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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaaatccaggttacatgaatatactcatcaatgaaaatccagtgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT

Basic information

species Glycine max
transcript GLYMA18G28130.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G28130.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ09619 (Selaginella moellendorffii), 3'ss of exon 10
agaaaaatccaggttacatgaatatactcatcaatgaaaatccagtgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
                                  |     ||   ||  || | ||| |||||||   ||  | |  |   || | |   | ||| | |||||||||| ||||| || || ||||||||||| || ||||||||||| 
---------------------------------gtacgtttctcatgacaactttct-tttgcaa---ttcatcc--aaccctctctttctatgtcgtagGTTCATCATGGAGGCGCGGGAACAACAGCTGCCGGTCTCAAAGCTGCG

upper sequence: GLYMA18G28130.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
agaaaaatccaggttacatgaatatactcatcaatgaaaatccagtgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
       | ||   |  ||   | | ||| || ||         |  ||| ||   |  ||  |||  |   | ||            | |||||| |||||||||||||| || ||||| ||||||||||| || |||||||| || 
------gtacaaagtttatt--tcttctcctcgattcgcgattcgcttgagttgagttcttttaaaactggatgctgga---------cttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG

upper sequence: GLYMA18G28130.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ18041 (Selaginella moellendorffii), 3'ss of exon 10
agaaaaatccaggttacatgaatatactcatcaatgaaaatccagtgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
                                  |     |    ||  || | ||| |||||||   ||  | |  |   || | |  || ||| | |||||||||| ||||| || || ||||||||||| || ||||||||||| 
---------------------------------gtatgtttgtcatgacaactttct-tttgcaa---ttcatcc--aaccctctctttatatgtcgtagGTTCATCATGGAGGCGCGGGAACAACAGCTGCCGGTCTCAAAGCTGCG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|15288220|gb|BI472111.1|BI472111
EST:     TATTGGATAATTGCCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTG                         GTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
genomic: TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTGgtaagattat ... tttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
EST: gi|22525980|gb|BU084791.1|BU084791
EST:     TATTGGATAATTGCCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTG                         GTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
genomic: TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTGgtaagattat ... tttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
EST: gi|9204101|gb|BE330325.1|BE330325
EST:     TATTGGATAATNGTNCTCATGATTGGCTNTTCTTGCGTTGCAAGGCTGTG                         GTTCATCACGGAAGTGCTTGCACAACAGCTGCGGGGCTCAAAGCTGCT
genomic: TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTGgtaagattat ... tttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
EST: gi|6566103|gb|AW233863.1|AW233863
EST:     TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTG                         GTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
genomic: TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTGgtaagattat ... tttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
EST: gi|51338437|gb|CO982303.1|CO982303
EST:     TATTGGATAATTGCCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTG                         GTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
genomic: TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTGgtaagattat ... tttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
EST: gi|58017155|gb|CX703897.1|CX703897
EST:     TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTG                         GTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
genomic: TATTGGATAATTGTCCTCATGATTGGCTTTTCTTGCGTTGCAAGGCTGTGgtaagattat ... tttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
                                         tccattt  CT-rich tract
     attatctatttgcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaaatccaggttacatgaatatactcatcaatgaaaatccagtgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT