Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgaagttttctctagtataaaaattacaaatagtctttaagggtttcatataaattatttgtcacccatggcaataggattccactttcttgc...

Basic information

species Glycine max
transcript GLYMA13G21480.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 5'ss of exon 12
GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgaagttttctctagt--ataaaaattacaaatagtctttaagggtttcatataaattatttgtcacccatggcaataggattccactttcttgc
|||||||| ||||| ||||| ||||||||||  || || ||||||||| | ||| |||| |||||||| ||||| ||||||||||| ||||| ||||| ||| |  | |    || |  |    ||   |  || | |  || |   ||  | |  ||| | |   |    |   |||   |||     |     ||||||
GCAAAGGGAATGAACTATCTACATAAACGTAGCCCTCCTATTGTTCATCGTGATTTGAAGTCTCCAAATCTTCTAGTTGACAAGAAGTATACCGTGAAAgtatgtttcataacttatacacctgattgcagctagacagggtatgatagtatgttttatgagtgcatgagtag--atgattataaatcacgttgatcttgc

upper sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 11
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 11
GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgaagttttctctagtataaaaattacaaatagtctttaagggtttcatataaattatttgtcacccatggcaataggattccactttcttgc--
|| ||||| |||||||||||||| || || ||||| || ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||||  ||||  |  ||     | | |       |    |    |||     ||| ||     || |  | ||  | |    |||  |||    ||| |     
GCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAGgtttgaatctaaattagaa-attgttgtgtccaatgttttgattttgatattttattcctcttgtgagacaagcttatatataa-attatgatttttaattc

upper sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 11
GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgaagttttctctagtataaaaattacaaatagtctttaagggttt-catataaattatttgtcacccatggcaataggattccactttcttgc
|| ||||| |||||||||||||||||||| ||||| |||||||||||| ||||| |||| |||||||||||| | |||||||| ||||| || |||||||||||| || | | | ||  ||  |  ||  || |  |   |||  |   |     |   |   |  |          ||  |    ||    |||     
GCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAGgtaagagtggaatat-cttgagcttgcaagatagacgtctacttcgataatcaatgttctagccaccttagttttgctgccttgcactttttgttttgatt

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|9820117|gb|BE555627.1|BE555627
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatga ... ctttttgtagGTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
EST: gi|21888649|gb|BQ741862.1|BQ741862
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatga ... ctttttgtagGTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
EST: gi|51335181|gb|CO979047.1|CO979047
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatga ... ctttttgtagGTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
EST: gi|19271170|gb|BM887426.1|BM887426
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatga ... ctttttgtagGTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
EST: gi|51344716|gb|CO985449.1|CO985449
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatga ... ctttttgtagGTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC
EST: gi|254346794|gb|GR856516.1|GR856516
EST:     AGAAATATACAGTGAAG                         GTTTGTGATTTTGGGCTTTCACGTCTGAA-GACAATACGTTTCTCTCATCC
genomic: AGAAATATACAGTGAAGgtaagaatga ... ctttttgtagGTTTGTGATTTTGGGCTTTCACGTCTGAAGGCCAATACGTTTCTCTCATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgaagttttctctagtataaaaattacaaatagtctttaagggtttcatataaattatttgtcacccatggcaataggattccactttcttgc

- - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA