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

...taagagtgttatgtcttcttttctctgatttgttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC

Basic information

species Glycine max
transcript GLYMA20G32790.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g73680.1 (Oryza sativa), 3'ss of exon 7
taagagtgttatgtct-----tcttttctctgattt-gttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
  ||  |||    |||     ||||| || |  |   | |||||  | |  || | ||||| | ||||   | |||  ||||  | |   | ||   |   |  |||||||||  || || ||||| ||||| ||||| ||||| || ||||| |||||||||||||| |||||||| || || ||||||||||| ||| |||| |
-cagcatgtgtcatctagaagtctttacttttgtaaagctgatttgtctt-tagaatacatgaatgag---tttgaggaattgcactg-atgtatatagcttatagGAATTTGTTGTAAGGAATGATATGGGCTGTGGTTCAACTATTGGCCCCATACTTGCTTCTGGTGTTGGCATACGGACTGTTGACTGTGGTATTCCTCAGC

upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G061127_T01 (Zea mays), 3'ss of exon 3
taagagtgttatgtcttcttttctctgatttgttg-attattatagtatattacataactga-ggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
||| | |||||  |  |       |    |  |   |  || |  |    || |     ||| ||  | || |    |     |  | ||   |      |||||||||  || || ||||| ||||||||||| || || || || || |||||||||||||| |||||||| || || || |||||||| ||  |||| |
taaaaatgttaaatgctagagaaacaagatgataacacaatcactgagccttccgc--ttgatggtttttggagtgatttgactgatgtaaataccacacagGAATTTGTTGTGAGGAATGATATGGGATGTGGCTCCACTATTGGACCCATACTTGCTTCTGGTGTTGGCATACGGACTGTAGACTGTGGTATCCCTCAGC

upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G04710.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------taagagtgttatg--tcttcttttctctgatttgttgattattatagtatattaca--------taactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
               |||   |   |||  ||| |   ||   ||| |  |   |  | |    || | ||        |||    |  ||    | | ||| |||||  ||| |    ||| |||| |||| ||| ||||| || ||||||||||| ||||| ||||| || ||| | ||||| ||||| || |||||||| ||||| ||||| || ||||| |
gttaggtgttcttcttaatgttaagatgaatctacacatcatagatcttctagatgctctgcactaatccacccacatttaagaatgaaatactgacatttagatttttgctattt---ctgcagGAGTTTGTGGTGAGAAACGATATGGGATGTGGTTCAACAATAGGACCTATATTGGCTTCAGGAGTAGGGATCCGAACCGTTGATTGTGGCATAGCTCAGC

upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0106g00700.t01 (Vitis vinifera), 3'ss of exon 8
taagagtgttatgtcttcttttctctgatttgttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaa---ctgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
  ||| | |   |   |   ||   || ||   |  |  | ||   |   |  | || |||| || | ||||    |  |  |  | | |||     ||| |||||||||  || ||||| || |||||||||||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| ||||| |||||||| |
--agaatatatagaggtagattacatgtttcactt-tcttcatttcaagatttaaaattgagacaccagaaactgcatctacttaccattcatttctctgtagGAATTTGTTGTGAGAAACGATATGGGATGTGGATCTACCATAGGTCCCATACTAGCTTCTGGGGTTGGCATCCGCACTGTTGATTGTGGTATTGCTCAGC

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|16347296|gb|BI972891.1|BI972891
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         GAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
EST: gi|151401885|gb|EV271698.1|EV271698
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         -AATTTGCGGTTAGAA-TGACATGGGATGTGGATCAACCATAG-CCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
EST: gi|14258779|gb|BG881687.1|BG881687
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         GAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
EST: gi|10232725|gb|BE801613.1|BE801613
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         GAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
      acataac  putative branch site (score: 3)
                                       tctactc  putative PPT
                   atctgaaaaattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagagtgttatgtcttcttttctctgatttgttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC

- -gagtgtt
- - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaaa