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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttaatcacattgatcatattgcagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG

Basic information

species Arabidopsis thaliana
transcript AT3G19960.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 18
----------------------------------------------------gttttaatcacattgatcatattg-cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                                    |   || |   |  | |||| ||  ||| ||||| ||||||||  | ||| |  | ||   |  ||| || || |||||||| ||||| ||||| || |||||||| || ||||| ||||||||||||                                    
gtaaataaaatatttgaacagtagtattgcatttctagttaccttttattttgcaatactgtaacagttcattttatcagGTATGGCTTTCTTCTTCTTGAGGATGTCGCATCTCAAGACCCACTTAGTGTTTCGGTTGCAATTCTTCACCAGTTTAACATTTTGCCTGAGATGTATCAA------------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 18
-------------------------------------------gttttaatcacattgatcatattg--cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                            ||| ||    | |  | |  ||   ||| |||||||||||||| |   || |  ||||   |  |||||| || |||||||||||||| ||||| |||||||| || || || || |||||||||||||||                                 
gtaagttgactctgaacaacggcaaaaaaattctgcaacctttttttaaaagttaatacttaatttaatcagGTATGGTTTTCTTCTTG---AGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTT---------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 18
--------------------------------------------gttttaatcacattgatcatattg--------cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                             |||| || | |  | | |||||         ||| ||||| ||||||||  | ||| |  ||||   |  |||||| || |||||||||||||| ||||| |||||||| || || || || ||||||||||||                                    
gtaagttaactctgaacaactgcagtaaatttctgccaacttttttttttataaaaaagttaatatttaatttaatcagGTATGGCTTTCTTCTTCTTGAGGATGTTGCATCTCAAGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAA------------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 17
----------------------------------------------------------------------------------------------gttttaatcacattgatcatattg---cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                                                                              ||| | ||    |||    | |||   ||||||||||||||| ||  | ||  |  |||||  |   ||||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||||||||||                                    
gtataataacagaaaactgatgatttatatcctttcaaatactatcaccttccacattccttctgccctggtgtttttacatgtgtctatccttgttcttattggcttgggtgtgttgaatcagATATGGTTTTCTCCTCCTTGATCATGTTGCTTCTCAGGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAA------------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 19
-----------------------------------------------------------------------------------------------gttttaatcacattgatcatattg---cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                                                                               ||| | ||    |||     ||||   ||||||||||||||| || |   | ||  ||||   |   ||||| || |||||||| ||||| ||||| |||||||||||||| ||| |||||||||||||||||                                 
gtataacgacagaaagactgataatttatatcctttcaaatactatcaccttccacattccctccgccctggtgtttttgcatgtgtctaaccttgttcttattggcttgggtgcattgaatcagATATGGTTTTCTCCTTG---ATAATGTTGCATCTCAGGATCCACTTAGTGTTTCGGTTGCAATTCTTCATCAGTTTAATATTTTGTCGGAGATGTATCAAGTT---------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 17
----------------------------------------------------------------------------------gttttaatcacattgatcatattg---cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                                                                    | | ||    |||       ||   ||||||||||||||||||  | || ||  ||||   |   ||||| || |||||||||||||| ||||| |||||||| || || ||||| ||||||||||||                                    
gtagaacaacaaagaaactatggtgattgatatcctttcaaattagtccccatcctagtgttttttgcacgtttctaacttttctgttattgatttgggagcggtgaatcagATATGGTTTTCTTCTCCTTGAAAATGTTGCCTCTCAGGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAA------------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 19
--------------------------------------------------------------------------------------------------------gttttaatcacattgatcatattgcagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                                                                                        ||| |   |       |  ||   ||||||||||||||||||  | || ||  ||||   |   ||||| || |||||||||||||| ||||| ||||| || || || ||||| ||||||||||||                                    
gtataacaacagagaaagaaactatggtgattgatatcctttcaaattacccccccgtcccctatcccctatccccgtgctttttgcacatttctaacctttctgttattgacttgggagtggtaaatcagATATGGTTTTCTTCTCCTTGAAAATGTTGCCTCTCAGGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAATTCAACATTTTGCCTGAGATGTATCAA------------------------------------

upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 18
-------------------------------------------------------------------------------------------gttttaatcacattgatcat--attg--cagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                                                                                            ||||       ||| |  |  ||||  ||| ||||||||||||||  |||||    ||||   |  |||||| || |||||||||||||| || || |||||||| |||||  |||| ||||||||||||                                    
gtacacatagatgacaaggttttattatctagttgtattgcacttataaattttgtattcttttcttaagaatctgtttttattttattttattttcccttgtttggttgttaattgaccagGTATGGTTTTCTTCTACTGGAGGGTGTTGCATCTCAAGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAA------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG
                          tgctgat  putative branch site (score: 3)
     ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttaatcacattgatcatattgcagatatggttttcttctggtggagaacattgctgatagagatcctctaagtgtttcagTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG