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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtcttgtcttgtgacacattgatgcctcacagttttggtgtttctatccctttagtttccctgctaagatgaaactgagtgcatatatctctaaattttgtagGTATCAACTCTTTCAAGTTTTTCCTAGCGTATAAAGGATCTCTTATGGTAACTGATGACCTACTCCTAGAAGGACTTAAAAGATGCAAATCCCTCGGTGC

Basic information

species Arabidopsis thaliana
transcript AT5G12200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g59340.3 (Oryza sativa), 3'ss of exon 7
gtaaatgtcttgtcttgtgacacattgatgcctcacagttttggtgtttctatccctttagtttccctgctaagatgaaactgagtgcatatatctctaaattttgtagGTATCAACTCTTTCAAGTTTTTCCTAGCGTATAAAGGATCTCTTATGGTAACTGATGACCTACTCCTAGAAGGACTTAAAAGATGCAAATCCCTCGGTGC
| |||| || |||  | ||  |  |  ||    || |   | | || ||   | |   ||  ||   |  ||   | |     ||    || ||  | ||  |||  ||| ||||| ||||||||||| ||| | ||||||||||| ||  | ||||| || ||||||||||||||  ||||  |  | | ||||||||| || |||||
gcaaatttcctgtagtctgcaatgtctat----cagaacat-gatgctttggtac---tatattgtatcgtagtctaagtgccagaatttaaattgccaatattt-cagGGATCAATTCTTTCAAGTTCTTCATGGCGTATAAAGGTTCATTGATGGTCACGGATGACCTACTCCTGCAAGGCTTACAGAAATGCAAATCTCTTGGTGC
















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|124860781|gb|EH945218.1|EH945218
EST:     GTGGGATGAAGGTGTTTCCAGGGACATGGAGATGTTGGTCAAGGAAAAGG                         GTATCAACTCTTTCAAGTTTTTCCTAGCGTA
genomic: GTGGGATGAAGGTGTTTCCAGGGACATGGAGATGTTGGTCAAGGAAAAGGgtaaatgtct ... aattttgtagGTATCAACTCTTTCAAGTTTTTCCTAGCGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttagtttccctgctaagatgaaactgagtgcatatatctctaaattttgtagGTATCAACTCTTTCAAGTTTTTCCTAGCGTATAAAGGATCTCTTATGGTAACTGATGACCTACTCCTAGAAGGACTTAAAAGATGCAAATCCCTCGGTGC
                                        ctctaaa  putative branch site (score: 3)
                                  atatatctctaaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtcttgtcttgtgacacattgatgcctcacagttttggtgtttctatccctttagtttccctgctaagatgaaactgagtgcatatatctctaaattttgtagGTATCAACTCTTTCAAGTTTTTCCTAGCGTATAAAGGATCTCTTATGGTAACTGATGACCTACTCCTAGAAGGACTTAAAAGATGCAAATCCCTCGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG