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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA

Basic information

species Arabidopsis thaliana
transcript AT2G20140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 3
gttccacaactggtgatccttaagttttc---tttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattatt-----agATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
       || |    ||   ||  ||||     |||    |   |||    |    |    |    | |||| | |  || |||   | | |     ||||||||||||| |||||||| ||||| || ||||||||| | ||||||||||| ||||| || || ||||| || || |||||||| || |||||||| |
-----gtaaatatccattagtatcttttagaacttcagaatgcatgataactgataagcagttcctttggttctca--tgaatgttgtgaatcgtgcagATACACACATCTAAGATGACATTGGCAGATGATGTGAACCTGGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 4
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattatt--agATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
            ||| |  |  |    | ||||   || |||    ||  | ||||   ||| |  ||| |||     |     |   |  ||||||||||||| |||||||| ||||| || ||||| ||| ||||||||||||| ||||| || || ||||| || || ||||| || || |||||||| |
------------gtgcttttcta-caatgtttcaagttctgt---cttattggaaa--cctgcttcgttcttatcaatagtttttgggtgcagATACACACATCTAAGATGACATTGGCAGATGATGTTAACCTAGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 3
gttccacaactggtgatccttaagttttctttctttttttgtgaat-tttctagaaagatctgatcggtttttaattgcatgcca--ttat-tagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
|| |    ||      ||  ||| |  |  |  ||   ||   ||| ||  ||  |   | || ||   || ||   |  ||  |  || |  ||||||||||||| || ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||||||||| || || |||||||| |||||||| ||||
gtactgtgac-----gtctgtaaatgataatatttgcattaacaatgttcttaataccctttgttcttattatagaaggttgtaaacttgtgcagATACACACATCGAAAATGACATTAGCTGATGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGACGAGTTTTCGGGTGCTGATATTAAGGCAATCTGCA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattatt-----agATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
|| |   |||     |||  ||     |  |  ||   || | ||| |||  | || | ||  | |   ||  | || | |   | |       |||| ||||||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||
gtgctgtaac-----atctgtagacagtaatatttgcattatcaatgttc--gtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgcc-attattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
|| |  | |   |||||    |  || |   || | || | | ||||    || | ||| || |        ||||   |    || |  ||||||||||||| || |||||  ||||||| ||||| ||| ||||||||||| | ||| ||||||| ||||| ||||| ||||| || ||||| || || |
gtgcttctat--gtgatgaa-agcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 4
-------gttccacaactggtgatccttaagttttctt-tctttttttgtga-attttctagaaagatctgatcggtttttaattgcatgccattatta-gATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
       | | |     || |  | || |   | | |  | | ||    ||| | ||| |  ||  || || |    | ||  |   |       |||| ||||||||| |||| |||||| || ||||| ||||| ||||| ||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| |
aacccaagatacgatgttgtttctgctgattctatgtgatatcttaacatgatactttgttcaatcatatgcttaaatgttc-tcatactttggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGACGAATTCTCCGGAGCTGATATAAAGGCAATATGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 4
----------------------gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcg---gtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
                        |   ||  |     | ||| | | || | ||||  | ||   ||| |    ||  || |||      | | |||      ||  |||  |||||||||||||||| |||||| || ||||| ||||| || |||||||| ||||| ||||| || || |||||||| |||||||||||||| |||||||| |
gtaggcacattttgtgaaagcaagttttcagttt-cactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatt--tagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTTGTTATGACCAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 4
------------gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcgg--tttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
             |       ||| |||| ||    | |  | ||||    ||   | ||| |  ||  || || |      || | ||    ||  ||||  ||||||||||||| | |||||| || ||||| ||||| ||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||||||||||||||| |
acccaacataagatgttgtttctgctgattct---atgtgatatcttaacatgcatactttgttcaatcatatgcttatacattctcatactttggaatta--agATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 4
-----------------------gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcg---gtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
                                 ||||  ||  | |  | ||||  | ||  | |    |   |||  | |||| |      | | |||  | | |   ||  ||||||||| || |||| |||||| || ||||| ||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| |||||||| |
gtcggaatgactagttctgtgaaaacatgtttttggttttcactgacatatcttaatattcctatt--ctacttagttatatctcactaaaaggtctta--tacttttgatatttagATACATACTTCAAGGATGACATTAGCTGATGATGTCAACTTAGAAGAATTTGTTATGACTAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gttccacaactg--gtgatccttaagttttctttc---tttttttg-----tgaattttctagaaagatctgatcggtttt--taattgcatgccatt-att--------agATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
                  ||   ||| ||   |  ||  ||  ||||| | |   || || ||     |||||   | |    |   ||||   | ||  |||    ||  |||| |||        ||||||| ||||||| |||||| |||||||| ||||| ||||| ||||| ||||| ||||| || || ||||| || |||||||||||||||||||||||||
gtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
                   | | || || ||| | ||| || |  |||  |        || | |    |||  || | |||       |||| || ||||| |  |||||  |  |||| ||||||||||| ||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||
------------------gtgacgtgttttttttctttgtgcgcgtttgttttt----cctaacca--ctttggtt-cttgc-------agATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 4
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcat-gccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
                               |    |  ||   ||||| |       | || |   ||   ||   | | |    |   |||| || ||||| |  |||||  |  |||| ||||||||||| ||||||||||| ||||| || || || ||||| |||||||| || |||||||| ||||
------------------------------gtgacgtcgtgcttattttttgtgcgcgtttgttt--ttcccaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGATGAATTCTCTGGAGCTGACATCAAGGCAATGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA
                                ttttaat  putative branch site (score: 3)
                               tttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT