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

TTGGGCAAATCGTGCATTTGCTCACACAAAACTGGAGGAATATGGCAGTGCAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcctgtgacaagatgttcctgtttcttcgtgtattcagccatattcactgattatctactgaatcacag

Basic information

species Arabidopsis thaliana
transcript AT2G42810.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42810.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 5'ss of exon 3
TTGGGCAAATCGTGCATTTGCTCACACAAAACTGGAGGAATATGGCAGTGCAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcctgtgacaagatgttcctgtttcttcgtgtattcagccatattcactgattatctactgaatcacag
 |||||||| |||||||||||||| |||||  | ||||||||||| |||||| | || ||||| || || || |||||| ||||| | |||||||| || |||   |  ||   | |  | ||||||   |   || |       | |||    |     | |  ||  |   ||
CTGGGCAAACCGTGCATTTGCTCATACAAAGTTAGAGGAATATGGAAGTGCAGTGCAAGATGCTTCAAAAGCAATTGAAATTGATGCTAGATACTCAAAAgtaa-gtgatggtgccatttcttcctgccacag-gtttgcaagttcctatcttttaccctttttttgt-ttgtag

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G126435_T02 (Zea mays), 5'ss of exon 2
TTGGGCAAATCGTGCATTTGCTCACACAAAACTGGAGGAATATGGCAGTGCAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcctgtgacaagatgttcctgtttcttcgtgtattcagccatattcactgattatctactgaatcacag--------------
 |||||||| ||||||||||| ||||||||| | |||||||| || |||||  | ||||||||  | || ||||| ||| ||||||| ||||| || || |||        || ||       |   |     | ||   |      | ||   || || | || | ||| | |               
CTGGGCAAACCGTGCATTTGCACACACAAAATTAGAGGAATACGGAAGTGCTGTGCAGGATGCTACAAAAGCCATCGAAATTGATTCTAGATATTCAAAAgtaagtgatgatgccagtgccacctcttgctgacatggtctttttacttttttttgtttctgtatttaatgaaattttattctgtgtag
















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|164218829|gb|EL992864.1|EL992864
EST:     CAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAG                         GGCTATTACAGGCGTGGTGCTGCGTATCT
genomic: CAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcct ... tgaatcacagGGCTATTACAGGCGTGGTGCTGCGTATCT
EST: gi|86073690|gb|DR369447.1|DR369447
EST:     CAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTATAAG                         GGCTATTACAGGCGTGGTGCTGCGTATCTTGCC
genomic: CAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcct ... tgaatcacagGGCTATTACAGGCGTGGTGCTGCGTATCTTGCC
EST: gi|86073689|gb|DR369446.1|DR369446
EST:     CAATACAGGATGCATCGAAGGCCATTGNAGTTGATTCAAGATACTCTAAN                         GGCTATTACAGGGCGGGGGTGCTGCGTATCTTGCCATGGGAAA
genomic: CAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcct ... tgaatcacagGGCTATTACAGG-CGTGG-TGCTGCGTATCTTGCCATGGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGGCAAATCGTGCATTTGCTCACACAAAACTGGAGGAATATGGCAGTGCAATACAGGATGCATCGAAGGCCATTGAAGTTGATTCAAGATACTCTAAGgtatcatcctgtgacaagatgttcctgtttcttcgtgtattcagccatattcactgattatctactgaatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG