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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatcatgtcttcttacattgaaaaaaccgtttatgttatttgagcctttaagtgatatttgactgttaataaaaatagtaatgatgatgataata...

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 6
CGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgta---tcatgtcttcttacattgaaaaaaccgtttatgttatttgagcctttaagtgatatttgactgttaataaaaatagtaatgatgatgataata
|| || || ||||||| ||| | |  |  ||| ||||| |||||  |||| || || || |||||||| || || ||||||||||||||||| || |||||||||||   | || || | ||    ||    ||   |||| ||    | | |   | || || | |  | | | | |        |  |||     |   | 
CGCAAGCCCTGGCCAAATATCACTCCTTGTGCTAAAGACTTTGTACAAAAGTTGCTTGTTAAGGATCCCCGTGCAAGATTAACTGCTGCTCAGGCATTATgtatgtaactttatatcatttttggatgtcttaa--atttaagtatgataatctgattagggaaactcta-tatcattttgggacatcttgaatgcaagtttg

upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 7
CGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatcatgtcttcttacattgaaaaaaccgtttatgttatttgagcctttaagtgatatttgactgttaataaaaatagtaatgatgatg--ataata---
|| || || ||| |||  |||| |     |||||||||||||||  ||||||||||||| |||||||| || || ||| |||||||||| || || ||||||||||  | | |  ||  |  ||||||||  |    |    |||   |  |   | |   |||||  |    |  | ||   || | |   ||  || ||    
CGCAAGCCTTGGTCAAACATTACTTCGAGTGCAAAAGATTTTGTACAAAAATTACTAGTTAAGGATCCCCGTGCAAGACTAACTGCTGCACAGGCATTATgtatgtgac-tatgatcc-atcttgaaaaataca---aaaccattaaggtttgctaatatgatttgtttccctagtataactttagtaagagtgccatgatgtaa

upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 5'ss of exon 7
CGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatcatgtcttcttacattgaaaaaaccgtttatg-ttatttgagccttt----aagtgatatttgactgttaataaaaatagtaatgatgatgataata
|| |||||||||||||| || || |||| ||| ||||||||||| || || |||||||| || || |||||||| ||| | ||||||||||| ||  |||||  |||||  ||  |  | | | || || |    | ||| |||||  || ||      || ||  |  ||  | |||| |||| || |  |  || || |    
CGCAAACCATGGCCAACCATAAGCAATGGTGCTAAAGATTTTGTAAAGAAGTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTCAGGCCCTATgtgagtatccagttcttctcc-tggagaatataaatgatgattattacagtctactggaaattggaacatgtgtcttaacaaaa-tacttcttgtgttggtt---

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|208136736|gb|GD939696.1|GD939696
EST:     ATCCTCGGGCGAGTATTTAACTTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATCCTCGGGCGAG-A-TTAAC-TGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193420116|gb|FK385554.1|FK385554
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193718228|gb|FK653036.1|FK653036
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193682134|gb|FK622910.1|FK622910
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193573663|gb|FK528351.1|FK528351
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193432686|gb|FK393406.1|FK393406
EST:     GGCGAGATTAACTGTCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: GGCGAGATTAACTG-CTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|207843720|gb|GD813905.1|GD813905
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193546146|gb|FK502323.1|FK502323
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193364409|gb|FK328914.1|FK328914
EST:     GGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: GGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|208217317|gb|GE010351.1|GE010351
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|208183682|gb|GD982898.1|GD982898
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193631037|gb|FK579088.1|FK579088
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|207825702|gb|GD797329.1|GD797329
EST:     ATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193567952|gb|FK526529.1|FK526529
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|193544365|gb|FK500310.1|FK500310
EST:     ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
EST: gi|208085782|gb|GD880636.1|GD880636
EST:     ATCCTCGGGCGAGTATTTAACTGCTGCTCAAGCTTTAT                         CACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA
genomic: ATCCTCGGGCGAG-A-TTAACTGCTGCTCAAGCTTTATgtatgtatca ... aatatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGGCGAGATTAACTGCTGCTCAAGCTTTATgtatgtatcatgtcttcttacattgaaaaaaccgtttatgttatttgagcctttaagtgatatttgactgttaataaaaatagtaatgatgatgataata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT