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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcataatcaagggctttagtttatgatttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG

Basic information

species Glycine max
transcript GLYMA09G34860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
----atcataatcaagggctttagtttatg-atttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
     |  | | |   | | |   | ||   |       ||| ||||  |    |  ||  ||||    |  | | || | | ||  | | ||  |      |||||||| |||||||| ||||||||||||||||| ||||| || |||||||| ||||| || |||||||||||||| || || |||||||| |||| |||||
ggtactgttgagcctagccctagatgtacataccacaacttgctatac-tgcttacagtttctttattttgcatccttttaagcatattgcaaccttc----cagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG

upper sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 3
-atcataatcaagggctttagtttatgatttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagta-atgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
 |   || ||| |||    |    |     ||  | | ||| |  |     |||| ||  ||   |   | ||||    ||   |  | ||   | | | |||||||||||||  | ||||||||||||||||||||||| || ||||| || ||||| || ||||| || || |||||||| || ||||| ||||||||||
aactttagtcaggggaaccaaac-acccccttcgtattgtacagtttcctcttgt-acagtttcctctcattttgcacccattaaacatattctgcttatagATAATTAATGCAGTCATGAGTGGAAGAGATGTTCTGGTCATAATGGCAGCTGGTGGAGGGAAGAGTCTATGTTACCAGCTCCCAGCTGTACTTCGTGATG

upper sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------atcataatcaagggctttagtttatgattttttt-ttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
               || |    |    ||  | |||||| || | |  |  | |    | | |  |  |  ||    |   |||||| |    | | ||||        |||| ||||| || || ||||  ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| || ||||| ||| | ||||||| ||
gtaagtgactttctgtattttctgatcctaaat-atgattcttgtgtccgcgtttgctagaaattcgtttgatgttcca---tttgttgattctttg-aatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG

upper sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------atcataatcaagggctttagtttatgattttttt-ttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG-----------------------------------------------
               || |    |    ||  | |||||| || | |  |  | |    | | |  |  |  ||    |   |||||| |    | | ||||        |||| ||||| || || ||||  ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| || ||||| ||| | ||||||| ||                                               
gtaagtgactttctgtattttctgatcctaaat-atgattcttgtgtccgcgtttgctagaaattcgtttgatgttcca---tttgttgattctttg-aatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG

upper sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
atcataatcaagggctttagtttatgatttttttttggtatatatagggattgtgacttttgggtaaaactttg-ttaacaagtagtaat---gtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
   ||  | |     |||| | | | ||||        | | |  |    ||||  | |          | ||| || ||||  | | ||    |   |  ||||| || |||||  | ||||||||||| |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||| ||| | ||||||||||
---attgttataaaattta-tgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaatttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG

upper sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S93_66V6.1 (Physcomitrella patens), 3'ss of exon 3
atcataa-tcaagggctttagtttatgatttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaat-gtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
 |  ||| ||||| | |     | | | |  ||  |   | | ||   || ||  | |||||   | ||||||          || |  | | |  || ||||| || |||||  | ||||||||||| |||||  | || || ||||| ||||||||||| ||||| || ||||||||||| || ||| |  | |||  ||
-ttgtaaatcaagtgatagctatcacggtacttgatatttgtgtacttggtttccg-cttttaaattaaacttaaccgtggtatattttttggctgtgccagATCATAAATGCAGTAATGAGTGGAAGGGATGTAATCGTAATAATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTACCAGCTCCCAGCTATGTTACGTACTG

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|213614933|gb|DB957013.1|DB957013
EST:     TTAGGTTGAATGTTTTTGGCATTTCCTCCTACCGTGCAAATCAAAGAGAG                         ATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCA
genomic: TTAGGTTGAATGTTTTTGGCATTTCCTCCTACCGTGCAAATCAAAGAGAGgtaataacta ... tcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCA
EST: gi|213600361|gb|DB970297.1|DB970297
EST:     TTAGGTTGAATGTTTTTGGCATTTCCTCCTACCGTGCAAATCAAAGAGAG                         ATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCA
genomic: TTAGGTTGAATGTTTTTGGCATTTCCTCCTACCGTGCAAATCAAAGAGAGgtaataacta ... tcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCA
EST: gi|213608200|gb|DB963060.1|DB963060
EST:     TTAGGTTGAATGTTTTTGGCATTTCCTCCTACCGTGCAAATCAAAGAGAG                         ATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCA
genomic: TTAGGTTGAATGTTTTTGGCATTTCCTCCTACCGTGCAAATCAAAGAGAGgtaataacta ... tcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
                           tgttaac  putative branch site (score: 2)
                   taaaactttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcataatcaagggctttagtttatgatttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - gggattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttgg