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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTGAATATTTCGAGTCCAAAGCTCTGGAACAGCAAGAAGCTGCACGAAATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaacatgagaatatgcactagatgactatggattgtaaaagaattaacaaaatagctatgatgtcagagtacaccctcaaatctattatttctt...

Basic information

species Arabidopsis thaliana
transcript AT4G28080.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G28080.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: LOC_Os02g15660.1 (Oryza sativa), 5'ss of exon 4
GGCTTGAATATTTCGAGTCCAAAGCTCTGGAACAGCAAGAAGCTGCACGAAATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaacatgagaatatgcactagatgactatggattgtaaaagaattaacaaaa--tagctatgatgtcagagtacaccctcaaatctattatttctt--
||||||||||||| |||||||| || || || ||||| ||||| ||||| ||||||||||| ||||| || || || ||  | |||| |||||| || |||||  |  ||||||      |  ||  |  |   ||  |  ||||||   |  |||||  |||   |||  |  |  |  |      |||| || || |||   
GGCTTGAATATTTTGAGTCCAAGGCACTAGAGCAGCAGGAAGCAGCACGTAATGGTACTCCAAAGCCTGATGCTTCAATAGCAAGCAGAGGCCACCTGAGgtag-atgacatgattgctcgt-ctttaccatgttgtttcataaaagtggttgcaaaagttaggattgagttttg--tttatttgtgaatcaatgatctctatt

upper sequence: AT4G28080.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA06G30000.1 (Glycine max), 5'ss of exon 19
GGCTTGAATATTTCGAGTCCAAAGCTCTGGAACAGCAAGAAGCTGCACGAAATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgta-ttaaaaca-tgagaatatgcactagatgactatggattgtaaaagaattaacaaaatagctatgatgtcaga-gtacaccctcaaatctattatttctt
|||| ||||| || ||||| || |||||||| || || || |||||||| |||||||| || || ||||| ||||| || ||||||||||| ||| | ||||| |||  ||| | ||||   |  | |  |   | |   |  ||   |  | ||   |     | | |  |||   | | ||  |||  |    |||   ||
GGCTAGAATACTTTGAGTCAAAGGCTCTGGAGCAACAGGAGGCTGCACGGAATGGTACACCTAAACCAGATGCCTCAATCTCCAGCAAAGGTCATTTAAGgtagttattacaattagaaccagttccactta--tgtcagtc-tatctggttcaattgatggcttttcagctcatttgaatacaatcatgtgctctatacatt

upper sequence: AT4G28080.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv11s0037g00850.t01 (Vitis vinifera), 5'ss of exon 2
GGCTTGAATATTTCGAGTCCAAAGCTCTGGAACAGCAAGAAGCTGCACGAAATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaa-aca-----tgagaatat-gcactagatgactatggattgtaaaagaattaacaaaatagctatgatgtca-gagtacaccctcaaatctattatttctt
||||||| || ||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||  |||     |||||  ||      |  ||| |   |  |    |    | |||  |  | |  | |||| | | ||| |   | ||    |||       
GGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCAAAGGTCATCTAAGgtaataattacaatttctgagagaattatgtgaattgagtccagtattcttacacctcaactgataatcgctcatgtaatgggtaaatgattaa-caaatt-------

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|116474176|gb|EG516768.1|EG516768
EST:     AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAG                         TGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
genomic: AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaac ... ccaataacagTGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
EST: gi|124765623|gb|EH855753.1|EH855753
EST:     AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAG                         TGTATCAGACCTGTTGG
genomic: AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaac ... ccaataacagTGTATCAGACCTGTTGG
EST: gi|125326792|gb|EL340872.1|EL340872
EST:     AATGGTACTCCCAAGCCAGACGCCTC-ATTTCCAGCAAAGGCCATCTCAG                         TGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
genomic: AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaac ... ccaataacagTGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
EST: gi|116474175|gb|EG516767.1|EG516767
EST:     AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAG                         TGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
genomic: AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaac ... ccaataacagTGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
EST: gi|125000418|gb|EL072687.1|EL072687
EST:     AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAG                         TGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG
genomic: AATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaac ... ccaataacagTGTATCAGACCTGTTGGATTATATAACCCCGGATTCTGGTATTAAAGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTGAATATTTCGAGTCCAAAGCTCTGGAACAGCAAGAAGCTGCACGAAATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCAAAGGCCATCTCAGgtattaaaacatgagaatatgcactagatgactatggattgtaaaagaattaacaaaatagctatgatgtcagagtacaccctcaaatctattatttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa