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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacatgttatttgcattttgagatccgaattctacttctgttttttttttttttttaattctattttctttttaattcag

Basic information

species Glycine max
transcript GLYMA13G09970.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G09970.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os04g52200.1 (Oryza sativa), 5'ss of exon 12
GAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtat-----ttacatgttatttgcattttgagatccgaattctacttctgttttttttttttttttaatt--ctattttctttttaattcag---
 ||||||||  | || ||||| || |||||||| ||||| ||||| ||||||||||| |||||   ||||||||| || | ||| ||||| ||| ||||||||        ||   |  ||| | | |       |   | |      || | | | ||  | || |     || | |  | | |   | |    
TAAGAAGCACATTAAGAATGGCAAGAATGTTTCGATGGGATTTGGCTTTGTTGAGTTCGACTCAGTTGAAACTGCAACCAGTGTCTGCAAGGATCTACAGgtacccctcccacccttcgttttcctctcttctctcttttccgcaccatgatctctgttgatgttcagcctgctgtatgttgtgtgtgttaatag

upper sequence: GLYMA13G09970.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G031529_T01 (Zea mays), 5'ss of exon 11
GAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacatgttatttgcattttgagatccgaattctacttctgtttttttttttttttta------------attctat-tttctttttaattcag--
|||||||||| | || || || || |||||||| ||||| ||||| |||||||||||||||||   ||||||||||||   ||| ||||| ||| ||||||||   ||   |   |    |||||   |||   ||   | ||| |   ||   |  |  ||            || |||  | | | |||  ||||   
GAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTACAGgtaac-acccatccctcctcttttgttttccttttttcgcctctttcccttagatgctcatatagatgtgcagcatgctaaatgtttctttggttcatag
















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|192306711|gb|FG998865.1|FG998865
EST:     TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAG                         GGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
genomic: TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacat ... tttaattcagGGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
EST: gi|51334771|gb|CO978637.1|CO978637
EST:     TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAG                         GGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
genomic: TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacat ... tttaattcagGGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
EST: gi|254313855|gb|GR831484.1|GR831484
EST:     TTGAGTTTGACT-CCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAG                         GGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
genomic: TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacat ... tttaattcagGGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
EST: gi|16348200|gb|BI973795.1|BI973795
EST:     TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAG                         GGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
genomic: TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacat ... tttaattcagGGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
EST: gi|193586810|gb|FK541342.1|FK541342
EST:     GTTTGCAAAGATTTACAG                         GGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
genomic: GTTTGCAAAGATTTACAGgtatttacat ... tttaattcagGGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
EST: gi|15287874|gb|BI471765.1|BI471765
EST:     TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAG                         GGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG
genomic: TTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacat ... tttaattcagGGGACAGTTTTGGACAGCCATGCTCTTATTTTACAACCTTGTAATGTCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTACAGgtatttacatgttatttgcattttgagatccgaattctacttctgttttttttttttttttaattctattttctttttaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG