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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCGTGATGTTAAGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatttctttccttccttctctatgcaccaagtaccctttgaccactagaatgataatccatgtagggttactttactttggagttacttatggt...

Basic information

species Glycine max
transcript GLYMA11G34050.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34050.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G12560.1 (Arabidopsis thaliana), 5'ss of exon 8
GTGGCGTGATGTTAAGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagat-tatttctttccttccttctctatgcaccaagtaccctttgaccactagaatgataatccatgtagggttactttactttggagttacttatggt
 ||||||||||| || ||||| ||||| ||| ||||||| ||| ||||||| || ||||| |||||| |   ||      |   | |    | || | ||  |  | | | ||    ||  | |||   |    | |   |  | | | || ||           
ATGGCGTGATGTAAAATTGCGTGCTTTCGAGGATGCAGATCATCGGACTTACGTGGACTTGAAGgtaaacacatcagacacaaacatgtaatctggaacatatcacgtcttacagtcaggttaatatctc----aagaacatgtgaatatgcag-----------

upper sequence: GLYMA11G34050.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv13s0019g01670.t01 (Vitis vinifera), 5'ss of exon 9
GTGGCGTGATGTTAAGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatttctttccttccttctctatgcaccaagtaccctttgaccactagaatgataatccatgtagggttactttactttggagttacttatggt--
|||||||||||||||  |||| |||||||| |||||| | ||| | ||||||||||| || |||||     || | |||   |  ||| |  | ||| || |   |    ||| || |  | ||| |   || ||  ||    |   |   | |   ||||| |  
GTGGCGTGATGTTAAACTGCGTGCTTTTGATAATGCAAAACATCGAACTTATGTAGATTTGAAGgtgaggaatctattttgctatttcacagtacac-aactggacaa-aacctcttgtctcatagtggctgcagaattcaagttgctcctattattttatgctag
















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|15203127|gb|BI425895.1|BI425895
EST:     AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAG                         GATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACATAGG
genomic: AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatt ... gtggatacagGATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
EST: gi|6455221|gb|AW185904.1|AW185904
EST:     AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAG                         GATAAATGGAAAACA
genomic: AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatt ... gtggatacagGATAAATGGAAAACA
EST: gi|298172245|gb|HO021837.1|HO021837
EST:     AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAG                         GATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
genomic: AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatt ... gtggatacagGATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
EST: gi|15663968|gb|BI701339.1|BI701339
EST:     AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAG                         GATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
genomic: AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatt ... gtggatacagGATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
EST: gi|14205474|gb|BG839152.1|BG839152
EST:     AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAG                         GATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
genomic: AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatt ... gtggatacagGATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
EST: gi|254341766|gb|GR852903.1|GR852903
EST:     AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAG                         GATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG
genomic: AGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatt ... gtggatacagGATAAATGGAAAACATTAGTGCACACCGCAACAATCTCCCCTCAACAAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCGTGATGTTAAGTTGCGAGCTTTTGAGAATGCAGACCATAGGACTTATGTAGACTTAAAGgtagattatttctttccttccttctctatgcaccaagtaccctttgaccactagaatgataatccatgtagggttactttactttggagttacttatggt

- - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctc