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

...gtaaatagtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG

Basic information

species Glycine max
transcript GLYMA13G39990.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
gtaaatagtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
       |||   || | | ||    ||  |      || |  | || |    ||   | |  | ||  | | |   ||||||| |        |||||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||||||  ||||||||||||||||||||
-------gtatgcagcacacatacttgtctacggcttttgcccatatca----tttccatctgtctggctgatt--attttaatct--------ttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 12
gtaaatagtaaatagtaaatat-gggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
       ||| |   ||  | | ||  ||  ||| |||         || ||  |  | |  ||| ||  | ||  | |  |   |||     ||   ||||| || || ||||| ||||| ||  |||||||||| ||||||||||| |||||  |||| ||||| |||||||||
-------gtataggttaccttttggctgttaaatttcaccggcctggtagaacttcattatgaatatg-ctcaccaaatgct---ttgtgcattt---cagCCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 12
gtaaatagtaaatagtaaatatgggggtgcaatctc-attacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatcc--ttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------
   |  || |   |  |  |||  |  | | ||||  |||| |   ||     |||   ||| || ||   ||||   ||||| | |  ||    || |  |||| || ||||| || ||||| ||  ||||| | ||||||||||||||||||| | ||||||| ||||||||||||                         
--tagcagcat-caacagttatatgattaccatctttattaatgtgatttcgactttagagctatatgcactactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G801369_T03 (Zea mays), 3'ss of exon 12
gtaaatagtaaat--agtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
|  |     ||    ||            | ||  ||    ||   ||  |    |  | |   ||      | ||    | | || | |    ||   |||||||| ||||| |||||||| ||  |||| || || ||||||||||||||||| || ||||| ||||| ||||||
gccatccacaacctgagcttccccctctttacatgctatccaccacaaccagtcatgtttactgatccaggattctcttatctgatctta--tgttaaacagCCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 12
---gtaaata-gtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------
     |  ||  | | ||  || |       ||   | ||     ||| ||   || | |         |||  |       ||| | || |||   | | ||||| || ||||| |||||||| ||  ||||| | ||||||||||||||||||  | ||||||| ||||| ||||||                         
tcaacagttatatgattaccaacttaattaatgtgctttcgac-tttatatgctatatgcacgatgtactgagctgggactcttttactttaat---tatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 12
-gtaaatagtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
   | ||  || ||  |   | ||||    ||| ||  |||     |    |  |||||    |  | |  | | || || | | | || |   ||| ||||| |||||||| ||||| |||||  |||||||||| |||||| ||||| ||||| | ||||||||||||| ||| 
cagatattttatatttttcttttgggctaacaacctttttatcagcaatctactttctatttgacatcaact-cataattgttactggattttctttacagCCTGCACATGAGAAAATCGGTGTGGTTGATTCACAGTGGATTATTCATAAAGTAGTACCTTCTCTTGGGAGCCAA

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|31464325|gb|CD406353.1|CD406353
EST:     ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|209728921|gb|BW654988.1|BW654988
EST:     AGTGCATGGATGGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: AGTGCATGGAT-GGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|20449491|gb|BQ253615.1|BQ253615
EST:     TTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: TTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|12691502|gb|BG157838.1|BG157838
EST:     ATCTATTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|10233381|gb|BE802269.1|BE802269
EST:     AGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: AGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|10234562|gb|BE803450.1|BE803450
EST:     ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|18848780|gb|BM567892.1|BM567892
EST:     ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
                                ttttaat  putative branch site (score: 3)
                                            tccttttgc  putative PPT
                aatttgatttacttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG

- - - - - - - - - - - gggggtg
- - - - - - - - - - - - - - -caatctc
- - - - - - - - - - - - - - - - - - - - - -aaataaa