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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtgctctgttcttatccaatttactgacaaattattgtttaatgaggatcttgtattatcacagcattaattgaaatctgtttcttgttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATGCAATATCATCTACCAATTATCAATCAACTACTTCATTTGTTGACAATCA

Basic information

species Glycine max
transcript GLYMA0048S00320.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 9
--acagtgctctgttcttatccaatttactgacaaattattgtttaatgaggatcttgtattatcacagcatta-attgaaatctgtttcttgttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATGCAATATCATCTACCAAT--TATCAATCAACTACTTCATTTGTTGACAATCA
  | |   |||| ||  |   | |||     |     |    ||||  ||| |  | | |||    |     |   ||||    | ||  ||  ||  |  ||| ||| | |||||||||||||||||||| ||||||||||| |  || |  ||    ||| || ||||   ||  | | ||  ||     ||| |     |  
gtatatcactctctttatcaactattagtgtattgtgtggattttagagagaagttagcattgcttcctttctgtgttgaggctttttcttttcttgttgtagCTCCAATGCATGGTTTTGCATTTTGGTTCGACGTTGAATTCAGCGGACCGGCCTCTTCACCTGCCAAGAATACTAGTGAA--ACCAGTATTGCTAGTGGTTC

upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0071g00750.t01 (Vitis vinifera), 3'ss of exon 10
acagtgctctgttcttatccaatttactgacaaattattgtttaatgaggatcttgtattatcacagcattaattgaaatctgtttcttgtttt---ctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATGCAATATCATCTACCAATTATCAATCAACTACTTCATTTGTTGACAATCA
||  | |||| | | |   || |  | | | |  || ||    |||||  | ||||   ||| | |  ||| ||   | |    || ||||  |    |||||| ||| | ||||| ||||| || ||||||||||||||||| ||||||| |||||| |   |||||| |  | | ||  |  | |  ||| |||    |  
act-tactctttaccttctcattacattaagatgttctttgccaatgataaacttga--tataaaaatattcatgttacttctatttttgtcctgatttccagCTCCACTGCATGGGTTTGCTTTCTGGTTTGACGTTGAATTCAATGGGCCTGCAATTTTTCCTACCAGTACTGATTCTCCATCCTTGTTTATTGGATCTTC
















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|58015381|gb|CX702123.1|CX702123
EST:     GAGTTTAGAATCTGTACCAGCCAAGTTTAAGTTCAATTCCATGATGCGAG                         CACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
genomic: GAG-TTAGAATCTGTAACAGCCAAGTTTAAGTTCAATTCCATGATGCGAGgtaccctcct ... ttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
EST: gi|208035428|gb|GD832482.1|GD832482
EST:     AGAGTTAGAATCTGTAACAGCCAAGTTTAAGTTCAATTCCATGATGCGAG                         CACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
genomic: AGAGTTAGAATCTGTAACAGCCAAGTTTAAGTTCAATTCCATGATGCGAGgtaccctcct ... ttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
EST: gi|193398322|gb|FK364678.1|FK364678
EST:     TCAATTCCATGATGCGAG                         CACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
genomic: TCAATTCCATGATGCGAGgtaccctcct ... ttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
EST: gi|193577963|gb|FK533795.1|FK533795
EST:     AGTTCAATTCCATGATGCGAG                         CACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
genomic: AGTTCAATTCCATGATGCGAGgtaccctcct ... ttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
EST: gi|58015722|gb|CX702464.1|CX702464
EST:     CCAAGTTTAAGTTCAATTCCATGATGCGAG                         CACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
genomic: CCAAGTTTAAGTTCAATTCCATGATGCGAGgtaccctcct ... ttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
EST: gi|193604571|gb|FK560348.1|FK560348
EST:     AGAGTTAGAATCTGTAACAGCCAAGTTTAAGTTCAATTCCATGATGCGAG                         CACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG
genomic: AGAGTTAGAATCTGTAACAGCCAAGTTTAAGTTCAATTCCATGATGCGAGgtaccctcct ... ttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaggatcttgtattatcacagcattaattgaaatctgtttcttgttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATGCAATATCATCTACCAATTATCAATCAACTACTTCATTTGTTGACAATCA
                      cattaat  putative branch site (score: 3)
                                  tctgtttcttgttttc  putative PPT
                       attaattgaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtgctctgttcttatccaatttactgacaaattattgtttaatgaggatcttgtattatcacagcattaattgaaatctgtttcttgttttctccagCACCATTACATGGTTTTGCATTTTGGTTTGACGTTGAATTTAATGGGCATGCAATATCATCTACCAATTATCAATCAACTACTTCATTTGTTGACAATCA

- - tgctctg
- - - - - - - - - - - - tactgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacagca