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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgcgctcattttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

Basic information

species Selaginella moellendorffii
transcript EFJ23280
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------------gtcggtgc--gctcattttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                      | | |        ||||| | | |   |||  ||   | |||    |||||||| || |||||||||||  | |||||||| ||||||||||| |||||||||||||| || || || ||  | |||||  | || || |||
gtatgtttatattaaactttatctacatctttctatatatttatgatttatctcaccatcttcatcctgtttgatattaaaatattttggctctactgatgctatgcattttatgcctgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTTAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
----------------------------------------------------------------gtcggtgcgctcattttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                  | ||  | | |||||   | |   |||  ||   | |||    |||||||| || |||||||| ||  | |||||||| ||||||||||| |||||||||||||| ||||| || ||  | |||||  | || || |||
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgat-attttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 14
----------------------------------------------------------------gtcggtgcgctc--attttagttttcgcgattttactgagttttctac-tgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                 |   |    |   || || | | |   |  | |  ||  |||| | | ||||||| || |||||||||||  | |||||||| ||||||||||| |||||||| ||||| ||||| || ||  | |||||  | || || |||
gtatgttatattatatggcagatcttttatatgcgtttttgtgtatatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgtggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------gtcggtgcgctcatttta---gttttcgcgattttac----tgagttttctac-tgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                 |  |    |  ||| |   |||| | |  || ||     ||  |||| | | ||||||| || |||||||||||  | || ||||| ||||||||||| |||||||| ||||| ||||| || ||  | |||||  | || || |||
gtatgttatattatatgacagatcttttatatgtgtgtgtgtgtgtatttatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgcggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------------gtcggtgcgctcattttagttt--tcgcgattttactgagttttct--actgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                     |   |   |||| |||  |||  | | |     |    || |||     |  ||  ||||||||| || ||| |||||||||||||||||||||||||| | ||||||||||||||||| || || || ||||| || ||||||
gttcgtaactgtgctcgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------------------------------------------------------------------------gtcggtgcgctcattttagttt---tcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                                     ||  |  || ||| |||   | ||    | | |    |   |  ||||||  ||||||||||||||  | || ||||| ||||||||||| ||||| |||||||| |||||||| || || ||||| || ||||| |||
gtatgctggtttttagtctccctttgcgttttactgcatgaacttacataagctatctgcacattacatcttctgtgttacattttgtaccaatgttaatttggtttgctgaataaatactatacatgttgcagAAAAATAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTCAACCGTCATCTCTTCAAGCTTGAGCAGGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------------------------------------------------------------------------------------------------------------------------------------------gtcggtgcgctcattttagtt-ttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                                                                                                   | | |       | ||| |  || || ||   |||    || || |||||||  ||||| || |||||  | || ||||| ||||||||||| ||||| |||||||| || ||||| || || ||||| || |||||||||
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcct-ctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------gtcggtgcgct----cattttagtttt--------cgcgattttactgagttttc---tactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                   |||||||  |     ||| ||||||         ||||  |  | |    | ||      ||||||| |||||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||||||||| ||||| || || || |||||||| 
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------gtcggtgcgctcatttta-gttttcgcgattttac---tgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                | |  ||  |||  | | |  ||    || |    || ||       ||||||| ||||||||||||||||| || ||||||||||||||||| ||  | ||||| ||||||||||| || || || || ||||| ||||| 
ctcttgtcgagcttttttgatgttaaaaccatcttttgatcttgcacagttttgcagattgcaagctaacgtatcttgattcttgtgtcggtctttgcagAGAAATAGTTTTGAGCAACTGTGTATAAACTATGCAAATGAGAGGCTGCAGCAGCATTTCAACCGTCATCTTTTTAAGCTCGAACAAGAA

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------------------------------------------gtcggtgcgctcatttta-gttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                                                                      | | || |||| | ||| | | | ||      | |    |    | ||||||  || |||||||||||  | ||||||||||||||||| ||||| || || ||||||||||| ||||| ||||| || || |||||||||
gtgaaatcttctcatacactagaatgagattgtaagcagtttattattaattgtttcctgatctagtcaaagctttgatttctggattgatg-gctcttcttatggtctagcttaagcatttccctcctgattgcagAAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------gtcg--gtgcgctcattttagttttcgcgattttactgagttttctac------tgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                         ||||   | | ||  |  |||  ||     | |  |    ||| |||       ||||||  || |||||||||||| | || ||||| ||||| |||||||| || || ||||||||||| || || |||||||| || |||||||||
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG

upper sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S17_368V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------gtcggtgcgctcattttagttttc-gcgatttta--ctgagttttc--tactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                            |||       |||| |   ||    |   |||||  ||  | ||||   | ||||||  || |||||||||||  | || || ||||| ||||| |||||||| || ||||||||||| || ||| ||||||| || |||||||||
ttattgtaggaacctgatacaagtaggttttacaaaattttcacgtcaaatttttcatctacattggaagttgttttaatcttcgctttcatgattgcagAAAAACAGTTTTGAGCAGTTGTGTATTAACTACGCAAACGAAAGATTGCAACAACATTTCAATCGTCACTTGTTCAAGCTTGAGCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcggtgcgctcattttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG
                                             ttttctact  CT-rich tract
                attttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgcgctcattttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA