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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACAGACCCGCAGTTTCTGTTATGTCTCCGACATGGTGGATGGACTTATCCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgcctttccattccaacatttaccttaacccctgtaactagagtgtggtgtttttgtttcatttgcttttttctaaaacccctctgtttctcag

Basic information

species Arabidopsis thaliana
transcript AT5G59290.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59290.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 10
ACACAGACCCGCAGTTTCTGTTATGTCTCCGACATGGTGGA---TGGACTTATCCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgcctttccattccaacatttaccttaacccctgtaactagagtgtggtgttt-ttgtttcatttgcttttttctaaaacccctctgtttctcag
                                  ||||| |   | |||   || | ||  |||||  ||      | |   ||   |   ||  | ||   |||  ||      | |   |  ||||   | |||   | |   |   |||  || || || ||    ||  ||    |  ||    ||   | |   ||
----------------------------------TGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTA-TGTCTCTGACAT-Ggtatgcaaaaataattataatttta---tgaccataggattgaccatgtattggttattattaagattatttgaagcccaattttcttcatgttaaag
















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|86075306|gb|DR371063.1|DR371063
EST:     CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAG                         GTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
genomic: CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgccttt ... tgtttctcagGTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
EST: gi|125186745|gb|EL201699.1|EL201699
EST:     CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAG                         GTGAGTTCACAATGGTGGAACTGGCTGAGACG
genomic: CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgccttt ... tgtttctcagGTGAGTTCACAATGGTGGAACTGGCTGAGACG
EST: gi|86075538|gb|DR371295.1|DR371295
EST:     CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAG                         GTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
genomic: CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgccttt ... tgtttctcagGTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
EST: gi|124890126|gb|EH969028.1|EH969028
EST:     TCGGTAACCCAG                         GTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
genomic: TCGGTAACCCAGgtccgccttt ... tgtttctcagGTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
EST: gi|124878334|gb|EH957771.1|EH957771
EST:     TCAACATCGGTAACCCAG                         GTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
genomic: TCAACATCGGTAACCCAGgtccgccttt ... tgtttctcagGTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAG
EST: gi|124760232|gb|EH850362.1|EH850362
EST:     CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAG                         GTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAGCTTA
genomic: CCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgccttt ... tgtttctcagGTGAGTTCACAATGGTGGAACTGGCTGAGACGGTTAAGGAGCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACAGACCCGCAGTTTCTGTTATGTCTCCGACATGGTGGATGGACTTATCCGTCTTATGGAAGGCAATGATACTGGCCCTATCAACATCGGTAACCCAGgtccgcctttccattccaacatttaccttaacccctgtaactagagtgtggtgtttttgtttcatttgcttttttctaaaacccctctgtttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG