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'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGAGATTCAGATAACAAAGCTGTTACTAAGATCATACTATGACATTGTAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccctcatccctttccccaagtttcttgcagtatctcaaacttgtacgatatatcatcaccttgatatttgattgccctttgaaattgtctttt...

Basic information

species Arabidopsis thaliana
transcript AT4G33650.2
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G33650.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA04G16340.1 (Glycine max), 5'ss of exon 17
AGTTGAGATTCAGATAACAAAGCTGTTACTAAGATCATACTATGACATTGTAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccctcatccctttccccaagtttcttgcagtatctcaaacttgta---cgatatatcatcaccttgatatttg-attgccctttgaaattgtctttt
  |||| ||     |||||||| || |  | |||||||||||||||||||| || || ||| ||||||| | ||| || |||||||| ||| ||||| ||| |  |  |||||||    |    | | ||  || |||||  |||   |  |   | |  || ||    ||||   ||||   |||     ||||||       
TATTGACATAACAGTAACAAAGTTGCTTTTGAGATCATACTATGACATTGTCAGAAAAAATGTTGAGGATTTGGTCCCTAAAGCAATTATGTATTTCTTGgtactttacctcatcttccttgt-aggatttgtgaagtattgcaattataaatttcaaagtagcaatctcttgtcttttgtgctgcatacagaaattagag---

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 5'ss of exon 18
AGTTGAGATTCAGATAACAAAGCTGTTACTAAGATCATACTATGACATTGTAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccctcatccctttccccaagtttcttgcagtatctcaaacttgtacgatatatcatcaccttgatatttgattgccctt--tgaaattgtctttt-
| |||| |||    | || || ||| | ||| ||||||| ||||||||||| |||||||||||||||||  | ||||| ||||| |||||||| ||||||| || |    | ||||  |   |  |   | ||    | | |     ||  | | | | | || ||||  | |     |||   ||  ||| ||  |  | | 
AATTGAAATTTCAGTCACTAAACTGCTGCTACGATCATATTATGACATTGTCAGGAAGAATATTGAGGATGCTGTACCTAAAGCCATCATGCACTTCCTGgtaattgttttaatcctatctgctcaccattttctgttcttttc--ttttcatgttctgttat-acctaaaaaaaatgttgaagttcatgagatcctgctgta

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: PP1S187_100V6.2 (Physcomitrella patens), 5'ss of exon 19
AGTTGAGATTCAGATAACAAAGCTGTTACTAAGATCATACTATGACATTGTAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccctcatccctttccccaagtttcttgcagtatctcaaacttgtacgatatatcatcaccttgatatttgattgcc-ctttgaaattgtctttt-------------------------------------------------------------------
  | || |||    | ||     || |||| |  || ||||||||||||||  ||||||||||| | ||||  ||||| ||||| ||||||||||||||||   |||   |  || |||    |  | |        |   ||||  |  |  ||  ||   |||      || | |   ||  |  |  | ||||   |                                                                    
TCTGGAAATTGCTGTGACTCGATTGCTACTTAAGTCCTACTATGACATTGTGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagttttctcacttatatcttgctgaagatgttgcttcaa-ttcattggacttactgtcataggtttactaggaggcagcaatacatttgttggtctatgaataagtttacatgtttccttggtcgaattttcaacctgatgactgttttcttgatataacag

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|116378698|gb|EG421290.1|EG421290
EST:     TTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTG                         GTAAACCACCCAAAACGTGAGCTGCATAACGTTTTCATCAAGAAGCTTTAC
genomic: TTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccc ... aatgcttcagGTAAACCACACAAAACGTGAGCTGCATAACGTCTTCATCAAGAAGCTTTAC
EST: gi|86083345|gb|DR379104.1|DR379104
EST:     TAAGGAAGAATATTGAGGACTCGGTACCAAAWGCAATCATGCATTTCCTG                         GTAAACCACACAAAACGTGAGCTGCATAACGTCTTCATCAAGAAGCTTTAC
genomic: TAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccc ... aatgcttcagGTAAACCACACAAAACGTGAGCTGCATAACGTCTTCATCAAGAAGCTTTAC
EST: gi|47828922|gb|CK118606.1|CK118606
EST:     TAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTG                         GTAAACCACACAAAACGTGAGCTGCATAACGTCTTCATCAAGAAGCTTTAC
genomic: TAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccc ... aatgcttcagGTAAACCACACAAAACGTGAGCTGCATAACGTCTTCATCAAGAAGCTTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGAGATTCAGATAACAAAGCTGTTACTAAGATCATACTATGACATTGTAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccctcatccctttccccaagtttcttgcagtatctcaaacttgtacgatatatcatcaccttgatatttgattgccctttgaaattgtctttt

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA