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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattctgcctgatattttttttcttcttccatcttattatcactgtcttacagtttgaaactcttttgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATATTAAAAACGTTCATGGAGGCCGAGTCAACTTTACCTGCTGGTACATTGA

Basic information

species Glycine max
transcript GLYMA06G43840.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 11
gtgaggattct-gcctgatatt---ttttttcttcttccatcttattatcactgtcttacagtttgaaactcttttgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATATTAAAAACGTTCATGGAGGCCGAGTCAACTTTACCTGCTGGTACATTGA
|| |||||  | || | |  ||   |||  |||  |||  |||   ||||||  ||| ||| |||      ||||  |   |||||||||||| || |||| ||||||||| |||||||||||||| |||||||| ||  | || ||  | || || ||| || || |  || ||||| || | |
gttaggatcatcgcattaacttgagtttcctctctttctctctgtatatcac--tctcacaatttttt-tcctttcctgcaccagAGTTATCAACTTGCAGAAGACTTGGGGAGAGCTTTCTCAGATCGAGCAATTTTGCAGACCTTTTTAGATGCTGAGGCAGCTGTGTCTTCTGGTCCACTTA
















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|192331591|gb|FK023438.1|FK023438
EST:     TCTCAGAATATCAATCTCGTGGAGAAAGCAAAGAGTCTGCCTTCATTCTA                         AGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATA
genomic: TCTCAGAATATCAATCTCGTGGAGAAAGCAAAGAGTCTGCCTTCATTCTAgtgaggattc ... tgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATA
EST: gi|37996941|gb|CF808530.1|CF808530
EST:     TCTCAGAATATCAATCTCGTGGAGAAAGCAAAGAGTCTGCCTTCATTCTA                         AGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATA
genomic: TCTCAGAATATCAATCTCGTGGAGAAAGCAAAGAGTCTGCCTTCATTCTAgtgaggattc ... tgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATA
EST: gi|58023823|gb|CX710564.1|CX710564
EST:     TCTCAGAATATCAATCTCGTGGAGAAAGCAAAGAGTCTGCCTTCATTCTA                         AGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATA
genomic: TCTCAGAATATCAATCTCGTGGAGAAAGCAAAGAGTCTGCCTTCATTCTAgtgaggattc ... tgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcttccatcttattatcactgtcttacagtttgaaactcttttgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATATTAAAAACGTTCATGGAGGCCGAGTCAACTTTACCTGCTGGTACATTGA
                       gtcttac  putative branch site (score: 3)
                                       ctcttttgtcttcc  putative PPT
         atcttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattctgcctgatattttttttcttcttccatcttattatcactgtcttacagtttgaaactcttttgtcttccagAGTTATCAGCTCGCAGGAGACTTGGGCAGAGCTTTCTCAGAACGAGCAATATTAAAAACGTTCATGGAGGCCGAGTCAACTTTACCTGCTGGTACATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG