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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatttctcctttcctttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

Basic information

species Selaginella moellendorffii
transcript EFJ30597
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
--------------------------------------gtgcatttctcctttc----ctttgtgcctgatttttcccttccggctttgc--attggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA
                                      ||     |||  || |      |      ||| ||   | |     || ||   ||||  ||||||| ||||||||||| ||||| |||||||| || || || || || || ||||| || || || |||||||| |||||||| || ||||| |||||||
ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA

upper sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------------------------------------------gtgcatttctcctttc---ctttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA
                                                                                                                        ||     |||  || |    | || | ||    ||     |  | || |   |||  ||||||| ||||||||||| ||||| ||||||||| |||  || || || ||  ||||||| || || |||||||| ||||||||||  ||||| |||||||
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA

upper sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
-----------------------------------------gtgcatttctcctttcc---tttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA
                                         ||     |||  || |    | || | ||    ||     |  | || |  ||||  ||||||| ||||||||||| ||||| |||||||| || || || || || || ||||| || || || |||||||| |||||||| || ||||| ||||| |
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA

upper sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
------------------------------------gtgcatttctcctttcctttgtgcctgatttttcccttccgg---------ctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA
                                    |||  ||     | |   |  |||  | |  ||  |                ||||   || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| ||||| |||||||
ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatg-cagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttctcctttcctttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA
                     gcctgat  putative branch site (score: 4)
                        tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatttctcctttcctttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA