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

...tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT

Basic information

species Arabidopsis thaliana
transcript AT2G38770.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttat---ttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT
            | ||  ||  |||   |    |         || |  ||||||     |  | |||||| |   |     |   || |||   |     |||| || ||||||||||||||||| || ||||| ||||||||||| ||  | |||||||| || || || || || || ||||| |||||||| |||||  
-----------gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC

upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 14
tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT
                   |||    || | |           |  |  ||          |  ||||| ||  ||||  | |   |  ||| |    |||| || || |||||||||||||| || || || ||||||||||| || || |||||||| || || || || || |||||||| |||||||| |||||  
---------------gtaatttccaataagtatggtgtttgctaacagtttgctggctttatttttttgggtactgac-atccatgtcatatct----agGTTACCACTGTGGACAAGTTCCAGGGCCAGCAAAATGATTTCATTTTACTTTCTCTTGTCCGTACCCGTTTTGTGGGTCATCTTCGTGATGTCAGAAGAC

upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 12
tttaggtttcgatt--ttggttttttggtatgcaatacccccctaagaaa-gttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT
 | | |||| |     | |  |   | |    |||||      |   |   || ||     | | |||| |    | ||  |  | ||| |   |   ||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||| |||||||| || || || || || ||||| ||||||||||||||||| |
atgatgttttggacagtagagtaaatagccatcaatattttttttgaagttgtgattctcaattaagttat---ctctgttttctataaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTCTTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT

upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
---tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT
   |   | ||| ||   | |  |   |  |     |       |||    || ||     | | |||| | | | || |||||   || |   |   ||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||| ||| |||| || || || || || ||||| ||||||||||||||||| |
gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgt---aaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT
                                   ttctaat  putative branch site (score: 2)
                                         ttttatttcctc  CT-rich tract
                                 tgttctaattttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - ggtttcg
- - - - - -attttgg
- - - - - - - - - -tttttgg
- - - - - - - - - - - - - - - caatacc
- - - - - - - - - - - - - - - - - - - - -taagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - tatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg