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

gtaaatagtcactttggattcatccactcatcgccttaaacattttggtttcctctgtctcttcttatttatgctgatgcaaatcatcaatgtgactactagGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAAATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTG

Basic information

species Arabidopsis thaliana
transcript AT1G17220.1
intron # 9
splice site 3'
intron type U2

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|47828854|gb|CK118538.1|CK118538
EST:     CAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAAGGTCGATGTACAG                         GGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAAT
genomic: CAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAAGGTCGATGTACAGgtaaatagtc ... tgactactagGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAAT
EST: gi|124917681|gb|EH991555.1|EH991555
EST:     CTTAGATTTGCATCAGCTTAATATCATCTTGAAGGTCGATGTACAG                         GGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGA
genomic: CTTAGATTTGCATCAGCTTAATATCATCTTGAAGGTCGATGTACAGgtaaatagtc ... tgactactagGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGA
EST: gi|116471513|gb|EG514105.1|EG514105
EST:     CAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAAGGTCGATGTACAG                         GGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAAT
genomic: CAGGCTTAGATTTGCATCAGCTTAATATCATCTTGAAGGTCGATGTACAGgtaaatagtc ... tgactactagGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctctgtctcttcttatttatgctgatgcaaatcatcaatgtgactactagGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAAATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTG
                        tgctgat  putative branch site (score: 3)
              ttcttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagtcactttggattcatccactcatcgccttaaacattttggtttcctctgtctcttcttatttatgctgatgcaaatcatcaatgtgactactagGGATCCATTGAAGCTGTAAGACAAGCCCTTCAAGTCCTCCCTCAGGAGAATGTCACCTTGAAATTCTTGCTACAAGCAACAGGGGATGTGAGCAACAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA