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'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggggacactaaagttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

Basic information

species Arabidopsis thaliana
transcript AT2G25760.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
---------gttggggacactaaagttatttgttttattt-cctggcaacttt----ccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
         ||| |     | ||  || |||  | | ||    | ||||| ||    ||||    | | ||   ||| | |||||  ||||||||||| ||||||||||||||||||||||| || ||||| || || |||||| || | |||||||||||||| |||||||| || || ||| | ||||
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattt--tagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
gttggggac-actaaagttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
|||       | | |  ||||   |||| | |     ||        | ||  |   ||| |           |||||||||||| |||||||| |||||||||||||| |||||||| || || |||||| || | ||  || |  |||| | ||| |||||||| ||||| ||||
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
gttggggacactaaagttatttgttttatttcctggcaact--ttccttgtcaatcattaacttggtctatt--tgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
   | | ||  |      |  |      |||| |    |||  | ||   | | |||     |  |   | |  | |||||| ||||| |||||||||||||| |||||||| |||||||| ||||| |||||| || | || ||||| || || |||||||| || || ||| | ||||
---gtgaactttgttacaacctccaaattttcttaattactgatccccccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 9
----------------------------gttggggacactaaagttatttgttttatttcctggcaact------ttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
                             ||    || |  |   | ||| | || ||   |    |||      ||  || ||  | |||   |   || ||||   ||||||||||||||||||| ||||| |||||||| |||||||| || || || ||  |||| ||  |  ||||||| |||||||| ||  | ||||| ||||
gttagtgtagttgatgttctgctcacctttttcttactcctactctttttttgtttttatttaaatactcacaaattttttatctgttattc-ttcaatcaattt---agGGAGAGAACAAAGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTCTGTGTGGAATCTGTCCACAACCTTTCCGGAATTTTGTTGAGT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
---------------gttggggacactaaagttatt--------tgttttatttcctggcaactttcc---------ttgtcaatcattaacttggtctatttgtt-agGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
               |||  || |||     || ||        | |||| |||      || |  ||         ||||   | |||    |  || ||   || ||||||||||||| ||||| ||||| |||||||| |||||||| || || || ||  || | ||  |  ||||||| |||||||| ||  | ||||| ||||
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
gttggggacactaaagttatttgttttatttcc--tggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
|||        |  |  || |  ||||| | |   | | || |     | | | || |||      | | | |   ||||||| || ||||| || ||||| |||||||| ||||||||||| || ||||||||| | || ||||| ||||||||||| ||||| || ||||| || |
gttattattgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactc-ttatgaaactttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
gttggggacactaaagttatttgttttatttcc--tggcaactttccttgtcaatcat-taacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
|||       ||  |  || |  ||||| | |   ||| || |     | | | || | | | ||  | | ||    ||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||||||| | || ||||| ||||| ||||| ||||| || ||||| || |
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgtta--cagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
gttggggacactaaagttatttgttttatttcc--tggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
|||           |  || |  ||| | | |   ||| || |          ||  |||      | | | |   ||||||| || ||||| || ||||| |||||||| |||||||||||||| || |||||| | || ||||| ||||| ||||| ||||| || ||||| || |
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------gttggggacac--taaagttatttgttttatttcctggcaactttccttgtcaatcattaactt-----ggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
                                               |||  |   |  |||| ||  ||  ||   |||||  ||| |||     |  ||  ||   ||       ||   |   |||||||||||||| || |||||||||||||||||||||||||| || || || ||| |||| || |||||||||||    |||||  | |||||||| || |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatagGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT

upper sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 9
gttgg-ggacactaaagttattt--gttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
||||   |   | ||| |||  |  | |||  ||    |  | | |     ||| ||  | |         ||  |||||||||||| ||||| | |||||||||||| ||||||||||| || || |||||| || | || ||||| ||||| || |||||||| |||||||| || |
gttgacagtttccaaacttaaataggattttcttttatgtgattctgtacatcattc--tgaaccaacagcttctttagGGAGAGAATAAAGGGTACCTTGTTTGCAAAAAGAAGATGGCAACATCTCCAGAAGCTTTGTGTTGCTTTTGTCCTCAGCCTTTTCGGCAGTTTGTTGAAT

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|124861961|gb|EH946398.1|EH946398
EST:     ACACTCTTGTTTTCCTTCTTCGAGGCCGGCTTCCATGGCAAGGGTACCAG                         GGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGG
genomic: ACACTCTTGTTTTCCTTCTTCGAGGCCGGCTTCCATGGCAAGGGTACCAGgttggggaca ... tatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT
                                cattaac  putative branch site (score: 2)
                                           tctattt  putative PPT
                             aatcattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggggacactaaagttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT