Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatgatgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC

Basic information

species Arabidopsis thaliana
transcript AT3G55770.6
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55770.6 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G03490.1 (Glycine max), 3'ss of exon 3
gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatg-atgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC
                                     | |     |    |  ||||   ||    | ||     |||     ||   || ||||  | || || |           |||      ||||| |  |  |||| |     ||||||||||  || || ||||||||||||||| | |||||||||||||| | |||||||||||| |||||||||||    |||| ||||||||| |||||| 
-------------------------------------cagacaggaccttaataatg---ttggacagtaattgacttagcatttgtgtgtatgagcttaaagttttacacggattaaag------ttgatgatctttatgttt-----caGCTGAGTAACTATTCCTCAATGGAAGGTGTTCTTTACTGTAAGCCTCACTATGAGCAGCTCTTCAAGGAGAGTGGCTCCTTCAGCAAGAACTTCCAGTCA-

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G34830.1 (Glycine max), 3'ss of exon 3
gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatgatgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC
                                     |||     |    || ||||   ||    | ||      ||     ||   | |||| || || || |    ||  ||          ||||| |  |  |||| |     |||||||| |  || || ||||||||||||||| | || ||||||||||| |||||||||||||| |||||||||||    |||| ||||||||| |||||||
------------------------------------tctgacaggaccttagtaatg---ttggacactaattgagttagcatttgtgt-atgagtttaaagttt----ta--cacggattatagttgatgatctttatgttt-----cagCTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G06800.2 (Glycine max), 3'ss of exon 2
gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatgatgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC
                                          || |||   | ||||  || || | || |  ||  | ||    ||||  |||  | ||| | |          ||   | ||  | |   |  || | || | || ||||| || |  || || || |||||||||||| | |||||||||||||||| |||||| ||||| |||||||  ||   |||||| |||||||| |||||||
------------------------------------------ttgattgctgcaatgcatt-actagtt-cttatgatattaaacaaattttgaggttaatttttgg-------gtatttaacttctcacttataaattttcatgtttcagCTCAGCAACTATTCCTCCATGGAAGGTGTTCTATACTGTAAGCCTCATTATGAGCAACTCTTCAAGGAGACAGGATCTTTCAAGAAGAACTTCCAGTCAC

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G42100.1 (Glycine max), 3'ss of exon 1
gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatgatgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC
                                          || |||   | ||||  || |  | || |  ||  | ||    |||   ||  || | | | || | |     |||        | ||||| | |    | | || ||||| || |  || || || |||||| ||||| | |||||||||||||||  |||||| ||||| |||||||  ||   |||||| |||||||| |||||||
-----------------------------------------cttgattgttgtaatgcatt-attagtt-cttatgatattaaacaaaatttgggttaattttatagtatt----taatttctcacttataaattta----catgtttcagCTTAGCAACTATTCCTCCATGGAAAGTGTTCTTTACTGTAAGCCTCATAATGAGCAACTCTTCAAGGAGACAGGATCTTTCAAGAAGAACTTCCAGTCAC

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g03280.t01 (Vitis vinifera), 3'ss of exon 2
gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatgatgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC
                                           |||||   |||      |||  |||   |  | ||  | ||  |     ||| || |    ||  || |   | |  |  ||| ||||   || || | ||||  |||||||| | ||| || |||||||| |||||| | |||||||||||||| |||||||||||||||||||||  ||| | |||||||||||| ||||||||||
------------------------------------------ataatttatggatctgacttaaaaat---ctgtgtttgttctctacaatagaaatgcaaaattaaagtgattgttattatatct-gata---tacatatgtttt--cagCTGAGCAATTATTCCTCAATGGAGGGTGTTCTTTACTGTAAGCCTCACTTTGAGCAGCTCTTTAAGGAGTCTGGAAATTTCAACAAGAATTTTCAGTCAC

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|47829977|gb|CK119661.1|CK119661
EST:     GATATCACAAGTCTTGCTTCAAATGCACTCACTGCAAAAGCAGGCTTCAG                         CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
genomic: GATATCACAAGTCTTGCTTCAAATGCACTCACTGCAAAAGCAGGCTTCAGgtctgattct ... ctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
EST: gi|124933262|gb|EL010437.1|EL010437
EST:     ATGCACTCACTGCAAAAGCAGGCTTCAG                         CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
genomic: ATGCACTCACTGCAAAAGCAGGCTTCAGgtctgattct ... ctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
EST: gi|125188651|gb|EL203605.1|EL203605
EST:     CAAATGCACTCACTGCAAAAGCAGGCTTCAG                         CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
genomic: CAAATGCACTCACTGCAAAAGCAGGCTTCAGgtctgattct ... ctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
EST: gi|164161910|gb|EL976291.1|EL976291
EST:     AAGCAGGCTTCAG                         CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
genomic: AAGCAGGCTTCAGgtctgattct ... ctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
EST: gi|301502045|gb|HO207585.1|HO207585
EST:     GATATCACAAGTCTTGCTTCAAATGCACTCACTGCAAAAGCAGGCTTCAG                         CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
genomic: GATATCACAAGTCTTGCTTCAAATGCACTCACTGCAAAAGCAGGCTTCAGgtctgattct ... ctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTT
EST: gi|124868917|gb|EH953354.1|EH953354
EST:     GATATCACAAGTCTTGCTTCAAATGCACTCACTGCAAAAGCAGGCTTCAG                         CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTA
genomic: GATATCACAAGTCTTGCTTCAAATGCACTCACTGCAAAAGCAGGCTTCAGgtctgattct ... ctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC
                                          tgtcttttt  CT-rich tract
                             ttgataaagtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgattctctcatctttgtattcatgttaacgatgctgctttaattagaggaatgagtttacgaattacccatcttcttgcttaaatgatgaattgaatgtctattgtaaccataagcagctcttgataaagtaaatgtctttttacagCTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC