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

...aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA

Basic information

species Glycine max
transcript GLYMA11G37650.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 6
aaataaagaactccgtctagcag--gattttcttacctgctgcactttcaattcagttagcacattta---taagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA
      | | |    ||||| ||    |||| |    |  |  || |   | |  |  |        |   |   ||   ||  | ||| |||      |  ||||| ||||| ||||| ||||| || ||||| ||  |||| || || |||||||| || || ||||||||||| ||||| ||||| |||||||||||||   
----gcatatcaatatctagtagtctgttttgtggttttataaacatattaattggacactgttcccagcctcccacattaaatagtttgaattgctcgtg-cagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAGAAAGTTGCTATGTTAATCGGAAAATGGGATGAAGCTATGTATTATGTTCTTGGGGATCCAAGTG

upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
----aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA
    || | |  | |   |||||   | |  |    |    ||  | | || |||   |     |     |  |||  |||    || ||||| | | |  ||||| ||||| ||||| ||||| || ||||| ||  | || ||||| ||||||||||| || ||||||||||| ||||| ||||| |||||||||||||   
ggttaagttagcagca--gtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattg-ttctaatcatttgtg-cagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG

upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA
                 ||| || ||  | ||   | |||   ||    |    | | ||    | |||             |  ||| |  ||   ||||| ||||||||||| |||||||||||||| || ||||| ||||| ||  | || || || |||||||||||||||||||||||| | || ||||| || |
----------------gtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaa------------tggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA

upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacattt--ataagactgaaagaacttttaatcttata-taacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA
    |||     |  ||   | | ||         |     | |         | ||  | |  |  |||    | ||   || |||     |||| |  ||||| ||||| ||||| ||||| ||  ||||||||||||||||||| |||||  | ||||| |||||||| |||||||| |||||  | || |||||||| |
---caaacggtgctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA

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|207683729|gb|GD665032.1|GD665032
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAGgtaggattat ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|13181499|gb|BG352839.1|BG352839
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAGgtaggattat ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|207799951|gb|GD768292.1|GD768292
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAAAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAGgtaggattat ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|51341985|gb|CO983302.1|CO983302
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAGgtaggattat ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA
                                    ttttaat  putative branch site (score: 3)
                             aaagaacttttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
aaataaa
- - - - - ctccgtc
- - - - - - - - - - - - - - - -tacctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaag