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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttaaaataattttctttagtcacaatgctgtaatatataaccattttgaagtatgcttgatatacgtttgccttgttgtttgttttggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG

Basic information

species Glycine max
transcript GLYMA15G01360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g06000.t01 (Vitis vinifera), 3'ss of exon 3
-tttttttaaaataattttctttagtcacaatgctgtaatatataaccattttg-aagta-tgcttgatatacgtttgccttgttgtttgttttggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG
 |    | |      || | ||||||    ||||  |  |    ||  |||||| ||||| |  ||  |       |   || ||  || | || | | |||||||||||||||||| ||| | ||||||| ||| | ||| |||||||| ||||| |||| |||||| |
ttaagatgatgcctgttctttttagttc--atgccttggtgc-caatgattttggaagtagtattttgttagtccataatttattcattttgtttgcttatagGAAGCACCTGCTGTGGTTCAGTCTTACTATGATAAAAGAATAGTTGGGTGCCCTGGAGGTGAAGGAG
















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|17400645|gb|BM177427.1|BM177427
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|254322314|gb|GR837728.1|GR837728
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|7589397|gb|AW705172.1|AW705172
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|10253522|gb|BE821288.1|BE821288
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|192320916|gb|FK013110.1|FK013110
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|192333618|gb|FK025435.1|FK025435
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGGTGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|298195945|gb|HO044336.1|HO044336
EST:     GAAGGGATATTCTTGAAATAAACCGTCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|21677694|gb|BQ630045.1|BQ630045
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|254322313|gb|GR837727.1|GR837727
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|33388406|gb|CA851613.1|CA851613
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCCGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|15814678|gb|BI786953.1|BI786953
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|192333647|gb|FK025436.1|FK025436
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGGTGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|14991330|gb|BI317003.1|BI317003
EST:     CTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
genomic: CTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC
EST: gi|5677887|gb|AI939017.1|AI939017
EST:     GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAG                         GAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGATGGATGC
genomic: GAAGGGATATTCTTGAAATAAACCATCCCGTCGGCCCTTTTGGCACAAAGgttagagtta ... tggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattttgaagtatgcttgatatacgtttgccttgttgtttgttttggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG
              gcttgat  putative branch site (score: 5)
                                      tttgtttt  putative PPT
                ttgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttaaaataattttctttagtcacaatgctgtaatatataaccattttgaagtatgcttgatatacgtttgccttgttgtttgttttggttgatagGAAGCACCTGCTGTTGTTAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG