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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT

Basic information

species Selaginella moellendorffii
transcript EFJ24973
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------------gtaagtattgctggaagt-tctttcgatcctttgtggtgatactatcttctt------------ctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                                                                             |      ||| | ||  | || || |   |  || | ||  |||   || ||            | || || ||| || || || || ||||| || |||||| | ||||| ||||| ||||| |||||||| ||||| |||  |||||||||||||||||| ||| | || || 
gtgagtcgtcgccctcgtcctcccccctcttgtgctctgctctgctctgctctgtcttcttttgagttttgagctttgagctcgttgtttgacttgtcgttggcggcgatgagatgtgactgggtttttgttgtggtggggcaacattacagGGCGAGCGATAAATGCCAGAGGGAGAAGCGCAAGACCATCAACGGCGACGACTTGCTGTGGGCGATGGCCACGCTGGGCTTCGAGGACTACATCGAGCCC

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G064426_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------gtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttctac--tttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                                                                                     | ||  | | |||   ||  |     | | | |      ||  || |  ||| |  ||||||| || |||||||||||||| || |||||| ||||||| ||||||||||| ||| |||| ||||| |||  ||||||||| || ||||| ||  | ||||| 
gtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttccttgtctgctgtttgcagGGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCC

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------gtaagtattgctggaagttctt-tcga-tcctttgtggtgatactatcttcttc-tactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                                                                        | ||  | |||||   ||  | | || |  |   ||   |   | | || | |   ||||||||||| |||||||||||||| || |||||| ||||||| ||||||||||| ||  |||| ||||| |||  ||||||||| || || || ||| | ||||| 
gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G05610.1 (Glycine max), 3'ss of exon 2
-------------------------gtaagtattgctggaa-gttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                         |     |||  | |   ||| ||    |   |||     |||   |    |  |  ||  |||||| || || ||||| || ||||||||||||||||| ||||| ||||| || ||||| ||||| |||| |||  | || |||||||||||  | || || 
gtacacttctttgtttctcatgcgcgctttcattttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------------------------gtaagtattgctggaa-gttctttcgatcctttgtggtgatact---atcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                                                                                               || |   |   |||   |||      |  |  | ||  |||  |   || || || | | ||  || || ||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| ||||| |||  |||  | || ||||| || ||| | || || 
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G37060.3 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------gtaagtattgctggaagtt--ctttcgatcctttgtggtgatactatcttcttct-actttg-----cagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                               | |   ||| | |   ||    ||  ||  ||  || ||  |   | ||  | | || |||     |||||| ||||| || || ||||||||||| |||||||| || ||||| ||||| ||||| |||||||||   ||  | || || || || ||| ||||||||
agtccttacattggttactctttcttgttgttcatctttgtttggctttgatgttgcatatttgatgatgcaatggtttttctatgacgttgatgagcagAGCGAGTGATAAATGTCAAAGAGAGAAAAGGAAGACTATTAATGGAGATGATTTGCTTTGGGCAATGGCTACTTTAGGATTTGAAGACTACATGGAACCT

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv06s0004g03490.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------gtaagtattgctggaagttctttcgatcctttgt-----ggtgatactatcttcttcta--ctttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                               |    | ||  |    ||| |||   |  ||  |     | | |    |   | ||||    |||| ||||| |||||||||||||| |  |||||||||||||| || ||||| ||||| ||  |||||||||||   ||| | || || || || ||  | || |||
cttttgtttttccggtaaccaaacggggttagggtttttttttttttgttttttttgtttttaatttcaagataaattgactctgttctgggttttgaagAGCGAGTGACAAGTGCCAGAAGGAGAAGAGGAAGACAATTAATGGTGATGATTTATTATGGGCAATGGCTACGTTAGGGTTTGAAGATTATATTGATCCT

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 3'ss of exon 1
--------------------gtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttctactttg-----cagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                     |   || |  | |  | |   | |||   | ||| || |  | |  | ||  | || |      || || ||||| || || || ||||||||||||||||| || ||||| ||||| ||||| |||||||||   ||  | || || ||||| ||  | || || 
gtatggctgatgcattttttctttttaattttaggcggtgcgt-gattgatggtgttgttggttttgtttttcaattggatgcctagGGCGAGTGATAAATGTCAGAGAGAGAAGAGGAAGACTATTAATGGGGATGATTTGCTCTGGGCAATGGCGACTTTAGGGTTTGAGGATTATATTGATCCG

upper sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------gtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                                                                                                     | | | || | ||       |        | | || |||||   | | |    ||| || || || ||||||||||||||  | |||||| |||| || || || ||||| ||| |||| ||||| ||||  ||| ||||||| ||||||||| |||| || 
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgc----actatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctggaagttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
                                  ctatcttcttctactt  CT-rich tract
                               atactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG