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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA

Basic information

species Selaginella moellendorffii
transcript EFJ18059
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
---------------------------------------------gtatatgcgtgggtt-tggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                                |||   |   |  | |  || | |  |  |  |    || | |   |   |||||| |  | |||||||| |||||  ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| || |||||||||||||| || || |
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
---------------------------------------------gtatatgcgtgggtt-tggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                                ||||  |   |  | |  || | |  |  |  |    || | |   |   |||||| |  | |||||||| |||||  ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| || |||||||||||||| || || |
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
--------------------------------------gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                          ||   |   | |     ||| |  |  |  || | |   || |   | ||||||||| | ||||| || |||||  ||||||| || |||||||| ||||| ||||||||| | || || |||||  | |||||||||||||| || || |
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgt-cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
--------------------------------------gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                          ||   |   | |     ||| |     |  || | |   || |   | ||||||||| | ||||| || |||||  ||||||| || |||||||| ||||| ||||||||| | || || |||||  | |||||||||||||| || ||||
gttagtatttatttgtttttggatattaatcttagatttctaattgataattataatcttagctaactgttgcaatggttgttatctgt-cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------------------------gtatatgcgtgggtttggctcta---ggtgctcatgacagtcggactt----ttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                  | ||| |   |||   | ||     || |||  | | | || |||    |||| |  ||||| || |||||||||| || || || || ||||| |||||||| || || ||||||||||| || || ||||||||||||||||| |||||  | || |
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------gtatatgcgtgggtttggctctaggtgctcatgacag-----tcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                       ||||    ||   ||      | ||| |  | |  |     | |   |||| | || ||||| |  | || ||||| || ||  | || |||||||||||||| || || ||||||||| | ||||| || || ||||||||||| ||||| || || |
gtaaaatctctctgaatgtaccatataaa-atgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------gtat-atgcgtgggtttggctctaggtgctcatgacagtcggactt---ttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                          ||| |||| |   ||    | |   ||||||||  | | |||  |   |    | ||||||||  | |||||||| |||||  | ||||||||||||||||| ||||| ||||||||| | ||||| || || || |||||||||||||| || || |
gttggtattcttgtcctcatctgtcttatgatgctttaattcatatttt--tgctcatg-tatttggatgtaattctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S342_4V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgc-atgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                                         |  |    |||||  ||| |  | | | |  |||| || | | || ||  |||||||||||||| ||||||||||| ||||||   || || ||||| || |||||||||||||||||  | || ||  |||  |||||||| ||||||||  |||
gcgatagaggtgcggtagtttgggaatggcggggaacaggggcagagcaggaggggagagtggaggtgggcgtggatggatgcggtgctgacggtggcatttgtgggatgcagATGCTGTCGAAGAAGGTGGACACGCTGGGGAAAGCGATGGAGGTGGAGGCGAAGAAGATGCGGCGAGAAGTGACAGTGATGGAGAAAGAGGTGGCATCGA

upper sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S228_73V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgc-atgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                                |  |    |||||  ||| |  | | | |  |||| || | | || ||  |||||||||||||| ||||||||||| ||||||   || || ||||| || |||||||||||||||||  | || ||  |||  |||||||| ||||||||  |||
gtgcggtagtttgggaatggcggggaacaggggcagagcaggaggggagagtggaggtgggcgtggatggatgcggtgctgacggtggcatttgtgggatgcagATGCTGTCGAAGAAGGTGGACACGCTGGGGAAAGCGATGGAGGTGGAGGCGAAGAAGATGCGGCGAGAAGTGACAGTGATGGAGAAAGAGGTGGCATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
                                          cttttgc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG