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

gtatgatgctttacccgccataacattaaattcttaatttctggctctgccagacagagttaatattggaaacaaactgaaacctgtggtcgaaaactctcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG

Basic information

species Arabidopsis thaliana
transcript AT4G17270.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G01180.1 (Glycine max), 3'ss of exon 7
gtatgatgctttacccgccataacattaaattcttaatttctggctctgccagacagagttaatattggaaacaaactgaaacctgtggtcgaaaactctcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
         | |      ||||   ||  |   | ||        || |  ||  |||||||   ||  | |   | | ||    ||  | |   |   |    ||||||| ||||||||||  || ||||||||||| || ||||||||||||
-------tttctgatgagcatacatttttaaattgaacagaaaattcaga-agttagagttatgtttatacaagcatttaa-tgggtcattgctgatatttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG

upper sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 8
gtatgatgctttacccgccataacattaaattcttaatttctggctctgccagacagagttaatattggaaacaaactgaaacctgtggtcgaaaactctcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
        |  |   | | |  |      | |   |||||  |   |||| | ||  |    | |||  ||  || ||   |    ||   | |   |||    | ||||| |||||||||| ||||||||| |||||||| ||||||||||||
-------accatcttcccaagtatgaaggactaaaaattttagtaactgctaaactaatgagacattttaacaaagctttgataaatg--tggattatcttcttttcagGAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG
















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|164011473|gb|ES115594.1|ES115594
EST:     GAATCTTCTCAGA                         GAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
genomic: GAATCTTCTCAGAgtatgatgct ... tcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
EST: gi|86088108|gb|DR383867.1|DR383867
EST:     AGTATGTGAGCTCGATGGATAACTTGAGGATTCTGATGAATCTTCTCAGA                         GAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
genomic: AGTATGTGAGCTCGATGGATAACTTGAGGATTCTGATGAATCTTCTCAGAgtatgatgct ... tcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
EST: gi|164097331|gb|EL999377.1|EL999377
EST:     GGATAACTTGAGGATTCTGATGAATCTTCTCAGA                         GAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
genomic: GGATAACTTGAGGATTCTGATGAATCTTCTCAGAgtatgatgct ... tcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagttaatattggaaacaaactgaaacctgtggtcgaaaactctcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG
   agttaat  putative branch site (score: 4)
                                          ctctc  putative PPT
     ttaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgctttacccgccataacattaaattcttaatttctggctctgccagacagagttaatattggaaacaaactgaaacctgtggtcgaaaactctcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC