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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaacttaacatcttgatactggctgaaatttcttacttgggttgaagattggttgcacaatttgtttttcactaaaagcatggaatttcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGAGATTTCATGTTTAG

Basic information

species Glycine max
transcript GLYMA20G16030.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16030.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0041g00100.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------------gtagaacttaacatcttgatactggctgaa-------atttcttac--ttgggttgaagattggttgcac---aatt------tgttttt-----cactaaaagcatggaatttcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGAGATTTCATGTTTAG
                                                               || |   ||  |||||  |  ||  |  |       || || |    |   | | ||   || ||  ||   ||||      |||||||      ||| ||| |||  | ||| || || || || ||| | |||||||||||||||||||||||||| ||||||||  |||||||||| ||| | |
gtatattattttctcttgttgctttctttatttctttatttttttaaatttctttataaatcttaaagagtagtatcttagtggtgtatctaccatcacatctcctgtgatcatgataaatcctgtttttactagaattatgtcctgtttttgtaattactgaaaacataaactttgttgaatagGCCTCCTTCCTGTTTAGTTCCTGGTGCTGGACTTGGGCGGCTGGCATTGGAGATTTCCTGTCTTG
















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|7685675|gb|AW756323.1|AW756323
EST:     CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAG                         TCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
genomic: CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAGgtagaactta ... tcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
EST: gi|308098770|gb|HO760511.1|HO760511
EST:     CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAG                         TCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
genomic: CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAGgtagaactta ... tcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
EST: gi|7146905|gb|AW508827.1|AW508827
EST:     CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAG                         TCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
genomic: CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAGgtagaactta ... tcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
EST: gi|9204212|gb|BE330436.1|BE330436
EST:     CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAG                         TCCACCTGCATGTTTAGTACCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA
genomic: CCTATACTTGACGAGCTTAATATGCTATTCCCTAATCGCAGTAAAGATAGgtagaactta ... tcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagattggttgcacaatttgtttttcactaaaagcatggaatttcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGAGATTTCATGTTTAG
                           cactaaa  putative branch site (score: 2)
                                           tttctt  putative PPT
                aatttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaacttaacatcttgatactggctgaaatttcttacttgggttgaagattggttgcacaatttgtttttcactaaaagcatggaatttcttaaacagTCCACCTGCATGTTTAGTTCCTGGTGCTGGACTTGGTCGGCTGGCCCTGGAGATTTCATGTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT