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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctcaaattatctgtgtttcagctttcgggtagggcttgttcaaaagctacttagatattagtgctcaaattctaaagctggtgcagtaactgg...

Basic information

species Glycine max
transcript GLYMA12G02920.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G02920.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G17330.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctcaaattatctgtgtttcagctttcgggtagggcttgttcaaaagctacttagatattagtgctcaaattctaaagctggtgcagtaactgg--------------------------------
|||| || || ||| |  |||||   | |    ||||     ||||||||||||| || || |||||||||||||| |||||||| ||||| || |||||||      |   |  | | | |    ||||| |    |   |||   || | || ||| ||| | | ||   |||||||  |  |  || | |   ||                                 
GTTTTAAAGACGAATTAGCAGGAGTAGCACTCTGTGAGTCTCTTCCAGAATTTGGGGTAGTTCAAGATGCTGATCGCCTTGATGCAATTGGCGCCATAGgtaagaatacgtctcttttctttagttgcttttgatatgtcattgccaaatatctgctttgatgtca-tgtgaaaattctctatgttatggaatttgtgctattagttgttgttgatctctttctgttatag

upper sequence: GLYMA12G02920.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0011g02070.t01 (Vitis vinifera), 5'ss of exon 5
GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctcaaatt-atctgtgtttcagctttcgggtag---ggcttgttcaaaagctacttagatattagtgctcaaattctaaagctggtgcagtaactgg
||||||| || ||| |  ||||   ||  ||| |||||     |||||| ||||| ||||| |||||||||||||| |||||||| |||||||| || ||||  || | || || |   ||| || |  ||    ||     | | | |  ||| ||||   |  |  ||||    |||   | | | | ||| | |    | 
GTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTGgtaagttttgaattttacgagtgctttaatttgatagtcatttgacctatctaaa-gctaaa-acttgatagtagataaaacattaggattgtg-attggtag-
















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|151398243|gb|EV268121.1|EV268121
EST:     ATTTGGAGTTGTGCAGGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|7693079|gb|AW761177.1|AW761177
EST:     ATATGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGG
EST: gi|209698483|gb|BW667280.1|BW667280
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|298164120|gb|HO013765.1|HO013765
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|24135503|gb|BU926013.1|BU926013
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGT
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGT
EST: gi|193419575|gb|FK383211.1|FK383211
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|193408566|gb|FK374124.1|FK374124
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCAAT
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCA-T
EST: gi|193393928|gb|FK358507.1|FK358507
EST:     TTGGTAGTTGTTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: TTGG-AGTTG-TGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|58022079|gb|CX708820.1|CX708820
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|213611749|gb|DB958871.1|DB958871
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|298177471|gb|HO023604.1|HO023604
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|193414153|gb|FK377853.1|FK377853
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGACACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTG-CACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGG
EST: gi|298168341|gb|HO014516.1|HO014516
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|193436738|gb|FK400883.1|FK400883
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGG
EST: gi|193429874|gb|FK395536.1|FK395536
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGG
EST: gi|298190152|gb|HO032273.1|HO032273
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
EST: gi|298185748|gb|HO028059.1|HO028059
EST:     ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCCATTGGTGCTATAG                         GAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG
genomic: ATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctc ... tcaatatcagGAATTGCACGTTGTTTCACCTTTGGTGGGAGTAGGAAGAGGTTGCTGCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAGgtattttctcaaattatctgtgtttcagctttcgggtagggcttgttcaaaagctacttagatattagtgctcaaattctaaagctggtgcagtaactgg

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT