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

...ttgtgtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT

Basic information

species Glycine max
transcript GLYMA08G09570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 3
ttgtgtgtgtcaatagtatcatgtt-ctgaagtatttttggtcagtttgaaatca--agttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT
   |   |||  ||  ||| ||||  |   | |   | |   |  | | |||| |  | |  ||  |||  |      ||  | | |  |       || |||||||||| ||||||||||| || |||||||| || ||||| || |||||||||||  |||||||||| || || |||||||||
---tccttgttgattatattatgtaaccatacttcctatatgctatgttaaattagtactccatagacttcataccaatgagttttaccatgacatgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT

upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g05080.1 (Oryza sativa), 3'ss of exon 3
------ttgtgtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT
      ||     | |  ||  ||| |||||  | ||  ||  |  |   || | | || |     || || |  || |    ||||   |||| |    || |||||||||| |||||||||||||| ||||| || || || || || |||||||||||  |||||||||| || || || ||||||
tttatgttacccttatgcattttattatgtta-gcagacttcctaatgctttagtagtccatagacttcacac--ggctgaattttactctgacatg---ttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT

upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008232_T01 (Zea mays), 3'ss of exon 2
---ttgtgtgtgtcaatagtatcatgttctgaagtatttttggt-cagtttgaaatcaagttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT
      |     | | | ||      ||      ||  || | | | |||    |||  | || || | | |   |  | |||| |  |   ||       |||| || || || |||||||| |||||||| |||||||||||||| || ||||||||| |||| |||||||| || || || |||
ctgcaatccccattatttgtgctgcattacttcatacattagttactgttgttgatcctgatggttcattatcaatact-gtttgttgt---ttcatgccacagAGACGACAGTTAAACAAATCGAGGATGCGTTCAAAGAATTTACTACGAGGGAGGATATTGCTATTGTGCTCATCAGTCAGTAT

upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G158766_T02 (Zea mays), 3'ss of exon 3
-ttgt-gtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttact--ctaggtttttgtttatcatgactttgatttt-cagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT
 || | |  || |   || | || | |       ||  ||| |   | |    |     ||||  | |   |  || |   |  |   ||  ||| |||   |||| || || || |||||||| ||||| || ||||||||||||||  ||||||||||| |||| |||||||| || || || |||
tttatagcatgccttcagcaacagggttc-----atgcttgtttcctctactgttgcaatgatccaatggtttagtatgaatacagtttgttttttattccacagAGACGACAGTTAAACAAATCGAGGACGCGTTCAAAGAATTTACTGCAAGGGAGGATATTGCTATTGTGCTCATCAGTCAGTAT

upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
ttgtgtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttactctaggttt-ttgttta------tcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT
    |||  |        |  ||| |     | | |||   |||| |  ||| ||||| ||  |   |   ||  |||  ||      ||||    ||  || | |||||||||||| ||||||||||| ||||||||||| ||||| || |||| ||| ||  |||| ||  |  | || |||||||||
----gtgaattgggcaacttgtgtacccttatttattt---cagtatctaatgaagtttatcaatggtcatttcattggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT

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|192319436|gb|FK005876.1|FK005876
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAATTTTCA                   
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTC--A-----Agtatgccact ... tgat
EST: gi|192319436|gb|FK005876.1|FK005876
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAATTTTCA                   
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTC--A-----Agtatgccact ... tgat
EST: gi|209720495|gb|BW674678.1|BW674678
EST:     GGAAATGTTGACATACGGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCGTTCAAAGAATTTACAACAAGGC
genomic: GGAAATGTTGACATACG-TAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|254338552|gb|GR845695.1|GR845695
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|9984254|gb|BE658362.1|BE658362
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|31470010|gb|CD412038.1|CD412038
EST:     GGGAAATGTTGACATACGTAGGAAGACCAATTACCTCATTGTGGATTCAT                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|21887354|gb|BQ740567.1|BQ740567
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|193682983|gb|FK625131.1|FK625131
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACCGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|58016543|gb|CX703285.1|CX703285
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|298198565|gb|HO040104.1|HO040104
EST:     GGGAAATGCTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|6952212|gb|AW424280.1|AW424280
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|192294996|gb|FG986715.1|FG986715
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|207759516|gb|GD733931.1|GD733931
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACCGTCAAACAA
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAA
EST: gi|193363933|gb|FK332147.1|FK332147
EST:     GGAAATGTTGACATACGTAGGAAGTACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGAAATGTTGACATACGTAGGAAG-ACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|213611466|gb|DB984002.1|DB984002
EST:     ATTGTGGATTCAA                         AAACAACTGGCAAACAAATTGAGGATGCATTCAAAGAATTTACTTCAAGGG
genomic: ATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|213604582|gb|DB966669.1|DB966669
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|8284082|gb|BE021641.1|BE021641
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|193347072|gb|FK311404.1|FK311404
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATTGTCATTCAAAGAATTTACAACAAG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGAT-G-CATTCAAAGAATTTACAACAAG
EST: gi|298165832|gb|HO008803.1|HO008803
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|213604487|gb|DB983519.1|DB983519
EST:     AGACAAATTACCTCATTGTGGATTCAA                         AAACAACAT-TCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGG
genomic: AGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAAC-TGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGG
EST: gi|13311850|gb|BG405501.1|BG405501
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|208299834|gb|GE099613.1|GE099613
EST:     GACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|298182781|gb|HO031516.1|HO031516
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|15813300|gb|BI785575.1|BI785575
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|6724545|gb|AW308944.1|AW308944
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|13252581|gb|BG363484.1|BG363484
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|254338553|gb|GR845696.1|GR845696
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|12497052|gb|BG047373.1|BG047373
EST:     GNAAATGTTGACATACGTAGGAAGACAAATTACCCTCATTGTGGATTCAA                         ACACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGAAATGTTGACATACGTAGGAAGACAAATTA-CCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|213594238|gb|DB966139.1|DB966139
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
EST: gi|193413995|gb|FK376589.1|FK376589
EST:     GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA                         AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG
genomic: GGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAAgtatgccact ... tgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaatcaagttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT
                                          ctttgat  putative branch site (score: 5)
                                                ttttc  CT-rich tract
                          tttttgtttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- gtgtgtg
- - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - aaatcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgac