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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGTGGAGTGTGACAGGAAAATTCAGAGGGCCCTAAAACGGCTTGCAGATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgctaggactcacttatatatcaattgcaaaagtttatttgtaacggaaactcttgatttgaggtgtattaaattgattgtattgtcaatgttcacag

Basic information

species Zea mays
transcript GRMZM2G069916_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 3
CATTGTGGAGTGTGACAGGAAAATTCAGAGGGCCCTAAAACGGCTTGCAGATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgctaggactcacttatatatcaattgcaaaagtttatttgtaacggaaactcttgatttgaggtgtattaaattgattgtattgtcaatgttcacag
||| |||||||| || ||||||||||||||||| || || || ||||| ||||| |||||||| ||||||||||| ||||| || ||||||||||||| ||||| |      |  ||  |||||    || |   ||  ||||||||   | |    ||| | ||||  ||       ||| |||  |||| ||  ||  |||
CATCGTGGAGTGCGAGAGGAAAATTCAGAGGGCGCTGAAGCGTCTTGCTGATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtattt------atccaactatatgc--atcg---aaacttatttgtctagaa----cttcaattgaattgc------ttgcttgc-ttgttaacatttgcag

upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 3
CATTGTGGAGTGTGACAGGAAAATTCAGAGGGCCCTAAAACGGCTTGCAGATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgctaggactcacttatatatcaattgcaaaag-tttatttgtaacggaaactcttgatttgaggtgtattaaattgattgtattgtcaatgttcacag
 ||||  |||||||||||||||||   |||||| ||||| ||||| |  ||||| ||||| || ||||| |||||||| ||||||||||| |||||||  ||         | ||   ||   |      |    ||| |||    ||  | |  | | |         |||  ||    | ||||| |||||  || |  |||
TATTGGTGAGTGTGACAGGAAAATAGGGAGGGCTCTAAAGCGGCTCGAGGATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAAgtg-------agtcttggttgagtccttgctatggaaggtttgccggtggcagtgatttt---------gtgagttgtgataattgttttgtct-tgcttgcag
















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|67033512|gb|CO462261.1|CO462261
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|211479946|gb|FL425922.1|FL425922
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|76292705|gb|DV032273.1|DV032273
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|211142603|gb|FL018649.1|FL018649
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAA
EST: gi|211024315|gb|FL368572.1|FL368572
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|149000973|gb|EE038213.2|EE038213
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|148932069|gb|EC875423.2|EC875423
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|76920400|gb|DV168155.1|DV168155
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|149014011|gb|EE043527.2|EE043527
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|88756297|gb|DY540438.1|DY540438
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|148952947|gb|EE152420.2|EE152420
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|87157671|gb|DY402460.1|DY402460
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAG---AC---G                         --G-ATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|71312972|gb|DR793008.1|DR793008
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|71330193|gb|DR801854.1|DR801854
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|87157020|gb|DY401809.1|DY401809
EST:     TGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: TGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|88756334|gb|DY540475.1|DY540475
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCATCTGTCAAAACAGATAAAGGAGAGAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
EST: gi|9952467|gb|BE639050.1|BE639050
EST:     ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTG                         ACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA
genomic: ATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgcta ... atgttcacagACGGATGACATACTGCAGCTGTCAAAACAGATAAAGGAGAAAATGGCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGTGGAGTGTGACAGGAAAATTCAGAGGGCCCTAAAACGGCTTGCAGATGATGATGCCAATGCTGCTATTGCGATATCGGTCTCTGAGGTTACTCTGgtatctgctaggactcacttatatatcaattgcaaaagtttatttgtaacggaaactcttgatttgaggtgtattaaattgattgtattgtcaatgttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT