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

gtaaaaaagactctttttgcttccattgaattgatcttatgtcacagttcaagcattgatggttttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G19270.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
------gtaaaaaagactctttttgcttccattgaattgatcttatgtcacagttcaag-----cattgatggt--tttgctgaatt-ttgttc----agGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG
       |  |||  | |  || || |  ||||   ||  |||    |   |  ||| |     |||||  |||  |||  ||  || ||||||    || ||  | || ||||| ||| |||||||||||||||||||||||||| || | || ||||
tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G342105_T02 (Zea mays), 3'ss of exon 7
--------------------------------gtaaaaaagactctttttgcttccattgaa--ttgatctta-tgtcacagttcaag----cattgatggt----------tttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG
                                 || ||  ||     ||| | |    ||||  |||||  || || ||       ||    |||| ||| |          |||  | || |   | |||| | || ||||| |||||||| |||||||||||||||||||| |   |  | || ||||
gtgattttctctctcattatttaacaaactaattacaattgatgtagtttccctttgatgaacgttgattctactgccaatccatgagaatgcattcatgttctaattttaatttatttaactgcatgcagGCTGCTAACTGGCTCGATTCTGGCTCATGAGATGATGCATGCTTACCTCCGACTTAAAG

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G017845_T01 (Zea mays), 3'ss of exon 10
-------gtaa-aaaagactctttttgcttcca-----ttgaattgatctt-atgtcacagttcaagcattgatggttttgctgaattttgttc----agGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG
        ||  |      | | |||| ||| |     ||||||   |    |||    | ||      |  |   ||||   |  ||||||||    || ||  | || ||||| ||| |||||||||||||||||||||| ||| || |||| ||||
ttctcctataccatgttgttttgtttggttctacattgttgaatcattaaggatgctcaaatttgtttgtatagacttttatggtgttttgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCATGGTTGCGGCTTAAAG

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 10
---------------gtaaaaaagactctttttgcttc-cattgaattgatcttatgtcac---agttcaagcattgatggttttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG
                |    |  || || |||  ||| ||   | ||  ||||   |||    | || |   ||  ||| ||||  |    |||   ||||||||||||||| || || ||||||||||||||||||||||| ||| || |||| ||||
gaaagaaaatccttcctccccaccaccctatttctttcacaacaactttgtctt-catcagttgattttatttatacatgatttttttcttcttttcacagGTTACTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 9
--------------------gtaaaaaagactctttttgcttccattgaattgatcttatgtcacagttcaagcattgatggttttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG
                        |      || |||  |  | | |   ||  || |||||   | ||||   |   |||  | |  |    |||  ||||||| |||||||| || || ||||||||||||||||||||||| ||| || |||| ||||
gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttt-tcatatgttg-atttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG

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|116457268|gb|EG499860.1|EG499860
EST:     ACACGGCAATGTGAAGTTACCGCCATTCTCATCTTATTCAGGCTCCCTAG                         GTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAG
genomic: ACACGGCAATGTGAAGTTACCGCCATTCTCATCTTATTCGGGCTCCCTAGgtaaaaaaga ... ttttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAG
EST: gi|116457269|gb|EG499861.1|EG499861
EST:     ACACGGCAATGTGAAGTTACCGCCATTCTCATCTTATTCGGGCTCCCTAG                         GTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAG
genomic: ACACGGCAATGTGAAGTTACCGCCATTCTCATCTTATTCGGGCTCCCTAGgtaaaaaaga ... ttttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAG
EST: gi|116435622|gb|EG478214.1|EG478214
EST:     ACACGGCAATGTGAAGTTACCGCCATTCTCATCTTATTCGGGCTCCCTAG                         GTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAG
genomic: ACACGGCAATGTGAAGTTACCGCCATTCTCATCTTATTCGGGCTCCCTAGgtaaaaaaga ... ttttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgatcttatgtcacagttcaagcattgatggttttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG
                          cattgat  putative branch site (score: 4)
                                             ttttgttc  putative PPT
                                           aattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaagactctttttgcttccattgaattgatcttatgtcacagttcaagcattgatggttttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG