Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggtctcagaacatggttctaggctagctgttggttccatctgcaaatttctataacagttttggattccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACATATCTTTGGTGGCTGCTAATACGACCACTATTGAG

Basic information

species Glycine max
transcript GLYMA03G02930.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G02930.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ09911 (Selaginella moellendorffii), 3'ss of exon 4
gtagggtctcagaacatggttctaggctagctgttggttccatctgcaaatttctataacagttttggattccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACATATCTTTGGTGGCTGCTAATACGACCACTATTGAG
                |   ||   ||  | |  |   ||  |||| || |  |  |     | |||| ||     ||||  || | |||||||||||||| |||||  | || ||||||||||||||||||||||| || ||||  || || ||||| ||||||
---------------gtcagtcgttgc-ggtttctttctcattctgaaactcgcccttttcctcttggctt-----cagTCCTAGATCTGGCCTTTGCACTCAGCGTACTTGGTTTTCTCATCATGCACATATCTTTAGTCGCTGGAAACACCACCACCATTGAG

upper sequence: GLYMA03G02930.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ04865 (Selaginella moellendorffii), 3'ss of exon 4
gtagggtctcagaacatggttctaggctagctgttggttccatctgcaaatttctataacagttttggattccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACATATCTTTGGTGGCTGCTAATACGACCACTATTGAG
                |   ||   ||  | |  |   ||  |||| || |  |  |     | |||| ||     ||||  || | |||||||||||||| |||||  | || ||||||||||||||||||||||| || ||||  || || ||||| ||||||
---------------gtcagtcgttgc-ggtttctttctcattctgaaactcgcccttttcctcttggctt-----cagTCCTAGATCTGGCCTTTGCACTCAGCGTACTGGGTTTTCTCATCATGCACATATCTTTAGTCGCTGGAAACACCACCACCATTGAG
















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|192301934|gb|FG995552.1|FG995552
EST:     AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCG                         TTTTAAACCTGGCCTTTGCACTGAGCGTCTTAG-ATT-CTCATCATGCACA
genomic: AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCGgtagggtctc ... ttccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACA
EST: gi|27424346|gb|CA935866.1|CA935866
EST:     AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCG                         TTTTAAACCTGGCCTTTGCACTGAGCGTCTTA
genomic: AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCGgtagggtctc ... ttccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTA
EST: gi|15287842|gb|BI471733.1|BI471733
EST:     AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCG                         TTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACA
genomic: AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCGgtagggtctc ... ttccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACA
EST: gi|151408618|gb|EV278426.1|EV278426
EST:     AGAAATTCCTGGAACACCTGGTTCTCTTGCTACAACTTTTCTTGCTTTCG                         TTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACA
genomic: AGAAATTCCTGGAACACCTGGCTCTCTTGCTACAACTTTTCTTGCTTTCGgtagggtctc ... ttccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctagctgttggttccatctgcaaatttctataacagttttggattccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACATATCTTTGGTGGCTGCTAATACGACCACTATTGAG
                             ctataac  putative branch site (score: 3)
                       aaatttctataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggtctcagaacatggttctaggctagctgttggttccatctgcaaatttctataacagttttggattccgtgcagTTTTAAACCTGGCCTTTGCACTGAGCGTCTTAGGATTTCTCATCATGCACATATCTTTGGTGGCTGCTAATACGACCACTATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT