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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttaacattcttcctcatggtttttacttttttactatgatttttctgtgtttgaccaaatattcaaatgtgattgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT

Basic information

species Glycine max
transcript GLYMA11G02410.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G25740.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattttaacattcttcctcatggtttttacttttttactatgatttttctgtgtttgaccaaatattcaaatgtgattgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT
||| ||| | | ||    | | ||   | | |  | | |    ||||      | | |||   | | ||      |  ||||||||   || || |||||||||| ||| |||||  |         ||||||||||||||||||||||||||| ||||| ||   || ||   |    || |     | |
gtagtttcatctttaaatcccttgacctgtccggtctga--gggattggctaatttctgat--attgttttggctt--ttgttttc---agAGGACCACCTCGCTCTGATGGAGACCGTCCCAGATTTGGTGACCGTGATGGATACCGTGGAGGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCT

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G25740.2 (Arabidopsis thaliana), 3'ss of exon 3
---------gtaattttaacattcttcctcatggtttttacttttttactatgatttttctgtgtttgaccaaatattcaaatg----tgattgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT---------------------
         || ||    | |       ||||  ||    |  ||   || |    | |  | | ||| | || |  | | ||     ||  | || |   ||| || |||||||||| ||| |||||  |         ||||||||||||||||||||||||||| ||||| ||   || ||   |    || |     | |                     
gcccacctggtgatcgccaaaggtagtttcatctttaaatcccttgacctgtccggtctgagggattggctaatttctgatattgttttggcttttgttttcagaggaccacctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------------gtaattttaacattcttcctcatggtttttacttttttactatgatttttctgtgtttgaccaaatattcaaatgtga-ttgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT
                                                                                                             ||| | ||      ||    ||| ||    | ||||  | |    ||  | || |  |  |    ||    ||  | ||||  |   ||| || |||||||||||||| ||||| ||   |     ||||||||| ||||| ||||||||||||||||| ||||||   ||||| || ||||||||||||
gtaatgactcaattttgagttgatgttcggtgatttatttatttatttatttatttattattctgttgttaaacaatttggtgcgcattggggttaatggtttgattacaatgtgaattgggatctgtttggattgccatgttttgtttttgagttcttatgatgtaaaatgggttttgttgaaaattgtgattttcagTGGTCCACCTCGCTTTGAAGGAGATAGACCAAGGTTTGGTGACCGGGATGGGTACCGTGGAGGTCCACGAGGACCTCCAGGTGAGTTTGGTGACAAGGGT

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|58014465|gb|CX701207.1|CX701207
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|208101481|gb|GD899022.1|GD899022
EST:     CGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: CGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|31475522|gb|CD417550.1|CD417550
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|22927028|gb|BU544167.1|BU544167
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|18041054|gb|BM309348.1|BM309348
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|9899073|gb|BE608041.1|BE608041
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|193471045|gb|FK436972.1|FK436972
EST:     CGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: CGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|208298767|gb|GE096292.1|GE096292
EST:     GCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|208234989|gb|GE028293.1|GE028293
EST:     CGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: CGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|254342456|gb|GR858618.1|GR858618
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|193335326|gb|FK299340.1|FK299340
EST:     GCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|11411498|gb|BF423509.1|BF423509
EST:     GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GCCAAGCCCGCGGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
EST: gi|18734547|gb|BM528246.1|BM528246
EST:     GGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAG                         GGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG
genomic: GGGAAGACCATTCGGTGGCCCACCCGGTGATCGCCCCAGgtaattttaa ... ttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactatgatttttctgtgtttgaccaaatattcaaatgtgattgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT
                  gtttgac  putative branch site (score: 4)
                                          ttgttttc  putative PPT
                          aaatattcaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttaacattcttcctcatggtttttacttttttactatgatttttctgtgtttgaccaaatattcaaatgtgattgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG