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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctacacatctttataggaaatttggtactgaggtcaataaggtgtattgattttagggtcctttaccattcctaactaatacatttatttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA

Basic information

species Glycine max
transcript GLYMA17G12070.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12070.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G156320_T01 (Zea mays), 3'ss of exon 11
-tctctacacatctttataggaaatttggtactgaggtcaataaggtgtattgattttagggtcctttaccattcctaactaatacatttattt---gttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA
   | |  |    || | |  |   |  ||| | |    |     || || |    |||  | |  | | | |      ||| |   ||| |||   |   ||| | |||||||| || |||  | ||||||| |||||||||| |||   |||||||||||| ||||||||||||||||||||| || | || ||||| ||||
aaatttcaatggtttgacacca---tcagtatttattataccgttgt-tactttgattaaagcctatcagcttagtgggctattttttttcttttgtgcctcagCTTGTGGAGCTTCTTGATCCTTCATTGCACAACTATTTTAGGCAAAATGACTGCTTGAACTATTTCTTCTGTTTCCGCTGGGTTCTTATACAATTCAAAA

upper sequence: GLYMA17G12070.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G52580.1 (Arabidopsis thaliana), 3'ss of exon 13
---------------------------tctctacacatctttataggaaatttggtactgag-gtcaataaggtgtattgattttagggtcctttaccatt---cctaactaatacatttat-ttgttaca--gTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA
                            ||||||| || |  ||     ||||  | ||     |||  |    | ||  || || |||    | | | |    | |  ||  | |||||    ||| |||  | |||| ||| |||| ||||| ||  | ||||| || |||||| ||  ||||||||||||||| ||||||||||||||||||||| ||||||| |||||||
gtctataattttttttcttcgagaacccctctaca-atttacattttgcatttcttcctttctatcagcattcggcatcaatgttgggggatctgaacctgaagcatttctttttcattttcactgtcacacagCTGGTAGAGTTGCTCGATAGCCCGCTACATAATTACTTTAAGGAGAATGACTGCTTGAATTACTTCTTCTGTTTCCGCTGGATTCTGATTCAGTTTAAAA

upper sequence: GLYMA17G12070.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv11s0016g05700.t01 (Vitis vinifera), 3'ss of exon 14
-------tctctaca-catctttataggaaatttggtactgaggtcaataaggtgtattgattttagggtcctttaccattcctaactaatacatttatttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA
       ||||      | ||       |   ||  |   ||   ||||||  |||  ||| |||    ||||| ||   | || | |  ||  || |       ||| |||||||| || | ||||| ||  | ||||| ||||||||||||  ||||||| | ||||||||||| |||||||||||| || | || || || ||||
tttcatgtctcagtggtacctcggctaaattctttttgtagacaacaataacatgttctgagtttctaatcctt-actgattctcaatgttatgttga-------cagCTGGTGGAGTTGTTAGATAGCCCGCTCCATAATTATTTTAAGCAGAATGACTGCCTAAATTATTTCTTTTGTTTCCGCTGGGTTCTTATACAGTTCAAAA

upper sequence: GLYMA17G12070.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S368_20V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------------------------tctctacacatctttataggaaatttggta---ctgaggtcaataaggtgtattgattttagggtcctttaccattcctaactaatacatttatttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA
                                      ||  || |  |||| ||      ||   ||   || |      |||     |    || |       ||        || || | | | |   |||  ||||||||||| || ||||||||| |||  ||||| | ||||| ||||||  ||||||||||||||| |||||||| ||||| |||||| ||||    |||||||
gtgagcttatatatgctaaggaactcatttagtcaaagtcctta-atctcttaatttactgttcaatatttctcacacgtttaaacaacagcttttctgcacgaattcgaagaatctgac-agttcgtgggtttactacagTTGGTGCAGTTGCTGGATAATCCTCTGCATGATTATTTCAAGCAGAATGACTGCTTGAATTACTTCTTCTGCTTCCGGTGGATTCTGATCTGCTTTAAAA

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|5509199|gb|AI855757.1|AI855757
EST:     TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAG                         TTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
genomic: TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAGgtttttctct ... tttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
EST: gi|9260051|gb|BE348198.1|BE348198
EST:     TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAG                         TTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
genomic: TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAGgtttttctct ... tttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
EST: gi|16348998|gb|BI974593.1|BI974593
EST:     TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAG                         TTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
genomic: TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAGgtttttctct ... tttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
EST: gi|7591273|gb|AW707009.1|AW707009
EST:     TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAG                         TTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
genomic: TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAGgtttttctct ... tttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
EST: gi|17153534|gb|BM143467.1|BM143467
EST:     TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAG                         TTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC
genomic: TTAATCGTGATCAAAACGGCATGCATTCTCAACTTTTTGCGCTATCTAAGgtttttctct ... tttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattgattttagggtcctttaccattcctaactaatacatttatttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA
                                         tttattt  CT-rich tract
                              taactaatacatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctacacatctttataggaaatttggtactgaggtcaataaggtgtattgattttagggtcctttaccattcctaactaatacatttatttgttacagTTGGTGGAGCTGCTGGATAGTCCATTGCATAACTATTTTAAGCAGCGTGACTGCTTGAATTATTTCTTCTGTTTCCGCTGGATTTTGATTCAATTTAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- -ctacaca
- - - - - - - - - - - - - - - ctgaggt