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'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcataacatgcacctgctgtgatgccgagtcttgtttttgtaatttgtgatttctttatgctgttttagatgtttctgttttaaaccttgggtttaattgttctgtgaatttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCTGTTACTGAAGCTGAAATTAAATCTTCAGCTGCATATGTGTTATTTTATC

Basic information

species Glycine max
transcript GLYMA20G36020.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G10570.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------gtaagttcataacatgcacctgctgtgatgccgagtcttgtttt-----tgtaatttgtgatttctttatgctgttttaga-tgtttctgttttaaaccttgggtttaattgttctgtg--aattttta-acagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCTGTTACTGAAGCTGAAATTAAATCTTCAGCTGCATATGTGTTATTTTATC
                            ||||||  |  |       |  |   || |  | |  |     |  | |      ||     ||  || ||   | |   |||  | | |    |   ||| ||  || ||||  |||||| |  |||||||| ||||| || ||||||| |||||||||||| |||||||| || ||||| | |||| ||||||| | |   ||||||||||||||  | || || |
gttggtgacttcatttggtctcactgcatcataatcttaattcatcatattatagacttatataatatatatccactcgacagttgtcccattgtgcttgccactagatcttctgtgagttctttatttgatcattatgtgtcaattttcatgcagTTGATTGATGACAACAAATGGTACCATTTCGACGACAGTCATGTGTCATCTGTAAATGAATCTGAAATCAGAAACTCAGCTGCATATGTTCTTTTCTACC

upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G10590.2 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------------------gtaagttcataaca-tgcacctgctgtgatgccgagtcttgtttttgtaatttgtgatttctttatgctgttttagatgtttctgttttaaaccttgggtttaattgttctgtga-atttttaa--cagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCTGTTACTGAAGCTGAAATTAAATCTTCAGCTGCATATGTGTTATTTTATC
                                      ||   ||  || |  | ||  |||    ||||    | ||         |   ||  |  |||| ||||  |     |  ||||  | | |    |   | | ||| ||  |||  |||||| |  |||||||| ||||| ||| |||||| |||||||||||| |||||||| || ||||| | |||| ||||||| |||   ||||||||||||||  | || || |
gtttgctgactaaacatttggtctcactatctattttggtttatttttacctcttcatatgcataaatgcatcatattacagactcgaca-gttgtccctttgtgct--tgctactagttcttctgtgagttctttatctgattattaggtgtcatttttcatgcagTTGATTGATGACAATGAATGGTACCATTTCGACGACAGTCATGTGTCATCTGTAAATGAATCTGAAATAAAAAACTCAGCTGCATATGTTCTTTTCTACC
















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|192306336|gb|FG996894.1|FG996894
EST:     GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAG                         TTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
genomic: GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAGgtaagttcat ... tttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
EST: gi|51343783|gb|CO984516.1|CO984516
EST:     GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAG                         TTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
genomic: GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAGgtaagttcat ... tttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
EST: gi|23731761|gb|BU764020.1|BU764020
EST:     GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAG                         TTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
genomic: GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAGgtaagttcat ... tttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
EST: gi|26269063|gb|CA820126.1|CA820126
EST:     GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAG                         TTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT
genomic: GCAACCATTATGGTGGTCTAGGTGGTGGGCATTACACTGCGTATTGTAAGgtaagttcat ... tttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagatgtttctgttttaaaccttgggtttaattgttctgtgaatttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCTGTTACTGAAGCTGAAATTAAATCTTCAGCTGCATATGTGTTATTTTATC
                           gtttaat  putative branch site (score: 4)
                                             ttttt  putative PPT
                                         tgaatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcataacatgcacctgctgtgatgccgagtcttgtttttgtaatttgtgatttctttatgctgttttagatgtttctgttttaaaccttgggtttaattgttctgtgaatttttaacagTTGATCGATGAAAATAAATGGTTCCATTTCGACGATAGTCATGTCTCTTCTGTTACTGAAGCTGAAATTAAATCTTCAGCTGCATATGTGTTATTTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC