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

...ttcataattgtggctactgaggttttatttccaattcgtggactcattttataatttccttgactttgacttgagtcctgtgaatttggttgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATCACCAACTTGCAGCAATCCTCTCAACAAGCAGAAGATGCGTTGTCTCAGG

Basic information

species Glycine max
transcript GLYMA13G26280.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G26280.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G361847_T07 (Zea mays), 3'ss of exon 6
ttcataattgtggctactg--aggttttatttccaattcgtggactcattttataatttccttgactttgacttgagtcctgtgaatttggttgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATCACCAACTTGCAGCAATCCTCTCAACAAGCAGAAGATGCGTTGTCTCAGG---------------------------------------------------------------
         |||   | ||  ||| ||  |||    |  |||  |||| |    || | |   |    ||| |||    |||   | | |     ||  ||||| || |  | |||  | |||||||| || ||||||||  || ||||| | |||||| | |||||||| || ||||||||||| ||||||||||| ||||                                                               
---------gtgagcattgtcaggcttcgttttttttctgtgtcctcact--ggaaatgcaaggttgctgatttg---tctgcataatggaaaatat--cagctcctagcgaatcacctcgagcctctaactgagcagcaaatgctgggtttgaccaacctccagCAATCTTCCCAACAAGCAGAGGATGCGTTGTCACAGGGCATGGAAGCACTGCAGCAATCTTTGGCAGAGACTTTGGCTGGATCTCTCGGTCCAGCAGGTT

upper sequence: GLYMA13G26280.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G361847_T02 (Zea mays), 3'ss of exon 6
ttcataattgtggctactg--aggttttatttccaattcgtggactcattttataatttccttgactttgacttgagtcctgtgaatttggttgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATCACCAACTTGCAGCAATCCTCTCAACAAGCAGAAGATGCGTTGTCTCAGG
         |||   | ||  ||| ||  |||    |  |||  |||| |    || | |   |    ||| |||    |||   | | |     ||  ||||| || |  | |||  | |||||||| || ||||||||  || ||||| | |||||| | |||||||| || ||||||||||| ||||||||||| ||||
---------gtgagcattgtcaggcttcgttttttttctgtgtcctcact--ggaaatgcaaggttgctgatttg---tctgcataatggaaaatat--cagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTGACCAACCTCCAGCAATCTTCCCAACAAGCAGAGGATGCGTTGTCACAGG
















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|10844047|gb|BF067384.1|BF067384
EST:     GAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: GAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|192329072|gb|FK021425.1|FK021425
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|9566058|gb|BE475629.1|BE475629
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|19346060|gb|BM890940.1|BM890940
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|13252262|gb|BG363165.1|BG363165
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|9902977|gb|BE611945.1|BE611945
EST:     GGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: GGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|254339872|gb|GR857997.1|GR857997
EST:     GTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: GTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
EST: gi|10843100|gb|BF067155.1|BF067155
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAG                         CTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttat ... tgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttataatttccttgactttgacttgagtcctgtgaatttggttgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATCACCAACTTGCAGCAATCCTCTCAACAAGCAGAAGATGCGTTGTCTCAGG
                  ctttgac  putative branch site (score: 4)
     ataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcataattgtggctactgaggttttatttccaattcgtggactcattttataatttccttgactttgacttgagtcctgtgaatttggttgcattgcagCTGCTGGTAAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATCACCAACTTGCAGCAATCCTCTCAACAAGCAGAAGATGCGTTGTCTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - tggctac
- - - - - - - - - - - - - - - - - - cgtggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgtga