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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGACACTTACTTCCAAAGACCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttgcagattttgtggctaatgactattattacatctaaattaatgacttatttccaggatttctcattttaaaatttaaattatggatatgtg...

Basic information

species Glycine max
transcript GLYMA03G40720.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 5'ss of exon 5
GCAAGACACTTACTTCCAAAGACCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttgcagattttgtggctaatgactat-tattacatctaaattaatgacttattt--ccaggatttctcattttaaaatttaaattatggatatgtg
| ||| | |  |||||||  ||| | |||||||||||||| |||||  | || ||  | |||||||| ||||| |||||||||||||| ||||| ||||||||| |   ||   || |     || |  |||  ||  ||| |||||  |    || |||     || |  |    |  ||  ||  |||  ||   ||    
GGAAGGCTCAGACTTCCACTGACAGGTTTGAGATGTGGGGTGATGGCCTCCAGACCCGGTCCTTCACATTCATAGATGAGTGTGTTGAGGGTGTTCTGAGgtatgca--gctacttgtcacattattatctagatagaaca-ctaaacca-cacctgattagatgagaagctggtctaatatgatacaaacaatttctag---

upper sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G124434_T01 (Zea mays), 5'ss of exon 5
GCAAGACACTTACTTCCAAAGACCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttgcagattttgtggctaatgactattattacatctaaattaatgact-tatttccaggatttctcattttaaaatttaaattatggatatgtg------------------------
| ||| | |  || ||||  ||  | |||||||||||||| |||||  | || || || |||||||||||||| || ||||| || || ||||| |||||||||  || |     ||||    || |  | | | |||      |  ||     |   | |   |  | |  || |  | |||  | ||| |       ||                        
GAAAGGCTCAGACATCCACGGAGAGGTTTGAGATGTGGGGCGATGGTCTCCAGACCAGGTCCTTCACCTTCATCGACGAGTGCGTGGAGGGTGTTCTGAGgtatgtct-gtgtgctttggatatactaccaaat-ttaagcaagagctagctgttgcctgtgttgtgtatagcaatggagaatcgacattgtatgacgatgatgcccacactgtgtgcactgcag

upper sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 5
GCAAGACACTTACTTCCAAAGACCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttgcagattttgtggctaatgactattattacatctaaattaatgacttatttccaggatttctcattttaaaatttaaattatggatatgtg
| ||| | |  |||||||  ||  | ||||||||||||||||||||  | || ||  | || || ||||| || ||||||||||||||||||||||| ||||     |  |   |  ||| | | | |     | ||| |  ||| |   |||  ||||| |   |||| |  ||||| |                    
GGAAGGCTCAGACTTCCACTGATAGGTTTGAGATGTGGGGAGATGGGCTTCAGACCCGTTCTTTTACCTTTATCGATGAGTGTGTTGAAGGTGTACTCAGgtgagggtatctcctgatgttgatgaagttgtatgttagacgtaattggctga--tattttcgtcattttt-gttttatag-------------------

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|16995884|gb|BM085256.1|BM085256
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
EST: gi|298178228|gb|HO023963.1|HO023963
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
EST: gi|13788218|gb|BG650810.1|BG650810
EST:     CTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
genomic: CTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
EST: gi|20448810|gb|BQ252934.1|BQ252934
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
EST: gi|298167582|gb|HO012845.1|HO012845
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATCGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT
EST: gi|193313333|gb|FK278672.1|FK278672
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCGGTGAATATTGGAAGTGATGAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGACACTTACTTCCAAAGACCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttgcagattttgtggctaatgactattattacatctaaattaatgacttatttccaggatttctcattttaaaatttaaattatggatatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG