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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G12360.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
-cttacatta--ctctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactctttt-ttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
  |||  |     | || |||||  |   ||    | |  |||| ||| |  | ||   |    | |  |||| ||     ||| || |   ||   ||   |||  ||| |  ||| | || |  ||||||||||| || |||||||||||  | ||||||||||| || |||||||| ||||| ||||| || || |||
atttatttggacatgtatgttgagttgcatg----agtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
-cttacattactctacg--ttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
  | |   || || | |  ||| | ||||| | ||   ||||||   | || | |     ||| |||  || | ||  |  | | |||  |  | ||| | ||| |||| |  ||  | || || | ||| ||||| || |||||||||||  | || ||||||||||| ||||||||||||||  | || || || |||
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgatagg--atccttttctttttgtaatgtaaat-gcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 12
cttacattactctacgttgatctatgtggtatactttatttg---gttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
        |  | | | || |   |   ||||    |  |||   | |     | | | |||  |   | |||  |||   | |  |   | ||   | | |||  ||| |  ||| | ||||| |   | |||||||| |||||||||||  | ||||| |||||||| ||||||||||||||| | || || || |||
aaagggccaagcaatgctgttagctaaagtattagctgcttgatagctgtgtcaatggatctggttaacatttattca---taggatctattttgagtgtcagATCTGGTGGAGAGTTATCTACCAAGCAGTTGCAGAAAATGGTTCAAGCTCTTCCACAATACAGTGATCAAATTGACAAGCTCACCCTTCATGTTGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
-cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttc-ttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
 || || |      ||| |  | |  |   | | ||| | ||  ||     | | | |  | | |  ||  |||  |||   |||  || | ||||| | |||   |  |  ||  | || ||||||||||| || || |||||||| ||  | |||||||||||||| |||||||| ||||| || || || || |||
actgacttccaaacacgattttgttagctatgttcttaacttc-ttgtttcaat-gttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactctttt---ttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
 |||  | |  |||  || || | | || |  |  ||  ||| ||     |    ||  ||          |   |  || ||  | | | ||   ||  ||||  | |   |||  | || ||||| ||  | || ||||||||||||||| | |||||||||||||||||||||||||||||||| ||||| ||||||
tttagctaagcctagatttat-tgtttgatggaagtt--ttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactct---tttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
| | ||||  |  | | |  |  |      || ||| || || |||   |  |        |    |  | || || |||     ||| |   |||   |||||| | | | |||  | || ||||| || ||||||||||||||||||||| | ||||| ||||| |||||||||||||||||||| ||||| ||||||
ccttcattcatgaatggtttttcaaaaaccattctt-atatgtttattta--ttatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
cttacattactctacg-----ttgatctatgtggtatactttatttggttagagaagtag-gtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
 ||  |  | |  | |     | ||||| |    ||||  ||  ||  |||   |  ||  ||| ||      ||| | ||| |||| ||     ||  |   ||||| | | | |||  | || ||||| || || || ||||||||||||||| | ||||| |||||||||||||||||||||||||| ||||| ||||||
-ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctagttactgtcatcataaactttaaacaactttgctt-----ttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactctttt---ttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
 |||  | |  |||  || || | | || |  |  |  |||  |||   |  ||| |||  ||         | || ||  ||  | | | ||   ||  |||   | |   |||  | |||||||| ||  | || |  || ||||||||| | ||||||||||||||||||||||| |||||||| ||||| ||||||
tttagctaagcctagatttat-tgtttgatggaagt-gtttctttattaatctagttctcgtcataacaaacttaaatt-attgaattttgttgtatttatagTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
cttacattactctacgttgatctatgtggtatactttatttggt--tagagaagtaggtcttctctcctt---ttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
   |  |  || |  | | ||||   |  | |  | || ||| |   || | | |  | |   |   |     |   | ||  |   |       | ||   ||||| ||| | |||  | |||||||| || ||||| |||||||||||||| |||||||| || ||||| |||||||| ||||| || ||||| || |||
---atgtatctttgtgat-atctggttaatct-ttctacttgatgccagtgtattcagaccagtaatccaggatgtgttaacctaaatatttatctgttatgtagAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaagtaggtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
                                   gtttgac  putative branch site (score: 4)
                               ttttgtttgactcttt  CT-rich tract
                     ttttgatcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
cttacat
- - - - -ctctacg
- - - - - - - - - - - - - - - - - - tatttgg
- - - - - - - - - - - - - - - - - - - - - - - -agaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga