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

...acttttctactgaaactagaagttctggtttttgtctttcacttatctcttccaaacaactgcttcaattttttctcatattgtttgtttcatgtgatagGTGGTTTGGAATACAGCTGAATCCTCAGTTTATGAGCATTGATCTCAA

Basic information

species Arabidopsis thaliana
transcript AT3G52940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g03930.t01 (Vitis vinifera), 3'ss of exon 5
acttttctactgaaactagaagttctggtttttgtctttcacttatctcttccaaacaactgcttcaattttttctcatattgtt------tgtttcatgtgatagGTGGTTTGGAATACAGCTGAATCCTCAGTTTATGAGCATTGATCTCAA
    || |  ||||  |  ||| | |||  |  |   ||  |||   |       | |   |  |    || |  | || ||| |      ||| ||||   |||||||||| || |||||||| ||||||||||||||| |||||||  ||||
----ttatgatgaa--tgaaagatttggcatgggctgtttgctttgtttccttggagactggactttgcttatcttgattttgctaatccttgtgtcattcaatagGTGGTTCGGGATACAGCTTAATCCTCAGTTTATGGGCATTGACATCAA
















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|125089633|gb|EL147927.1|EL147927
EST:     AAGGGTTCTTCCCTAAAGCCTCATGTCTCAGGAAATCTTGTACATGACTG                         GTGGTTTGGAATA
genomic: AAGGGTTCTTCCCTAAAGCCTCATGTCTCAGGAAATCTTGTACATGACTGgtactaacat ... catgtgatagGTGGTTTGGAATA
EST: gi|124709469|gb|EH800871.1|EH800871
EST:     AGCCTCATGTCTCAGGAAATCTTGTACATGACTG                         GTGGTTTGGAATACAGCTGAATCCTCAGTTTANGAGCATTGATCTCAAGTT
genomic: AGCCTCATGTCTCAGGAAATCTTGTACATGACTGgtactaacat ... catgtgatagGTGGTTTGGAATACAGCTGAATCCTCAGTTTATGAGCATTGATCTCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttccaaacaactgcttcaattttttctcatattgtttgtttcatgtgatagGTGGTTTGGAATACAGCTGAATCCTCAGTTTATGAGCATTGATCTCAA
                                      tttgtttc  CT-rich tract
                     aattttttctcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttttctactgaaactagaagttctggtttttgtctttcacttatctcttccaaacaactgcttcaattttttctcatattgtttgtttcatgtgatagGTGGTTTGGAATACAGCTGAATCCTCAGTTTATGAGCATTGATCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA