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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggcattgttgatgagaacacatatagctgtatgttatactaaaatagtttgctttgtctag

Basic information

species Arabidopsis thaliana
transcript AT3G19980.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggca--ttgttgatgagaacacatatagctgtatgttatactaaaatagtttgcttt--gtctag
||| || || ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||||||||| ||||| || ||||| || ||  ||||||| ||||||  ||  || |  | || | |  |||| | |    | |  | | |    |  | ||  | |||   | ||||     || ||
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagt--ttgtttggacattttgtaagttgtcggttt--ataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G055905_T03 (Zea mays), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggcattgttgatgagaacaca-tatagctgtatgttatactaaaatagtttgctttgtctag
|||||| || || |||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||| || ||||| || ||  ||||   |||||||   |   |||  |      |  | |  | | | ||   |||  | | | ||  |||  ||||  | ||||   |  ||
CTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCATTAATGGTCAAgtaagtacctc--tagggaaaaaatacaggttttcatatcatgctatctcggcaagtc-tacctaaattatatgctggattcag

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttgg-cattgttgatgagaa----cacatatagctgtatgttatactaaaa--tagtttgctttgtctag-------------------------------------------------
 ||||| |||||||||||||||||||| || |||||||| ||||||||||| ||||||||||||||||||||||| || || || ||||||||||| || |||| |   || |||    ||    || |  |  |   |     |  || |   |||| |   |  | ||   |  |||  ||| | | |                                                 
TTATGATGAATGCCAGAGGAAGTATGGGAATGCTAATGCTTGGCGATATTGTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctctttttactctctccatcagtcctcctcctatttttcttatgtgcatgtaggcagtggtcaaggtttttttattttattttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttag

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G23310.2 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggcattgt-tgatgagaacacatatagctgtatgt-tatactaaaatagtttgctttgtctag----------------
 ||||| |||||||||||||||||||| || || ||||| ||||| ||||| |||||||| ||||||||| | || || || || ||||| ||||| || |||| | || | |||    ||   | |    |    |   | ||| |  || | ||  | |       ||| || ||   | ||                 
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTATTGATGGAACTgtaaat-atcttttactccctcctcttcaagtatctaccccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttgttgt

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G23310.4 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggcattgt-tgatgagaacacatatagctgtatgt-tatactaaaatagtttgctttgtctag-------------------------------------------------------------------------
 ||||| |||||||||||||||||||| || || ||||| ||||| ||||| |||||||| ||||||||| | || || || || ||||| ||||| || |||| | || | |||    ||   | |    |    |   | ||| |  || | ||  | |       ||| || ||   | ||                                                                          
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTATTGATGGAACTgtaaat-atcttttactccctcctcttcaagtatctaccccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttgttgttctattagaatgttgcttgttcaaaattgagttttctatatgctatgcttgacccag

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G43470.1 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggcattgt-tgatgagaacacatatagctgtatgt-tatactaaaatagtttgctttgtctag-------------------------------------------------------------------------
 ||||| |||||||||||||||||||| || || ||||| ||||| ||||| |||||||| |||||||| || || || || || ||||| ||||| || |||| | || | | |    ||   | |    |    |   | ||| |  || | ||  | |       ||| || ||   | ||                                                                          
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTACCTAACTCTTTCTGCAATTATTGATGGAACTgtaaat-atctttcactccctcctcttcaagtatctatcccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttatagttctgtttgaatggttcttgttcaaaattaagttttatatatgttatgtttgacccag

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaag----tgatttcttagcaacttggcattgttg---atgagaacacatatagctgtatgttatactaaaatagtttgctt----tgtctag---------------------------------------
|||||| || |||||||||||||| || || |||||||| ||||| || |||||||||||||||||||| || ||||| || || || |||||||| || ||||     | | ||  |  |    | |||||  |    |  ||      | |   ||| |||  |  ||| |||  |   ||    ||||||                                        
CTATGATGAGTGCCAGAGGAAGTACGGAAATGCTAATGCATGGCGGTACTGCACAGATGTTTTTGACTACCTAACCCTCTCTGCGATAATAGATGGAACTgtaaacctctcactttatctctctcttgcattaatctgtaccagtgtgtgtgtgtgtgtgtgtgtttttaatatatctaagttgtagtgtctatctgttaatgttatatgtctcattgtttttggaattccag

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaag--tgatttcttagcaacttggcattgttgatgagaacacatatagctgtatgttatactaaaatagt-ttgctttgtctag---------------
 ||||| ||||| ||| | |||||||| ||| | ||||| ||||| |||||||| || ||||||||||| || || || || ||||| |||||||| |  ||||   | |    |   |   |      |||   || | |     | | |   || ||  |  || |   | ||| |   |||                 
TTATGATGAATGTCAGCGTAAGTATGGAAACCCAAATGCTTGGCGGTATTGCACTGACGTTTTTGACTACCTGACACTCTCGGCTATCATAGATGGAAGGgtaaagttcaaacttgcacggttaaattctgtccgtgtgtatgttca-acccagattttcgataaagagcctcttggtagatctcatcgtgctgtaggatt

upper sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 5
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtg--atttcttagcaacttggcattgttgatgagaacacatatagctgtatgttatactaaaa------tagtttgctttgtctag-----------
 ||||||||||||||| |||||||||| ||| | ||||| ||||| || ||||| |||||||||||||| ||||| || ||||| || |||||||| |  ||||| |  |    |  |    |    |||| |  |  |      | || || |||||| |   || |       |||     |  ||  |           
TTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAATAGATGGAAGGgtaagggggaaacttacgtggttaaatattgcttgtatg--tctgtttaactttatgttttgagaagagtctatcagtagatgtcatcatggttgaggatta

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggcattgttgatgagaacacatatagctgtatgttatactaaaatagtttgctttgtctag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT