Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag

Basic information

species Glycine max
transcript GLYMA11G11670.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 3
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtga-aattatagccttataagtgggactgattgtttctagaacatactgtttaacag
 |||||||  ||||| || ||  ||||||| || || || ||||| |||||||| || ||||||||||| ||||||||||| || || || ||||||||||||     ||| || ||   ||    | |     | | ||| ||  ||     || ||||||    | ||  | | | ||    || |  |||  || | |  |  || ||||  |    ||  |  |  || ||  |  || | ||||||  | ||||       || |                            
GGAGAATTTCAATGAGAGAGTTTTGCCTTCAATCATTCATGAAACACTCAAAGCGGTGGTTGCACAGTACAATGCCAGTCAACTAATCACACAGAGAGAGgtactgtcttatcatatctatctgtgttt---aaatatctaata--tgtttccatggtatgc----tatgctagtttaag----agctaatatagtagtat--gatatttagtttaagagctaatatagtaggatatatggtaataattattcctttatc--caacacag----------------------------

upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 5'ss of exon 3
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaatt-cacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag
 |||||||  ||||| || ||  ||||||| || || || ||||| |||||||| || ||||| ||||| |||||||||||||| || || ||||||||||||     | | || ||   ||    | |     | | ||| ||  ||     || ||||||    | ||  | | | ||    || |  |||  ||   |    | | ||  |  |   |   | ||||   |  ||| | | |     |   |  | |                                      
GGAGAATTTCAATGAGAGAGTTTTGCCTTCAATCATTCATGAAACACTCAAAGCGGTGGTTGCGCAGTACAATGCCAGTCAGCTAATCACACAGAGAGAGgta--ctgtcatcatatctatctgtgttt---aaatatctaata--tgtttccatggtatgc----tatgctagtttaag----agctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacag-----------------------------------

upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 3
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt-accagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag
 ||||| |  ||||| || ||  ||||||| ||||| || ||||| || |||||||| || ||||| || ||||| |||||||| || || ||||||||||| || |  | | || || |||    ||  ||| |    ||  ||  ||   |    ||   |||    ||        | |||   ||||| |||   ||     |||| ||                                                                                     
GGAGAACTTCAATGAGAGAGTTTTGCCTTCAATTATCCATGAAACACTTAAAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacctgaacatatgcttttt-atagtctttttttcttatatttga--tgggggtcaacattacttgggggcgctaactg---tttgtttcactctcc---aaatccag-------------------------------------------------------------------------------------

upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: AC217358.3_FGT005 (Zea mays), 5'ss of exon 3
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtat-gcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag
 ||||| |  ||||| || || |||||||| || || || ||||| ||||||||||| ||||| || || |||||||| ||||| || || ||||||||||||   ||| |   |  |   | | || |||   | |  ||  |||||   |  | | || | |||   | ||            ||||  | ||||    |   || ||   |  |                                                                                 
GGAGAACTTCAATGAGAGAGTTCTGCCTTCAATCATTCATGAAACACTCAAAGCTGTGGTTGCTCAATACAATGCCAGCCAGCTGATCACCCAGAGAGAGgtac-cattcatgcgtctagacacgatgttccccata--taacaactgtcttgctaggattggatgagat-taggatatgttaacagttcat-tcatgcattc--gattccgatgcag--------------------------------------------------------------------------------

upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 4
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccag---attcttccccatcttctgtacagct---agtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag
|||||| || |  || || || || |||||||| ||  |||| ||| | |||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||| | |  |  | |   ||   |   |||||| | |     |   ||||| ||   |  ||  |    |  || |   |||||     |                                                                                                                 
TGAGAACTACAGCGAGAGAGTTCTACCTTCTATAATCAACGAGACTTTGAAAGCTGTGGTTGCTCAGTACAATGCAAGCCAGCTTATTACTCAGAGAGAGgtatacaaatgactgtgaatatatgatcatcttttttctctttcttagtaagtgaagttcttaaagatttattccgggcttctc--tcag-----------------------------------------------------------------------------------------------------------------

upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 5
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag
|||||| || |||||||| ||||||||||| || || || |||||||| |||||||| ||||||||||||||||| || ||||| ||||||||||||||||||  | |  ||     ||||     |||| |  |||| |  ||| ||  | ||||  | | |||    |||      |  | | | | |     |||  |||||| | |  |                                                                                    
TGAGAACTACAATGAAAGAGTCCTGCCTTCAATAATTCATGAAACTCTGAAAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctgaactg---tctt-----tcttttaaacagttt-taattg--caaatttgaagtatga---gtatcagataaatagtgatagctgtttaagattaggattttgttt-----------------------------------------------------------------------------------

upper sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 5
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag
|||||| || |||||||| |||||||| || || || || |||||||| |||||||| ||||||||||||||||| || ||||| ||||||||||| ||||||  ||   |||    ||||     |||| |  |||  |           |||||| |    ||   | | | | |||| |  |   ||    ||||   |   |   |||   |||   |||||                                                                       
TGAGAACTACAATGAAAGAGTCCTGCCCTCAATAATTCATGAAACTCTGAAAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggta---accg---tctt-----tcttttaaacaatt----------ttaattgcaaatttgaagtatgagtatcagataaatagtg----ataactatttaagattag--gattttgttttgc----------------------------------------------------------------------

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|254330517|gb|GR841782.1|GR841782
EST:     AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAG                         AATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
genomic: AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt ... tgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
EST: gi|192301953|gb|FG995571.1|FG995571
EST:     AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAG                         AATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
genomic: AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt ... tgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
EST: gi|15287791|gb|BI471682.1|BI471682
EST:     AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAG                         AATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
genomic: AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt ... tgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
EST: gi|17962874|gb|BM269622.1|BM269622
EST:     AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAG                         AATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
genomic: AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt ... tgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
EST: gi|12688335|gb|BG154671.1|BG154671
EST:     AAGCTGTAGTTGCACAG-ATAATGCCAGTCAGCTCATTACTCAGAGAGAG                         AATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
genomic: AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt ... tgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
EST: gi|23735502|gb|BU766034.1|BU766034
EST:     AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAG                         AATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT
genomic: AAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatattt ... tgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAATTATAATGAAAGGGTCCTGCCTTCTATTATACACGAAACTCTCAAAGCTGTAGTTGCACAGTATAATGCCAGTCAGCTCATTACTCAGAGAGAGgtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA