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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcactcaatcctcttaattggttttcaagattagatataaatctgtgtaccgggttgggtttattgattcatacacaagtaagaagcaatctttgttgttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA

Basic information

species Arabidopsis thaliana
transcript AT1G64550.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 17
gtactcactcaatcctcttaattggttttcaagattagat-ataaatctgtgtaccgggttgggtttattgattcatacacaagtaagaagcaatctttgttg-ttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA
                            | ||  | ||||  |  || |  ||         | |   |||      |  | | | | |||| || |  ||   |||||   || | |||||||||||||||||||| |||||| |||| |||||||| ||| | ||||| ||||| || |||||| |  | || |||   || || ||| | |||||||
---------------------------gtaaaactaagatcgttcattttggtgtaaaagctgatgacttggcat-cattctaattacaagctatatgggtgacttgttatcttttacagGTGAGTCACGACGAGCACCTGATAACGGGGAGCGTGGATGAGCTTTGGGTGGTGTCGGAAGGCAGGGTGTCGCCTTTCGCAGGCACGTTCAAGGACTACA

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 17
gtactcactcaatcctcttaattggttttcaagattagatataaatctgtgtaccgggttgggttta--ttgattcatacacaagtaagaagcaatctttgttgttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA
            |||| ||  |    | |||   || | ||   || |  | |     |  |  | |  |  |  || ||    |    |  | |    |||   ||||||  | |||||||||||||||| |||||||| ||  | ||||||||||||||| | ||||| ||||| || |||||| |  | || |||   || || ||| | |||||||
------------tcctgttt-taatctctcaccgtttggta---atttagggattaaatgagactaaaatcaaaccaaacg-gggcctaagacgacgagtgtg--tgtttgcat-tgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTGGTGTCGGAAGGCAGGGTGACCCCGTTCTCGGGCACTTTCAAGGACTACA

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 16
gtactcactcaatcctcttaattggttttcaagattagatataaatctgtgtaccgggttgggtttattgattcatacacaagtaagaagcaatctttgttgttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA
                  |  |    ||||||  |||  |  |  |  |||  ||           | |  || ||  |   | |   |   || ||| |  || |  | ||  ||||||||||||||| |||||||| || || ||||||||||| ||  | |||||||| || ||||| ||  | |||||||||||||| || ||||| || || |
---------------gtatgttattctttcaatgttattt-catttgagtgctcctaaactaaaacaatattttatttatctgaattgattgatgtttatgtttat--gctttggcagGTGAGTCACGATGAGCATCTCATCTCTGGAAGCGTGGAGGAACTATGGGTTGTATCCGACGGAAGAGTGGCACCATTCCATGGCACATTCCAAGATTATA

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ22634 (Selaginella moellendorffii), 3'ss of exon 17
gtactcactcaatcctcttaattggttttcaagattagatataaatctgtgtaccgggttgggtttattgattcatacacaagtaagaagca-atctttgttgttgtttgtttgtg-cagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA
                                                                           ||    |  |    |    | |||  |  || || |||    |||||||| || |||||||| |||||||| ||||||||||||||| | ||||||||| |||| || |   |  | ||||| || ||  | ||||| |||||||
--------------------------------------------------------------------------gtaggagaacattgtgtttgttttttctaatgattttttacaacagGTGAGCCATGACGAGCACCTGATATCCGGAAGCGTGGACGAGCTCTGGGTTGTGACAGAAGGAAAAGTATCGCCATTTCACGGCTCGTTCCAGGACTACA

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ11792 (Selaginella moellendorffii), 3'ss of exon 17
gtactcactcaatcctcttaattggttttcaagattagatataaatctgtgtaccgggttgggtttattgattcatacacaagtaagaagcaatctttgttgttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA
                                                                          ||    |  |         | ||| |  |  ||| ||    |||||||| || |||||||| |||||||| ||||||||||||||| | ||||||||| |||| || |   |  | ||||| || ||  | ||||| |||||||
------------------------------------------------------------------------gtatgagaacattgtgtttgttttttctaatgattttttacaacagGTGAGCCATGACGAGCACCTGATATCCGGAAGCGTGGACGAGCTCTGGGTTGTGACAGAAGGAAAAGTATCGCCATTTCACGGCTCGTTCCAGGACTACA

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|164228754|gb|ES129673.1|ES129673
EST:     AAGGCGGTATTTGCATG                         GTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTT
genomic: AAGGCGGTATTTGCATGgtactcactc ... gtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgattcatacacaagtaagaagcaatctttgttgttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA
  tattgat  putative branch site (score: 3)
                                          tttgttt  putative PPT
       attcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcactcaatcctcttaattggttttcaagattagatataaatctgtgtaccgggttgggtttattgattcatacacaagtaagaagcaatctttgttgttgtttgtttgtgcagGTGAGTCACGACGAGCATCTGATATCGGGAAGCGTGGACGAGTTGTGGGTTGTGTCAGACGGCAGGATTGCACCATTCCATGGAACCTTCCATGACTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA