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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcttctgtctccctcctgcctttctagcatatttggtttaagaaatttaaatctgaattttgtccctttttattttattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA

Basic information

species Arabidopsis thaliana
transcript AT3G11710.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G386714_T01 (Zea mays), 3'ss of exon 12
-------gtaaaatcttctgtctccctcctgcct-ttctagcatatttggtttaagaaat-ttaaatctgaattttgtccctttttattttattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA
        |       | ||  ||  || || ||  |  ||  ||    |||  |   || ||   | | |   |  |    | |  |  ||||    || | |||||  | ||  ||||   |||||||||||| ||||| || |||||||| || || ||||| |||||||| ||||| || ||||| || ||     
tcttggccttttggagtttgggtcaatcatgtctgctacagagtaccctgttagaattatatttggtataatactgatgtgctctgctgctattggatagTTAGTTGGGCATTTCTTGGAGGAGACATGTGTGAATCCAACATTTATCATCAATCATCCAGAGATAATGAGTCCATTGGCAAAGTGGCATAGGTCTCGAC

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G21870.1 (Glycine max), 3'ss of exon 12
------gtaaaatctt---ctgtctccctcctgcctttctagcatatttggtttaagaaatttaaatctgaattttgtccctttttattttattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA
       |  ||| ||   |  |     |  ||| |   ||   |||||   ||| ||| | |      ||| | |     | ||  ||| || ||||||||||||||  | ||| |||||  ||||||||| || || || ||||| || ||||| || ||||||||||||||||| || || ||||||||||| ||  
tttcagttttaattttgcacaattctaataatgcatcgttaatgtatttttattatgaagtgtctgcaggaaatataattatattcttttcatattgcagCTTGTTGGTCACTTTTTGGAAGAGACATGTGTAAATCCTACATTCATAATAAACCACCCTGAGATCATGAGTCCTTTAGCAAAGTGGCACAGATCAAAAC

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G08040.1 (Glycine max), 3'ss of exon 12
------gtaaaatcttctgtctccctcctgcctttctagcatatttggtt---taagaaatttaaatctgaattttgtccctttttattttattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA
       |  |   ||||   |      |   | |      | ||  | |   |  ||  | |      ||| | |     | ||  ||| || ||||||||||||||  | ||| |||||  ||| ||||| || || || |||||||| ||||| || ||||||||||||||||| || || ||||||||||| ||  
taaattttgcacaattctaattaatgtatttttattcgttgttttgagcttcctgtgaggtgtctgctggaaatataattatattcttttcatattgcagCTTGTTGGTCACTTTTTGGAAGAGACGTGTGTAAATCCTACATTCATCATAAACCACCCTGAGATCATGAGTCCTTTAGCAAAGTGGCACAGATCAAAAC

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv15s0024g00700.t01 (Vitis vinifera), 3'ss of exon 13
------gtaaaatcttctg-tctccctcctgcctttc-tagcatatttggtttaagaaatttaaatctgaattttgtccctttttatttt---attttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA
      | || || || || | |   |  |  ||||  |    |||      |   |||||| |    || ||||     ||   |||||   || ||||||||||| ||  | ||||| ||   ||||||||| || || ||||||||||  ||||| || || || |||||||||||||| || ||||||||||||||  
tttgctgcaacattttgtgatttaaattgtatcttttatgatgtatagcacattttaaatttta--tggatttttaattattgccattttgcaatgttgcagCTTGTGGGGCATTTTCTTGAGGAGACATGTGTAAATCCTACTTTCATCACTAACCATCCTGAAATAATGAGTCCTTTGGCAAAGTGGCACAGATCGAAAC

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0060g02350.t01 (Vitis vinifera), 3'ss of exon 28
------gtaaaatcttctgtctccctcctgcctttctagcatatttggtttaag--aaatttaaatctgaattttgtccctttttatttt---attttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA
      | || || || ||  |           || ||  || | | | |||    |||||| |    || ||||     |||  |||||   || ||||||||||| ||  | ||||| |||  | | ||||| || || ||||||||||||||||| || || || |||||||||||||| || ||||||||||||||  
tttggtgcaacattttgtgatttaaattgtatcttttatgatgtatagcttattttaaatttta--tggatttttaattatttccattttgcaatgttgcagCTTGTGGGGCATTTTCTTGAAGAGGCCTGTGTAAATCCTACTTTCATCATCAACCATCCAGAAATAATGAGTCCTTTGGCAAAGTGGCACAGATCGAAAC

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|86083865|gb|DR379624.1|DR379624
EST:     TTGATGTCAAATGCCCTCCTCCTCAGACAACAGCTCGTCTGTTAGATAAA                         CTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATC
genomic: TTGATGTCAAATGCCCTCCTCCTCAGACAACAGCTCGTCTGTTAGATAAAgtaaaatctt ... tattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATC
EST: gi|125034760|gb|EL107029.1|EL107029
EST:     AGCTCGTCTGTTAGATAAA                         CTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATC
genomic: AGCTCGTCTGTTAGATAAAgtaaaatctt ... tattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATC
EST: gi|124989101|gb|EL061441.1|EL061441
EST:     TTGATGTCAAATGCCCTCCTCCTCAGACAACAGCTCGTCTGTTAGATAAA                         CTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCAT
genomic: TTGATGTCAAATGCCCTCCTCCTCAGACAACAGCTCGTCTGTTAGATAAAgtaaaatctt ... tattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtttaagaaatttaaatctgaattttgtccctttttattttattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA
                           ttttgtccctttttat  CT-rich tract
      tttaagaaatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcttctgtctccctcctgcctttctagcatatttggtttaagaaatttaaatctgaattttgtccctttttattttattttgcagCTTGTTGGAGAATTTCTGGAACCGACATGTGTGAACCCAACTTTCATCATCAACCAGCCCGAGATCATGAGTCCTTTGGCTAAATGGCACAGATCGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA