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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatcaacgtctttaacatatgattgatacatcttccagagagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT

Basic information

species Arabidopsis thaliana
transcript AT5G13300.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
-------------------------gttgatcaacgtcttta-acatatgatt-gatacatcttcca----gagagtactattaacatttcttggtgc-------tttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
                         ||| ||   | |  |||    || | |  |   ||  || ||    |  | | |   | | ||||    |||        |||||||| || || ||  | ||||| |||||||| || |||||||||||| ||||||| ||||||||||||||||| ||||||||||| ||||| |||||| | |
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gttgatcaacgtctttaacatatgattgatacatcttccagagag--tactattaacatttcttgg--------tgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
||    |  | |  || ||     ||| |  | || | |||| |   || || |  |||| ||           |   ||||||| || || ||  | |||||||| ||||| ||| ||||||||||| ||||||  || |||||||||||||||||||| ||||| || || |||||||| |
gtaccacttcctggttcactaggaattaaagcttcatgcagacattctagtactgtcattcctgaaacaaagtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
-----------gttgatcaacgtctttaacatatgattga----tacatcttccagagagtactattaacatttct-tggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
            | |  |||     |  | ||   |   |    ||||  ||  | | |  |   | ||   |  | |  | ||| |||||  | || ||  | ||||||||||| || ||| ||||||||||| ||||||  ||||||||||||||||| || || ||||| || || |||||||| |
gtaagacaccgatagtccaatacactggagatccaaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 11
--------------gttgatcaacgtctttaacatatgattgatacatcttcc---agagagtac--------tattaacatttcttgg--tgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
                 ||  |   || |  |   |||||| |   || |      |||   | |        || | | |  |   |   |  |||||||| || || ||  | ||||| ||||| |||||  ||||||||||| ||||||| || |||||||| ||||| ||||| || ||||| || |||||| | |
tgctggaactctccaaagacaatattcatgcatgcatgattaagtaatttcataaaagaagatgcatgttttatactgaaacgtaaggaactattttcagGTTCAGACCATTCGCCAAGGCTATCTATCTAAGAGATCTTCAAACTTGAGAGGTGATTGGAAAAGGAGGTTCTTTGTCCTCGACAGTCGAGGAATGTTGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
----------------------gttgatcaacgtctttaacatatgattgatacatcttccaga---gagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
                      ||||||  | ||  ||||||| |  ||  | |   |    ||      || ||||    | | ||  |  ||| |||| ||||| ||  | |||||||||||||| || || || |||||| | || || ||||||||||| || |||||||||||||| || ||||||||||| |
gttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtcttttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
----------------------gttgatcaacgtctttaacatatgattgatacatcttccaga---gagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
                      ||||||  | ||  ||||||  |  ||  | |   |    ||      ||   ||    | |  |  |  ||| |||| ||||| ||  | |||||||||||||| || || || || ||| | || || ||||||||||| || |||||||||||||| || ||||||||||| |
gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------------------------------------------------gttgatcaacgtctttaacat-atgattgatacatcttccagagagtactattaacatttcttggtgc-----tttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
                                                                              | ||||  | |  ||  | | ||| |   |  || |      |  |  | ||  | | |||   |       |||||||| ||||| ||  | |||||||| ||||| ||||| || |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||| |
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT

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|164215024|gb|ES145835.1|ES145835
EST:     CAATCTGCTGCAAGAGGAAAG                         GTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGA
genomic: CAATCTGCTGCAAGAGGAAAGgttgatcaac ... gtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgattgatacatcttccagagagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
                              tattaac  putative branch site (score: 1)
                                              tgctttc  putative PPT
                           tactattaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatcaacgtctttaacatatgattgatacatcttccagagagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG