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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA

Basic information

species Glycine max
transcript GLYMA15G15310.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcatta--atgaaagctcaccaagtaaatgc-attcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
    |  || |  || |     |  |   |     | | |    |   ||||||| || |   |||  ||   |   ||||   |   | || |    | |||| || |||||  |||||||||| |||||||| ||||| ||| |||| || || ||||||||||| || |||||||| || ||||| ||||||||||||||
---aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgttatacctattgttcttacagaagcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
ggggatctttgttcactgatactgtcc-ctcttgtttttctgttttgttatttcttcttcttggtat-cattaatg-----aaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
         |  |  || ||||  |   |   | || ||| |     |   |  | | | |    || || || |      | ||||| |  | |   |  || |||| || || ||  |||| ||||| |||||||| ||||| ||| | |||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||
-------gctcctttctaataccatttacatatattattcaggaaaatatgtgttgcatatgcacattcactagttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
 |||  | || || | ||  ||        | |||    | ||||||    | | ||| |||       | |  |||    ||    | | |  || |||| || |||||  |||| ||||| |||||||| ||||| ||| | ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
ggggatctttgttcactgatactgtccctcttgtttttctgtt-ttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
    ||| |   |     |||||    ||    |   | ||||    ||  |  ||| |  | | |||  |  | ||||||  |    |   |  || |||| || |||||  |||| ||||| |||||||| ||||| ||| | || ||||| ||||| || ||||| ||||||||||| ||||| ||||||||||||||
ccttatcatatatgttgcatactacagcttaaatgcatttgttgccattcctatttcattctagcatccctt-taaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
          || |  |  |  |||       ||     ||||  |  |         ||||  || |||  |  ||  |   ||  |    || | |||||||||||||||| ||||||||||||||  | ||| | ||| |||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||
----------gtacgtt--tcttgttttggacgtagagttgttaagggagcatgcagacttg--attattccttgaatgtttacattttggcgc-tgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
--ggggatctttgt-tcactgatac-tgtccctcttgtttttctg-----ttttgttatttcttcttcttggtatcattaatg----aaagctcacca-agtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
    |  | ||||| | | |||||  ||        |||               | |  |  ||  | || ||||    | |     ||   ||  || | |   ||| | ||||||||||||| || || ||||| |||||| | ||| ||||| | |||||||| ||||| || || ||||||||||||||||| || ||||| ||||||||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgc-tgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA

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|27426345|gb|CA937865.1|CA937865
EST:     CATTGCCACTGGTTCAGTTCCTTTTGTTCCAAAGGGCATTGAGGTTGATG                         GAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTG
genomic: CATTGCCACTGGTTCAGTTCCTTTTGTTCCAAAGGGCATTGAGGTTGATGgtacgtcata ... atgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTG
EST: gi|13562493|gb|BG550713.1|BG550713
EST:     CATTGCCACTGGTTCAGTTCCTTTTGTTCCAAAGGGCATTGAGGTTGATG                         GAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTG
genomic: CATTGCCACTGGTTCAGTTCCTTTTGTTCCAAAGGGCATTGAGGTTGATGgtacgtcata ... atgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
                               agctcac  putative branch site (score: 3)
                  tatcattaatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA

- - - - -tgttcac
- - - - - - - - -gatactg
- - - - - - - - - - - - -ccctctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaccaa