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

gtaaaaatggggatccatgcttctcatttccatgccatgcttttcgttttctcacggatatacttttttcttccttctggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAATGACAAGTTGCAGCGCTCCTATAATGAGCTTATGGAGTACAAGTTGGTTC

Basic information

species Arabidopsis thaliana
transcript AT4G39080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 3
--gtaaaaatggggatccatgcttctcatttccatgccatgcttttcgttttctcacggatatacttttttcttccttctggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAATGACAAGTTGCAGCGCTCCTATAATGAGCTTATGGAGTACAAGTTGGTTC
  ||   ||| |  ||  ||  |||    || ||||| |   | |   | |           || | ||||    ||| ||  |    || ||||||||||||| || ||||||||||| | |||| | ||||| || ||||| |||||  ||||  |||| ||||||||  |||||||||     ||||
gtgtgtcaatcga-atggatttttcctgattgcatgc-agaatataaatcta---------gtattattttaacacttttgaataac-agATAAAGCTTGGAGAACTGGAAGCTGAACTAGCTGAAGTTAATGCAAACAATGAAAAGTTAAAGCGGACCTACAATGAGCTGTTGGAGTACAGTACTGTTC
















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|164196238|gb|EL982582.1|EL982582
EST:     CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAG                         GTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAA
genomic: CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAGgtaaaaatgg ... ggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAA
EST: gi|116448634|gb|EG491226.1|EG491226
EST:     CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAG                         GTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
genomic: CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAGgtaaaaatgg ... ggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
EST: gi|301501304|gb|HO206844.1|HO206844
EST:     CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAG                         GTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
genomic: CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAGgtaaaaatgg ... ggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
EST: gi|86064751|gb|DR360508.1|DR360508
EST:     CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAG                         GTAAAGCTTGNAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
genomic: CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAGgtaaaaatgg ... ggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
EST: gi|116444120|gb|EG486712.1|EG486712
EST:     CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAG                         GTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
genomic: CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAGgtaaaaatgg ... ggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
EST: gi|116415767|gb|EG458359.1|EG458359
EST:     CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAG                         GTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT
genomic: CCAAGGAAATGCAAGGGAAAGAAAATGACATTGACTTGGATGATGTTGAGgtaaaaatgg ... ggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatgcttttcgttttctcacggatatacttttttcttccttctggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAATGACAAGTTGCAGCGCTCCTATAATGAGCTTATGGAGTACAAGTTGGTTC
               ttctcac  putative branch site (score: 2)
                             cttttttcttccttct  putative PPT
                        atatacttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatggggatccatgcttctcatttccatgccatgcttttcgttttctcacggatatacttttttcttccttctggcttgttagGTAAAGCTTGGAGAGCTAGAAGCTGAACTTGTTGAAATCAATGCTAATAATGACAAGTTGCAGCGCTCCTATAATGAGCTTATGGAGTACAAGTTGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT