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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 12
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctc----atctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
     ||||   |||  |   ||| ||||      |||||||||   |     || ||  |||| | ||  |    | || | ||          |||||| |  |||||||||||||||| || ||||| || || || ||| | || ||| |  | |||||||||||||||||||||||||||||||  ||||||||  | ||| 
----acttaaaagtt--aagattgttata-actcattcgtgttgattttttgaatatctattttatgttaatattctaatgggcaatgccacatttttgttatccagGCTGAAATGCCTGCAGATAGTGGTTACCCTGCTTATTTGGCTGCAAGACTGGCATCTTTCTATGAACGTGCTGGTAAAGTAAGGTGTCTTGGAAGTCCAA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagttta---ttgacacctat--tttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
       || |   ||   ||| |         || ||  | |  |    |    |||| || |     | | |    |||| ||  ||  |||| |   |||   |||||||||||||||| || ||||| || || || ||| | || |||||||| ||||| || || |||||||||||||| || |||||||| ||  | ||||
-----actaggaaatta--tttggagtcgaaagtgctctcgctagctagttactgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttc-cagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgtttta---tagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
      | ||  |    |||||     | ||  |  | ||||||  |   | |||| ||   | | ||    ||    ||   |  |   |||| || |     ||||||||||||||||||| ||||| || ||||| ||  | || |||||||| ||||| || ||||||||||||||||| ||||||||||| ||  | ||||
------taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
---------gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
          |||| | |     ||||   || || | | | || || | ||   | ||| | |  | ||||   | ||  | || |      ||||| ||| ||     ||||||||||||||||||| ||||| || ||||| ||  | || || ||||| ||||| || ||||||||||||||||| || ||||| || ||  | ||||
agctatgagataatatgaaatacttcaaactt-ctgttttgttgatcatttt--tcacattttatctgtctt---cacaactaatgg---tgcattttccttggtcc---agGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------------gtaatcttatgcgtttcacttttgctatatggatgtt----cgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
                                                                         ||||      || |  |   | || |  ||        |  |    | |||   | |   | ||   ||| | ||||   |   || ||| | | ||  | |||| ||||||||||| || ||||||||||| || || || || ||||||||||| |||||||||||||||||||| || ||||||||||| || || || |
gtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattga-tcaatgtattttgatg-atattgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCTTTCTATGAACGTGCTGGGAAGGTAAAATGTCTAGGAGGCCCTG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 13
gtaatcttatgcg-tttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
 |   ||  ||    |  ||  ||  ||||    |   | ||     | |||   | |   | ||   ||| | ||||   |   ||  || | | ||  | |||| ||||||||||| || ||||||||||| || || || || ||||||||||| || ||||||||||||||||| || |||||||||||||| || || |
cttgactagtgtaactagacaatttatataccattaaccatgaga--cacatgggaatggacattga-tcaatgtattttgatg-atgctgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCGTTCTATGAACGTGCTGGGAAGGTAAAATGTCTTGGAGGCCCTG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 13
--gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
   | || | ||     |   |||||  |||| ||| ||    |      | | || |||| |||  ||| |    ||||||| |||   |  ||| ||    |||| |||||||| || |||||||| || || || ||||| |||||||||||||| ||||||||||| |||||||||||||| || || |||||||| ||||
gcatgatttcatataactgcattttgaaatattgattttgtaatctgaagcgtgtctctttgcttactctgaa--aattgacaacta---taatttcttaatcagGCAGAAATGCCAGCAGACAGTGGTTACCCTGCTTATCTGGCAGCACGTTTAGCCTCTTTCTATGAGCGTGCTGGTAAAGTTAAGTGCCTTGGTGGGCCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
gtaatcttatgcgtttcact-tttgctatatggatgttc-gtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
      ||||   |||   | ||||    ||   | ||  |   | |     | | | |  ||| |  || | |  | |      | | ||  ||| |   | ||||||| |||||||| || ||||| ||||| || ||| | |||||||||||||| ||||||||||| || ||||| ||||| |||||||| ||||||||||
---tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggcttactccaatat--tttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 13
--gtaatcttatgcgtttcacttttgctat--atggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
    | | |  |    |||| ||  | ||   | ||| | |   |   | ||| ||  |  |    ||||     |||       || | | |   | ||  |  ||||||| |||||||| |||||||| || ||||| || ||||| ||| | ||||| |||||||||||| | || || ||||| || ||||| ||  | ||  
ttacattgtattatccttcagttaaggtaggaacggaagatgaggaaatgctcttcagatatcatgtttttcttattt-------ccaactgtatgtggtgctgcagGCTGAGATGCCTGCGGACAGTGGTTACCCAGCTTACCTAGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCAGGGAAAGTTAAGTGTCTGGGGAGCCCGA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctca--tctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
 | ||  |||       |  ||||||    | ||   |      | |  |  |   ||||| |   |  |  | | ||        | ||    | |   |  ||||||| ||||||||||||||||| |||||||| || || || ||| | ||||| |||||||||||| | || || ||||| || ||||| ||  | ||  
-tcataatatttaaaa-atatttgctcagggcatagccagacaattcagaaatgctactttccagatattttgctaatatgtgatcactt---gtggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCCGGGAAAGTGAAGTGTCTGGGAAGCCCGA

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|116463760|gb|EG506352.1|EG506352
EST:     ACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTG                         GCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTA
genomic: ACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttat ... tgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTA
EST: gi|163986288|gb|EL994859.1|EL994859
EST:     CTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTG                         GCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCAC
genomic: CTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttat ... tgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCAC
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     ACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTG                         GCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTA
genomic: ACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttat ... tgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTA
EST: gi|124903142|gb|EH977222.1|EH977222
EST:     GCAGAAGCATTAAGAGAAATTTCAGGACGGCTG                         GCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTA
genomic: GCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttat ... tgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTA
EST: gi|124961392|gb|EL035922.1|EL035922
EST:     GAAATTTCAGGACGGCTG                         GCTGAAATGCCTGCTGACAGTG-ATATCCAGCCTATCTAGCAGC
genomic: GAAATTTCAGGACGGCTGgtaatcttat ... tgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG
                         tattgac  putative branch site (score: 2)
                                     ttttgctttgtttt  putative PPT
                                           tttgttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA