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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacttgagacctctagattttgtagctctcatgtgcatagctgtttatattatgttttattatttggaatatttaaacttttatctttgtcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAAAAGCTGCAGTGGTTTTTAGATGCAGTGAAGGAGCTTCCTAATG

Basic information

species Glycine max
transcript GLYMA03G33830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33830.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12224 (Selaginella moellendorffii), 3'ss of exon 2
aaacttgagacctctagattttgtagctctcatgtgcatagctgtttatattatgttttattatttggaatatttaaacttttatctttgtcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAAAAGCTGCAGTGGTTTTTAGATGCAGTGAAGGAGCTTCCTAATG
                                        |    |  | ||    |||   || | |  |  |    ||   || ||| |     | |||||||||||||||| || || || || || ||||| || ||||||||| | || || ||||| ||||||||||| ||||   | ||  ||| ||| ||||
----------------------------------------gtgagtggtgtttcaattt--catctagcgtgctcgcgctca-atgtttctt----tcagGTTCATCCTTATGTCGCGACAGGCAACAAAAACTCCAAGTTTGGCATTCGCAACGAGAAGCTCCAGTGGTTTTTGGATGAGATAAAACAGCATCCCAATG
















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|7590650|gb|AW706398.1|AW706398
EST:     GGATTAACCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGATTAACCCTGATGTGGATCCACAGgtatgttgtt ... tcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|193355263|gb|FK321780.1|FK321780
EST:     AAGAAGGTCAAATAGTTTTACTTCGGATTAACCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: AAGAAGGTC-AAT-GTTTTACTTCGGATTAACCCTGATGTGGATCCACAGgtatgttgtt ... tcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|308098900|gb|HO760741.1|HO760741
EST:     GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTTGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAGgtatgttgtt ... tcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|192325345|gb|FK017146.1|FK017146
EST:     GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAGgtatgttgtt ... tcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|14258605|gb|BG881513.1|BG881513
EST:     GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAGgtatgttgtt ... tcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|192320763|gb|FK013853.1|FK013853
EST:     GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GAAAGAAGGTCAATGTTTTACTTCGGATTAACCCTGATGTGGATCCACAGgtatgttgtt ... tcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatattatgttttattatttggaatatttaaacttttatctttgtcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAAAAGCTGCAGTGGTTTTTAGATGCAGTGAAGGAGCTTCCTAATG
                                 cttttatctttgtc  CT-rich tract
     ttatgttttattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacttgagacctctagattttgtagctctcatgtgcatagctgtttatattatgttttattatttggaatatttaaacttttatctttgtcgtggttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAAAAGCTGCAGTGGTTTTTAGATGCAGTGAAGGAGCTTCCTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT