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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggcatttctgtataatagattggctgatatttagcatccggttttcttgatgacatgattggtattttttgagattgtgtgtgtagtatttaatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA

Basic information

species Glycine max
transcript GLYMA10G35320.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 2
gtaagttggcatttctgtataatagattggctgatatttagcatccggttttcttgatgacatgattggtattttttgagattgtgtgtgtagtatttaatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA
                                                 ||| ||  ||  |  | | | |   |     | ||||  |||      ||   | || |  | ||   ||||| |  |     |  | |  | ||    | ||||| || ||||| |||    |||| |||||||  |  |     || ||||| || ||||| ||||| ||||| ||||||||| |||||||||||||  || 
-------------------------------------------------ttttttagtggaaacaataggagagtgccccactgtgaatgtctagaatagattgatgc-gcactgtccttatgtgtg---acatgttcggagttttggtgcagATAAATCCTGAAAAGGCCCGGGAGGAGTTTCGGACAGTAAGTCAAAAAAATGGAGGAACAGGAGTAAAAGATTTCATGGATAGCATGGGCCTTGGGGTGC

upper sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaagttggcatttctgtataatagattggctgatatttagcatccggttttcttgatgacatgattggtattttttgagattgtgtgtgtagtatttaatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA
                                                           |  || |||| |||   |  | |    | | | || | |    | ||     |   | |  ||||    || || ||  |  |||     |||||| ||||||||||||  ||||||||||||||  | |||| | ||||  || || ||||| || || ||||| || |||||||| ||||| ||||||||| 
---------------------------------------------------------gtatgtgtttggaattacctttggtgcattttttggtttctgtggtgatgatcttacactcaaattttgagttttaattgatagctttgca-acagATAAACCCTGAGAAGGCTAGGGAAGAGTTTCGTAGTGCCTCGCAGATGAATGGAGGAACTGGGGTGAAAGATTTTATGGATGGTATGGGACTTGGAATGC

upper sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 3
----gtaagttggcatttctgtataatagattggctgatatttagc----atccggttttcttg--------atgacatgattggtattttttgagattgtgtgtgtagtatttaatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA
    |||      | || |||||| |     ||  |  | || ||     ||   ||| |||          |||| | |||||||||| |   |     |  ||  | | ||  ||          |  |   ||| | |  ||  | | |  ||  |||||  |||||| |||||||| |||  | ||||||| || |  |||||    |||||||| || ||||| || |||||||| ||||||||||||||||||||||||||| 
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtattatggcaatgcatccgttaaattttctatgaggctttgttgcctcattactcagtttaattggtagtt--ttcat--acagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC

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|207787687|gb|GD761485.1|GD761485
EST:     GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAA                         ATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
genomic: GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
EST: gi|298195047|gb|HO043575.1|HO043575
EST:     GTGCATTGGTGCCAGAGGAAGGACCTGATTATCCACTTTTTGCTCTTGAA                         ATTAACCCTGAGA
genomic: GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATTAACCCTGAGA
EST: gi|7692581|gb|AW760684.1|AW760684
EST:     GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAA                         ATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
genomic: GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
EST: gi|9564725|gb|BE474234.1|BE474234
EST:     GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAA                         ATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
genomic: GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
EST: gi|209716152|gb|BW662337.1|BW662337
EST:     GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAA                         ATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG
genomic: GTGCATTGGTGCCAGTGGAAGGACCTGATTATCCACTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA
                                     tccttac  putative branch site (score: 2)
                                    ttccttacttcattt  CT-rich tract
                    ttatttaagtttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggcatttctgtataatagattggctgatatttagcatccggttttcttgatgacatgattggtattttttgagattgtgtgtgtagtatttaatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA