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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaacttggaagaatgtaaagctttctccatgagttttttgtgttgcatacttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA

Basic information

species Glycine max
transcript GLYMA20G23670.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 5
gtagaacttggaagaatgtaaagctttctccatgagttttttgtgttgcatac-ttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA
   | | || |  | | | | |   ||     |  |||| |    |||   |  ||  ||  |||| | |||   |  ||   |||   | |||||||||| |||| ||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| ||||| |||||||||||||
---gtattttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattctgatattgaatttag---atcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA

upper sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S291_29V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gtagaacttggaagaatgtaaagctttctccatgagttttttgtgttgcatacttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA
         |   | ||      ||   ||  | |    |  |  | |  |       ||||||  ||   || |    |          |  || || |||||| ||||||| | ||||||||||| ||||| ||||  || ||||||||||| ||||| |||||  | || ||||| |||||  | ||| | |  || |
gtatgcatatgtgaatttcttacattcgaacatctgctgactatatctcagcagcttctacttgacagaacgattaatcctgttcagaggtgcttttgtagGTTCTAGCTGCTCGAGATGAAATGCAGTGGGGAGAGGCTGGGCCACCTCCATTACTGGTGAAAATCTCACCCGATTTATCAAAGCAGGACTTGGCGGACA

upper sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S29_152V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gtagaacttggaagaatgtaaagctttctccatgagttttttgtgttgcatacttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA
             | ||  | | ||    |   |    |  | | | |    ||    | |||  ||   |    ||       |  |  |  |  |  |||||| ||||||| | ||||||||||| ||||| ||||  || || ||||| || ||||| ||||||||||| |||||||||||  | ||| | |  || |
gtactgatacgtgagttttatgtattctgattatctgtctggcggtatcgaggtaatctccttttgacagtacaactgattcggta-gtatactcttacagGTTCTAGCTGCTCGAGATGAAATGCAGTGGGGAGAGGCTGGTCCGCCTCCGTTACTGGTGAAAATTGCTCCTGATTTGTCAAAGCAGGACTTGGCTGACA

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|26058429|gb|CA801343.1|CA801343
EST:     CTTGTGAAGAAG                         GTTCAAGCTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCA
genomic: CTTGTGAAGAAGgtagaacttg ... ttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCA
EST: gi|17022514|gb|BM093548.1|BM093548
EST:     GCATGCTTCAAGGAAGAAAGCAATTGAAGGATCTTGTGAAGAAG                         GTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCA
genomic: GCATGCTTCAAGGAAGAAAGCAATTGAAGGATCTTGTGAAGAAGgtagaacttg ... ttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCA
EST: gi|12691517|gb|BG157853.1|BG157853
EST:     GTTTGCGCATGCTTCAA-GAAGAAAGCAATTGAAGGATCTTGTGAAGAAG                         GTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCA
genomic: GTTTGCGCATGCTTCAAGGAAGAAAGCAATTGAAGGATCTTGTGAAGAAGgtagaacttg ... ttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgttgcatacttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA
                     gcttgac  putative branch site (score: 4)
                                      tttgccttttt  putative PPT
                                  aaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaacttggaagaatgtaaagctttctccatgagttttttgtgttgcatacttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA