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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G19960.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatt-tcttgatttatgt---gtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                                                            |||  ||||| | |  | |   |  | || ||| |    |   ||  | || || |  ||| ||      | ||||||| || || || || |||||||| || |||||||| ||||| || ||||||||||| || || |||||| | || ||||| |||||||||
-------------------------------------------------------------------------------------------------------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttact-tctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 12
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                       |  || |  ||  | |    | | |   | | | ||| |     | ||| ||    |  |  |    ||  || |    || | |  |   || ||||  ||||| |   ||| || |||  |||||  || || || ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||| |||||||| | || || |||
---------------------------------------------------------------------gtatgtttatattaaactttatctacatctttctatatatttatgatttatctcaccatcttcatcctgtttgatattaaaatattttggctctactgat--gctatgca--ttttatgcct--gcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTTAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 12
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcc---tctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                              || ||  ||  ||    ||||  |       |     | | | | ||| |     | |  ||    |  || |||| |     |  ||| | || | || |   |  |||       ||||||  || || || ||||||||||||||||||||||||||||||||||| || |||||||| || |||||| |||||||| | || || |||
------------------------------------------------------------------------------gtatgttatattatatgacagatcttttatatgtgtgtgtgtgtgtatttatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgcggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatt-tcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                 |    | |||  ||||  |  | |    |    || ||||| ||||   | |        | |  || || || || | |    |  | |     || |  ||| || |||  |||||  || || || || |||||||| ||||||||||||||||||||||| ||||||||||| || |||||| |||||||| | || || |||
--------------------------------------------------------------------------------gtatgtttatattaaactttatctacctcttt--ctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccct--gcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 14
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacag---tgccaaata-gtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                              || ||  ||  ||     |||   |   | ||  ||     | ||||||  | | ||| |    ||  |||| || |  | | ||   | ||| | ||   |  |  ||| || | |  |||||  || || || ||||||||||| ||||||||||||||||||||||| || |||||||| || |||||| |||||||| | || || |||
------------------------------------------------------------------------------gtatgttatattatatggcagatcttttatatgcgtttttgtgtatatcactatccttatcctatttaattttttaaaatgtttgctctgttg-tatgtggt--ggattttatgcat--gcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 13
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                     ||||||  |   |||  |   |   |  | | | |   |     | ||     ||      ||  ||||||   |       |||     |||   ||   ||  ||  |||| ||||||||| ||||||||||| |||||||||||||||||||| |||||||| ||||||||||||||| |||||||| | |||||||||
-----------------------------------------------------------------------------------gtatgatattatttagtttctgctgtaaataatttttcattccccccattccccattgtccccctaaatttataaat-------attcatgttacatattctgtttttc--cagAGAAATAGCTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGGTTGCAGCAGCACTTTAACCGTCATTTATTCAAGTTAGAGCAAGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                      |  |  | | |  |     ||  || |||  | | |  || |      || || |   ||      | | || |||   |||||   | |     |       || |||||| |||||| || |||||  | |||||||| ||||||||||||||  ||||||| || || ||||||||||| || ||||| || ||||| 
-------------------------------------------------------------------------------------ctcttgtcgagcttt-tttgatgttaaaaccatcttttgatcttgcacagttttgcagattgcaagctaacgtatct---tgattc-ttgtgtcggt-------ctttgcagAGAAATAGTTTTGAGCAACTGTGTATAAACTATGCAAATGAGAGGCTGCAGCAGCATTTCAACCGTCATCTTTTTAAGCTCGAACAAGAA

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                     |   |    ||  ||  |   | | | | ||   | ||  ||   | | || ||    ||| |    | | | ||||   |  | |  | |  ||||||         ||||| |||||| ||||||||  | |||||||| ||||||||||||||  |||||||||| || |||||||| || || ||||| |||||||| 
-------------------------------------------------------------------------------------aacctgttgaatcgtttcgttttgcaaatctacgt-tcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgat--tcttatctcggacttt---------gcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                    |  | || ||     ||      |  ||  || |     | |   || | |   | ||| || | |   || |  | || ||  | |        ||| |  |||   |||||||||| || || ||||| || |||||||||||||| ||||| || ||||| ||||| || || |||||||| |||||||| |||||||||
------------------------------------------------------------------------------------aggggtatcaggacctg------accaggtcttttacaatgtccactgtcgaaat-ccacttttcg---ta-gaattttttttgtctcaagctttactatggttct--tgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 12
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcct-ctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                                                                                   | | |      || ||| |  || || ||   |||    || || |||||||  ||||| || |||||  | || ||||| ||||||||||| ||||| |||||||| || ||||| || || ||||| || |||||||||
--------------------------------------------------------------------------------------------------------------------------------------------------gtcggtgcgctagttttagtt-ttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcct-ctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                                                                                                                                                   | | |       | ||| |  || || ||   |||    || || |||||||  ||||| || |||||  | || ||||| ||||||||||| ||||| |||||||| || ||||| || || ||||| || |||||||||
--------------------------------------------------------------------------------------------------------------------------------------------------gtcggtgcgctcattttagtt-ttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG
                    tattgat  putative branch site (score: 3)
                                      ctttcattcctctgc  putative PPT
                   ttattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA