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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttttgaacttaagcttagaaatgtatgtttgatattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G53090.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G461948_T01 (Zea mays), 3'ss of exon 12
gtttgtttttgaacttaagcttagaaatgtatgtttgatattc----tgtttggtaattttgttttcttac------ttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
 |  ||| |||   ||      ||  || |    |||| | ||    |||    ||| |||||||    |       |  |   | || | |  |  || ||||  | ||||||    | ||||||||  | |||||||| |||||||||||  | |||||||||||||| || ||||||||||| || |||
-tccgttcttggtttttc-tacagtgatatcaacttgagactcataatgtgctctaaatttgtttatgcaagaacgataattaacgttgttacttgatgtagGTTCCATGTGATGTAACACTTTGGGCATCAATTGGAGGCCAAGATGTAGATCGTCTTCCATCTGCTTCCACATGCTACAATACGCTCAAG

upper sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 13
------gtttgtttttgaacttaagcttagaaatgtatgtttgatattct---gtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
         |  |  |  | | | |  | ||||       |  | ||  |    | |  | |||   ||   | || ||  ||  | ||  | | |  |||||  | ||||||    ||||||||||  | ||||||||||||||||||||  |||||||||| ||||| || ||||||||||||||||||
tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaacattcatgtctatttgtttac-acagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG

upper sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G37310.2 (Glycine max), 3'ss of exon 14
-------gtttgtttttgaacttaagcttagaaatgtatgtt----tgatattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
         |  |  |  |  |   | || |||   |   |     | |||   ||| |  | |||   ||   |  | ||  ||  | ||  | | |   ||||  | ||||||    ||||||||||  | ||||||||||||||||||||  | |||||||| ||||| || ||||||||||| ||||||
tttgcaacatcatgatccagttatgggttggaagaatccctaaaaataataaaatgtct--tgattccattgattggcattcatgtctatttgtttacaa-agGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGGCTTCCATCAGCTTCAACCTGCTACAATACCCTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
                       ttcttac  putative branch site (score: 2)
                ttttgttttcttactt  CT-rich tract
             taattttgttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttttgaacttaagcttagaaatgtatgtttgatattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG