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'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcattgaagaagttttgaggcagttgcatgccctaatggatcatttgggttttgaattaaatacacgctttaactatgatcttatatttggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG

Basic information

species Glycine max
transcript GLYMA07G00630.2
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 28
-tggcattgaagaagttttgaggcagttgcatgccctaatggatcatttgggttttgaattaaatacacgctttaact-----atgatcttatatttggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
 | ||  || || |  |||  | ||||      | ||  ||     ||||   | | ||  | ||  | | |   |       ||| | |   ||     |||||| ||  |  |  ||||||||||||||||||||||||||||  |   |
ttagc--tgcagcaaatttatgtcagtatttatctctgttgc----tttgaagtgtcaaaaatatttatgttagcagcgctaaatggtttctcatcatcttttcagGGAGCCATTGGTAACAAATATCATGTGGAGAAACTTGATTATCATG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 27
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 29
tggcattgaagaagttttgaggcagttgcatgccctaatggatca--tttgggttttgaattaaatacacgcttt--aactatgatcttatatttggctt-tcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
     ||      | |||  || |  |  | |     |  ||  |  ||| ||||||  ||| | |||| | | |  |   |||||  | | ||||  || |||||||| ||||||| ||||||||||||||||| ||| | ||| | |||
----ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattga-tacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
















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|16996275|gb|BM085647.1|BM085647
EST:     ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAG                         AGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
genomic: ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattg ... tggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
EST: gi|33390180|gb|CA853387.1|CA853387
EST:     ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAG                         AGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAGGCTGT
genomic: ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattg ... tggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAGGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggttttgaattaaatacacgctttaactatgatcttatatttggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
                        ctttaac  putative branch site (score: 3)
                                                ctttc  putative PPT
                         tttaactatgatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcattgaagaagttttgaggcagttgcatgccctaatggatcatttgggttttgaattaaatacacgctttaactatgatcttatatttggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - -gcagttg
- - - - - - - - - - - - - - catgccc
- - - - - - - - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacacgc