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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaataaatttaagagtcaaccataacggcacagaaatttctaaaaatacaccagaattttttcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag

Basic information

species Glycine max
transcript GLYMA04G43340.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 4
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaa-----gaaagaaataaataaatttaagagtcaaccataacggcacagaaatttctaaaaatacaccagaattttttcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag
 |    | ||||||||| |||||| |||||||||| || ||||| || ||||||||||||||| | || ||||| ||| |  |||| |||||||||||||||  | |      || | || | |||    |   | | |  |||  |       |   ||    || |  ||  ||  ||| | || | || ||  |||                                                    
AGCCAGCAAAGGAAGAAAGCTTTTGTAGTGATTGGGATCAACACTGCATTCAGTAGCAGGAAGCGTCGGGATTCTGTTCGGCAGACCTGGATGCCTCAAGgttcatacttttcaatgcaacacatagtactgcaa-tgagacatggctatttgcatgctttactaactttactgga--tttcttattcatagttagaagccat------------------------------------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 4
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaataaatttaagagtcaaccataacggcacagaaatttctaaaaatacaccagaattttt-tcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag
 |    |||||||||||||| ||| | || |||||  ||||||| || ||||| ||| | ||| | |||||||| ||  ||||||| |||||||||||||||    |           |||| |||| |  | ||| |  | | |      |||  |   |  |||    | ||||  |||||   || |  ||||   |                                               
AGCCAACCAAGGAAGAAGGCATTTGTTGTAATTGGAGTAAACACCGCATTCAGCAGCCGCAAGCGCCGTGATTCAGTGCGAGAGACATGGATGCCTCAAGgttgctatttcttgtattataactttatggatgaactagcaagacggttctattattgttag-acatttcatttttaatcatcatcatctccaaggctctt----------------------------------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G133613_T02 (Zea mays), 5'ss of exon 4
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaat-----aaattta---agagtcaaccataacggcacagaaatttctaa----aaatacaccagaattttttcat------ccctatttttaaggggatag----tggccctaattg--atttctaaaatgttgtgttg-gcgt-tttgatcag-----------
 ||   |  ||||  | ||  ||  | ||||| ||  | ||||| || ||||| ||||||||| | || |||||||| || ||||| |||||||||||||||             |   |       | | |   ||||  ||  || | |   ||| | | |||      |  ||       || ||||| |       || ||     |||  |||     | |  || | ||  ||||||    |||| |  || || | | ||| | |           
AGTAAGCAGAGGAGAAGGGTGTTCGTGGTGATCGGGGTCAACACCGCCTTCAGCAGCAGGAAGCGTCGGGATTCCGTGAGGGAGACCTGGATGCCTCAAGgttcgtgattctttgtctttcccccggactgatgcagaggaaatgatgatgatgcaggattctctctgtttatttatttttatatattttcttgaaagatccaatggcgcaggaaatatccattagggctgactgctatttctcttttgttttactgtgcttgtctgacctgctgtttatcag

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 4
lower sequence: EFJ30358 (Selaginella moellendorffii), 5'ss of exon 4
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaataaatttaagagtcaaccataacggcacagaaatttctaaaaatacaccagaattttttcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag
| ||  ||  |  |||| | |||| | ||||| || |||||||| ||||| || ||  | ||| | |||||||||||| ||||||| ||||||||||||||||||          | ||   |||    |||    | | ||       |  | |   |                                                                                       
GCTGAGCCTCGACAGAAAGTTTTTGTTGTGATCGGAATAAACACCGCTTTTAGCAGTCGTAAGCGTCGTGATTCCGTTCGAGAGACATGGATGCCTCAAGgtaaattcggc----tcaacgcattctcaagtg---cttgactcttttcatttcttccag--------------------------------------------------------------------------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 4
lower sequence: EFJ28470 (Selaginella moellendorffii), 5'ss of exon 4
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaataaatttaagag-tcaaccataacggcacagaaatttctaaaaatacaccagaattttttcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag
| ||  ||  |  |||| | |||| | ||||| || || ||||| ||||| || ||  | ||| | || ||||||||| ||||||| ||||||||||||||||||        ||   ||    | ||| | |  || ||             |||| |                                                                                        
GCTGAGCCTCGACAGAAAGTTTTTGTTGTGATCGGAATCAACACGGCTTTTAGCAGTCGTAAGCGTCGCGATTCCGTTCGAGAGACATGGATGCCTCAAGgtaaattcggctcaacgcatt--ctcaagtgcttgactattttcattt-----tttccag---------------------------------------------------------------------------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 4
lower sequence: EFJ21395 (Selaginella moellendorffii), 5'ss of exon 4
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaataaatttaagagtcaaccataacggcacagaaatttctaaaaatacaccagaattttttcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag
  |  ||  ||  | ||||| ||  | ||||| ||||||||||| |||||||| ||| ||||| | ||||| || |||||||| || |||||||| || ||| |           |   |    ||  ||||      ||   || ||   ||  ||      ||     |                                                                           
AATCATCAGAGACAAAAGGCCTTCGTGGTGATCGGCATAAACACGGCTTTCAGCAGCCGGAAGCGTCGTGACTCTGTTAGAGAAACATGGATGCCACAGGgtgagtcccgcactttttttcttcttttgagtt--ttttatttgctcatgtatcacttgtttcacttttcag--------------------------------------------------------------------------

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|19054062|gb|BM732729.1|BM732729
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAAC
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAAC
EST: gi|7796823|gb|AW782217.1|AW782217
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|213615386|gb|DB965651.1|DB965651
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGGATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|23052841|gb|BU577332.1|BU577332
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|151395197|gb|EV265068.1|EV265068
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|31561426|gb|CD487264.1|CD487264
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|209720190|gb|BW674528.1|BW674528
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|16104724|gb|BI892464.1|BI892464
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|17023237|gb|BM094271.1|BM094271
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
EST: gi|8283506|gb|BE021065.1|BE021065
EST:     CAGTAGCAAGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGG
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGG
EST: gi|192305500|gb|FG994294.1|FG994294
EST:     CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAG                         GTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA
genomic: CAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaa ... ttttgatcagGTGAACAACTTCTTCAATTGGAACGGGAGAAGGGAATTGTTATCAGATTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCTCCAAGGAAGAAGGCTTTTATAGTGATTGGCATAAACACAGCTTTCAGTAGCAGGAAGAGGCGTGATTCCGTTAGAGAGACTTGGATGCCTCAAGgtaaaaagaaagaaataaataaatttaagagtcaaccataacggcacagaaatttctaaaaatacaccagaattttttcatccctatttttaaggggatagtggccctaattgatttctaaaatgttgtgttggcgttttgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG