacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
     | |||     |     | | |   |   ||| || |||| | |||   || | |    |  ||  | |   |   |   |||  || ||||| ||||| ||||| |||||||| |||| |||||| ||||||||||||||   ||||||||||||||||||||||||| | ||||| |||||||  || |
---gtgctatatgcttttatagcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggttggctggttatggttgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 5
-----------------------gtctggttattgttctcctctggaagcatctctctagatcttgagtcaatccctctgtctcttgcatgattaactccataaatatattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
                        | |  | | |  |    | ||   | || |   || ||  |  | ||    || | | | | |      |  ||         || |  |||| || || ||||| |||||||| |||||||||||||| ||||||||||| | ||| ||||||||||||||||||||| | ||||| || || |  || |
gtgctatattgttactgaaggagatatattaaattgttgattatgtgtgtatttggttacatgatatgcca--tactatatttatggtgctcctggct------ggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAAGTGGTTCAAAGGGTAGAAAGTTTCGTA

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 5
-----------------------gtctggttattgttctcctctggaagcatctctctagatcttgagtcaatccctctgtctcttgcatgattaactccataaatatattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
                        | |  | | || |    | ||   | || |   || ||  |  | ||    || | | | | |  ||  |  ||         || |  |||| || || ||||| |||||||| || ||||||||||||||||||||||| | ||| ||||||||||||||||||||| | ||||| || || |  || |
gtgctatattgttactgaaggagatatattaaatggttgattatgtgtgtatttggttatatgatatgcca--tactatatttatggtgtggctggct------ggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCTAGAGAACTAAAGAAAGCAGCTGAGGCACTCCATCAGGAAGAAAGAAGTGGTTCAAAGGGTAGAAAGTTTCGTA

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 4
-----gtctggttattgt------tctcctctggaagcatctctctagatcttgagtcaatccctctgtc-tcttgcatg-attaactccataaata--tattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
     || | |||| ||       | |  |           | | |   | ||  || |     | || | |  |  ||  ||    | | |   |   || |  |||| || || ||||| |||||||| |||||||||||||| ||||||||||| | ||| |||||||||||||||| |||| | ||||| || || |  || |
gtgctgtattgttactgaaggagatatattaaattgttgattatgtgtgtatttggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtctggttatt-gttctcctctggaagcatctctcta---gatcttgagtcaatccctctgtctcttgc--atgattaact-ccataaatatattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
                               || |    ||| |   |  |||  |    | |   ||   |||  ||  |   | | | | ||  |  |  |||  |   |  |||  ||||  |  |||| || || |||||||||||||||||||||||  | |||||||| |||||||  || ||||||||||||||||||||| | ||||| || || ||||| |
gtgctgctttttttctttttaatagtgcatcgtgtatccatttgaaattatctaaatatttttggttatgtgatgatggatatttgcatgtttcaatcacttatggatggttgtcattgatatcctgtagGAAGCCACTGAACTAGGTAAAAAGGCAAGAGACTTGAAGAAAGCGGCTGATGCGCTCCATCAGGAAGAAAGAAGTGGTTCCAAGGGTAGAAAGTGGCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgagtcaatccctctgtctcttgcatgattaactccataaatatattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
                              gattaac  putative branch site (score: 2)
                               attaactccataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggttattgttctcctctggaagcatctctctagatcttgagtcaatccctctgtctcttgcatgattaactccataaatatattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT