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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaaacaaaagaaaccttgttctgtacttattatgtaggtaataattggtattactctcttgactctctttcatattttttgttctattccagAGGACGGTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTCCCTGATGTCGGGTTTTCATATATAGCAGCTCATAGCCCTGGAGGAGGATCTGTTG

Basic information

species Arabidopsis thaliana
transcript AT4G13360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 3'ss of exon 4
---gtacaaaaacaaaagaaaccttgttctgtacttattatgtaggtaataattggtattactctcttgactctct--ttcatattttttg-------ttctattccagAGGACGGTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTCCCTGATGTCGGGTTTTCATATATAGCAGCTCATAGCCCTGGAGGAGGATCTGTTG
         |||     | |||  || | |  | ||  |||||   | ||   |  | | | | | |  | | |     ||| | | || |       | || || ||||||||| | || || |||||||||||||| |||||||||||||| || || || ||| | || || |  ||  |    || ||||| ||  ||||||
gcaagtttgaaatttctgtaactctgatttagattt--tatgttcatcatttgtattctcagtatttgaattgtaaggctcaaaatgttcgcatgcactactgttacagAGGACGCTCCTGGCTATGCCAGAAAATGGTATTGGCTTGTTCCCGGACGTTGGCTTTGCTTACATTGGTGCCAAAGCTCCAGGAGGTGGTGCTGTTG

upper sequence: AT4G13360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ14541 (Selaginella moellendorffii), 3'ss of exon 4
gtacaaaaacaaaagaaaccttgttctgtacttattatgtaggtaataattggtattactctcttgactctctttcatattttttgttctattccagAGGACGGTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTCCCTGATGTCGGGTTTTCATATATAGCAGCTCATAGCCCTGGAGGAGGATCTGTTG
                                   | ||| |    | |       |  | ||    ||    ||    ||| || |   ||  ||||||||||||||||||||||| || |||||||| |||||||| || || || || ||| |||||||||||||||  |  |||| |   ||| |||| |
----------------------------------gtctgtggcgttttaccttggctcgtttcgaagctaagctttgcgtttgttttgtgat--cagAGGACGGTTCTTGCCATGCCTGAGAATGGAATCGGCTTGTTTCCAGACGTTGGTTTTGCATATATAGCAGCTCGAACTCCTGCAAATGGAGCTGTAG

upper sequence: AT4G13360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ26244 (Selaginella moellendorffii), 3'ss of exon 4
gtacaaaaacaaaagaaaccttgttctgtacttattatgtaggtaataattggtattactc-tcttgactctctttcatattttttgttctattccagAGGACGGTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTCCCTGATGTCGGGTTTTCATATATAGCAGCTCATAGCCCTGGAGGAGGATCTGTTG
                                                  ||   |  ||| | | ||  ||      |   |||| || |  || |||||||||||||||||||||| || |||||||| |||||||| || || || || ||| |||||||||||||||  |  |||| |   ||| |||| |
-----------------------------------------------gtctgtggtggctcgtttcgaagctaagctttgcgtttttttgtgatc-agAGGACGGTTCTTGCCATGCCTGAGAATGGAATCGGCTTGTTTCCAGACGTTGGTTTTGCATATATAGCAGCTCGAACTCCTGCAAATGGAGCTGTAG

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|301502043|gb|HO207583.1|HO207583
EST:     GATTTGGTCTTGGTCTTTCTGGACATGGTCGCTACCGTGTGATAACAGAG                         AGGACGGTTCTTGCCATG
genomic: GATTTGGTCTTGGTCTTTCTGGACATGGTCGCTACCGTGTGATAACAGAGgtacaaaaac ... tctattccagAGGACGGTTCTTGCCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaataattggtattactctcttgactctctttcatattttttgttctattccagAGGACGGTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTCCCTGATGTCGGGTTTTCATATATAGCAGCTCATAGCCCTGGAGGAGGATCTGTTG
                   tcttgac  putative branch site (score: 3)
                         ctctctttcatatttt  CT-rich tract
                              tttcatattttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaaaacaaaagaaaccttgttctgtacttattatgtaggtaataattggtattactctcttgactctctttcatattttttgttctattccagAGGACGGTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTCCCTGATGTCGGGTTTTCATATATAGCAGCTCATAGCCCTGGAGGAGGATCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT