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

...attcattgggttcttttgtcctctagatgattgtgatcctgtaacgtaagctttagcttttgctagttcttattatacatttgatatttgattcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA

Basic information

species Glycine max
transcript GLYMA08G17810.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17810.5 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 3'ss of exon 2
attcattgggttcttttgtcctctagatgattgtgatcctgtaacgtaagctttagcttttgctagttc--ttattatacatttgatatttgat-tcatg-cagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA
||| ||| | ||| |   |     ||   |     ||    |  | |      |  |   ||| || |   | ||| | ||    ||||||| | |  |  ||||||| |||||||| || ||||| ||||||||||| ||||| ||||| || || |||||| |||| 
atttattagattcctccattacacaggctaggtccataaaattgcttggttcct--ccaatgcaagcttaataattttgcaa--aatatttggtgttgtaacagCTGCTAATGGAGTAGTTATTGCCACCGAGAAGAAGTTGCCTTCTATTTTAGTGGATGAAACATCT

upper sequence: GLYMA08G17810.5 (Glycine max), 3'ss of exon 3
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
attcattgggttcttttgtcctctagatgattgtgatcctgtaacgtaagctttagcttttgctagttcttattat-acatttgatatttgattcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA
        | || ||   |  ||||    | |  ||       | |  |  ||||        |   | |  | || |    || | |||  || |||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||||| || 
--------gttttttcaatgatctaatcaaattcga------gaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT

upper sequence: GLYMA08G17810.5 (Glycine max), 3'ss of exon 3
lower sequence: AT1G16470.2 (Arabidopsis thaliana), 3'ss of exon 2
attcattgggttcttttgtcctctagatgattgtgatcctgtaacgtaagctttagcttttgctagttcttattatacatttgatatttgattcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA
              ||||||      ||||| |  ||  | ||  |     |  |   ||||    ||  |  |    | ||| | | | | |   |||||| | ||||||||||||||||| || || ||||| ||||| |||||  |||||||||||||||| 
-------------gtttgtcaatgtcatgat-gaaattgtttatagatcaatgaaaaatttgtagatttcttctgataacttggtttcttact---gcagCTTCTAATGGAGTTGTCATTGCAACTGAAAAGAAGTTGCCTTCTATTCTGGTTGATGAAGCATCT

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|12688055|gb|BG154391.1|BG154391
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|7690855|gb|AW758992.1|AW758992
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|27446035|gb|CA953158.1|CA953158
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|15815476|gb|BI787751.1|BI787751
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|19268728|gb|BM884984.1|BM884984
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|4305924|gb|AI443831.1|AI443831
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|27425474|gb|CA936994.1|CA936994
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|37996790|gb|CF808379.1|CF808379
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGTTTCCGACAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|15285795|gb|BI469686.1|BI469686
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|12687912|gb|BG154308.1|BG154308
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|26058340|gb|CA801254.1|CA801254
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|298195959|gb|HO044350.1|HO044350
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|15000807|gb|BI321621.1|BI321621
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGTATTTTGCCATCTATATTG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAG-AAATTGCCATCTATATTG
EST: gi|8283306|gb|BE020867.1|BE020867
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|26058444|gb|CA801358.1|CA801358
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|13563115|gb|BG551335.1|BG551335
EST:     GCATGCTTTGACGGCTGTCGGTTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTGGTCATTGCTACCGAGACGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|208056326|gb|GD853305.1|GD853305
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|298192268|gb|HO036350.1|HO036350
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|17023069|gb|BM094103.1|BM094103
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|6567102|gb|AW234729.1|AW234729
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|27424967|gb|CA936487.1|CA936487
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|24135847|gb|BU926357.1|BU926357
EST:     GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAG                         CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACGGCTGTCGGGTCTGGACAAACGTCTTTGGGAATTAAAGgtgattgatt ... attcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagctttagcttttgctagttcttattatacatttgatatttgattcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA
                                        atttgat  putative branch site (score: 5)
                     ttcttattatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcattgggttcttttgtcctctagatgattgtgatcctgtaacgtaagctttagcttttgctagttcttattatacatttgatatttgattcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC