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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

Basic information

species Glycine max
transcript GLYMA12G06980.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 8
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   || ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     ||  |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| |  ||||||||||| ||||| |||||||| || || |
gtaaatttcttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 7
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   |  ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     ||  |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| |  ||||||||||| ||||| |||||||| || || |
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   |  ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     |   |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----aatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   |  ||  ||  ||| |  |  |||| ||   |  ||| |||| |  | |   |    | || |||    |    | ||| |     | |     |||| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | |||||| || || |
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaacttt----ttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 7
-aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  |   |  |  | | | | |  | |  ||| | | |||| ||  | ||   ||   ||     || | | |   |  |  |  | |   | | |   |||||||  |||| |||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |
gtaaatttgttca-tctgacaattgcaatatatttgctttgattttcataaattatcattcaagttatctta-cggttttgatttgattttttctat-cagGAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
-aatgatcatcgactttaatat-ataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTC-GGAGTTGTTATGATGAGGGCAAGCGTGTTGCA-GAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  |   |  |  |  | || ||   |  |||| ||   |  ||| |||| |  | |   |    | || |||     ||  |  |  |||   | |      ||| |||  ||||||||||||||||||| |||||||| ||| || || |||||||| || ||||| |||||||| || || |
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
        | |   | || |  || |   | |    | | | | |     | ||  |  |  | ||  |  ||| | |       |  |||     | ||| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| || ||||| |
-------gtaggagtaaacacttatcagcttttaattctcaacttatctgcgtgtcaattcacattctt--ataacttggtttctattatg-----atagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 6
aatgatcatcgactttaatatataccttatctgtccttttatcatg-----atctcttgatatgttgcttttatcaatagcctaaacataa---aaatg----tgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
                    || |||| |  ||| ||  | | ||      ||||  |   || |   ||||  ||      ||||| |||      ||    | |  | ||| ||||||||||| ||||| || |||||||| || || ||||| ||||||||||| || || || || || || || |
-------------------gtaaacctcaaatgttctcatcttatagaggaatcttcttgcatttcagtttttacagctttgtaaacttaacctggttgctattatcaaaagGGGTTCGGAGTTGCTATGACGAAGGCAAGCGGGTAGCCGAAACCTTGATGTTTGACTACCACAGACAACATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtg---cacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
|||  |  |   |||   | | |     |  ||      | || |||    |   ||||    |||          || || |||        ||    ||||| || ||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||||| || || || |
aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaat---tatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

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|209703509|gb|BW656547.1|BW656547
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
EST: gi|192298392|gb|FG989143.1|FG989143
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTTGATG
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTT-GATG
EST: gi|193540711|gb|FK494361.1|FK494361
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
EST: gi|209703510|gb|BW656548.1|BW656548
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
EST: gi|192330026|gb|FK020842.1|FK020842
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
                             gcctaaa  putative branch site (score: 3)
                                taaacataaaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

- - - - - - - - - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa