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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtttcagttttcagaaggaagaagcacctctctcttttttttttgtcatagtttctcagtgcctaattcatgtgatttgtgtgctttcgaccgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G25740.1 (Glycine max), 3'ss of exon 8
tctgtttcagttttcaga-aggaagaagcacctctctctttttt---ttttgtcatagtttctcagtgcctaattcatgtgatttgtgtgctttcgaccgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAG
  || || |    | | | |  ||  |  ||   |    ||| |   |||     |  ||| | || |   ||   |  | |||  |    |       |||||||||| |||||||||||||||||||| |||||  | ||||||||||| || ||||| || || ||||| || || || ||  | |   | || |  || |
--tgatttatcaataaaataataaatattactaatgaaatttgtagatttcacgctgcttttttagggaacaaa--aattaattgataaattcctctgtgacagCTTCTTTATGAAACATGTCTCTGCATATGGCTCTTATCCTATTATGAGCCAGCAATTGAATATTTGGCTACTTCTAGAACCCTTCCGCGACTTATTGATG

upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G06710.1 (Glycine max), 3'ss of exon 8
tctgtttcagttttcaga-aggaagaagcacctctctcttttttttttgtcatagtttctcagtgcctaattcatgtgatttg-tgtgctttcgaccgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAG
  || || |    | | | |  ||  |  ||   |    ||| |   | |||  ||   |  ||    ||   |  | | ||| |    |      || |||||||| |||||||||||||||||||| |||||  | ||||||||||| || ||||| || || ||||| || || || ||  | |   | || |  || |
--tgatttatcaataaaatattaaatattactgataaaatttgtagatttcacggtgcttttgtagggaacaaaaattaattgataaattcctcttcggcagCTTCTTTATGAAACATGTCTCTGCATATGGCTCTTATCCTATTATGAGCCAGCAATTGAATATTTGGCTACTTCAAGAACCCTTCCGCGACTTATTGATG

upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv16s0039g01610.t01 (Vitis vinifera), 3'ss of exon 8
tctgtttcagttttcagaaggaagaagcacctctctcttttttttttgtcatagtttctcagtgcctaattcatgtgatttgtgtgctttcgac-cgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAG
        || |||    |  |    |    |  |   |         |||| ||  |  |||  || |   |  ||| | |  |   |||      |||||| || |||||||| ||||| ||  | |||||  | || ||||||||||||||||| ||||||||||| || || || ||  | | | | ||    || |
------gtagcttttgtcattattg-gtggttaacaagtaagaaccaatcatcgtagccaagttactga---aaatgact-gcatatcttctttgtaacagCTACTTTATGAAACTTGTCTTTGTGTTTGGCTCTTATCTTATTATGAACCTGCAATCGAGTACTTGGCTACTTCTAGAACCCTACCACGACTAGTAGAGG

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|125001585|gb|EL073854.1|EL073854
EST:     AGTTACTTGTCCCTTTAATTTCCCCAGCATCCACTCAGCAGTCTATCCAG                         CTTCTGTATGAAACATGTCTACTGCATCTGGCTTCTGTCCTATTA
genomic: AGTTACTTGTCCCTTTAATTTCCCCAGCATCCACTCAGCAGTCTATCCAGgtaactgtat ... cgaccgacagCTTCTGTATGAAACATGTCT-CTGCATCTGGCTTCTGTCCTATTA
EST: gi|125311162|gb|EL325247.1|EL325247
EST:     AGTTACCTGTCCCTTTAATTTCCCCAGCATCCACTCAGCAGTCTATCCAG                         CTTCTGTATGAAACATGTC
genomic: AGTTACTTGTCCCTTTAATTTCCCCAGCATCCACTCAGCAGTCTATCCAGgtaactgtat ... cgaccgacagCTTCTGTATGAAACATGTC
EST: gi|86031301|gb|DR327054.1|DR327054
EST:     AGTTACTTGTCCCTTTAATTTCCCCAGCATCCACTCAGCAGTCTATCCAG                         CTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCT
genomic: AGTTACTTGTCCCTTTAATTTCCCCAGCATCCACTCAGCAGTCTATCCAGgtaactgtat ... cgaccgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatagtttctcagtgcctaattcatgtgatttgtgtgctttcgaccgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAG
                  gcctaat  putative branch site (score: 3)
                                       tgctttc  putative PPT
                     taattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtttcagttttcagaaggaagaagcacctctctcttttttttttgtcatagtttctcagtgcctaattcatgtgatttgtgtgctttcgaccgacagCTTCTGTATGAAACATGTCTCTGCATCTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
-ctgtttc
- - - - - - - -agaagga
- - - - - - - - - - - agaagca
- - - - - - - - - - - - - - -cctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatttgt