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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtaactgtgctcgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G27370.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA12G34780.1 (Glycine max), 3'ss of exon 16
-------gttcgta--actgtgc---tcgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
       ||| |||  |  |||    | || | || ||||    | | | | || || || ||    | |  | ||  |  || ||| |||| || || ||||||||||| ||||||||||| ||||| || || || ||||||||||| || ||||| ||||||||||| || |||
gtatgcagtttgtattaacgtgtttattgatgcttcatagatagactctttgttaatagttta----tta--tttttatt-ttgtagAATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 15
-------gttcgta--actgtgct---cgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
       ||| |||  |  ||| |    || | || ||||    | | | | |   |  | |||   |    | ||  |  || ||| |||| || || ||||||||||| ||||||||||| ||||| || || || ||||||||||| || ||||| ||||||||||| || |||
gtatacagtttgtattaacgtgtttattgatgcttcatagatagactctttgtatgtattctaatagtttattatttttctttgtagAATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 14
-------gttcgtaactgtgctcgaggttttatagtctcaatttcttttgattgtg-------taaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
        |||  |  | |   |   ||   ||  |   |||    | ||||| |         |||||||   |||||    ||| || | || || || |||||| | || ||||||||||||||||| || ||||| || |||||||| || |||||| ||||||| ||||| |||
gtatacaattcacatttatctgcttagtc--atgtttctaatggaatatgattataacactcacaaggatcttatcttcaaattttcagAAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAG

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------gttcgtaactgtgctcgaggttttatagtctca---atttcttttgattgtgtaaggat-caggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
                     |||   | |     | ||  ||  | ||| |     ||| |     |  || |   ||| |  || |  ||  ||  ||   |||||||| || ||| | || ||||||||||||||||| || |||||||| ||||||||||| ||||| ||||| || |||||||| 
ctcttgtcgagcttttttgatgttaaaaccatcttttgatcttgcacagttttgcagattgcaagctaacgtatcttgattcttgtgtcggtctttgcagAGAAATAGTTTTGAGCAACTGTGTATAAACTATGCAAATGAGAGGCTGCAGCAGCATTTCAACCGTCATCTTTTTAAGCTCGAACAAGAA

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------gttcgtaa--ctgtgctcgaggttttatagtctcaatttcttttgatt---gtgtaaggatcaggtcttcgtggttt-tagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
                    || | ||  ||  | |||  |   |||||| |     | | |    |   | ||   |||       |||   |||  ||   ||||||||||| ||| |||| ||||||||||||||||| || |||||||||||||||||||| || || ||||| ||||| ||||| 
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------------------------gttcgtaactgtgctcgaggttttatagtctcaatt------tcttttgattgtgtaag--gatcaggtct-tcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
                                                    |||      | |  || | | |||    |||  |||      |||| | || || ||     | ||  ||  || || ||  || | || ||||| || || || ||||||||||||||||| |||||  |||| ||||||||||| || ||||| ||||| ||||| ||||||
gtgaaatcttctcatacactagaatgagattgtaagcagtttattattaattgtttcctgatctagtcaaagctttgatttctggattgatggctcttcttatggtctagcttaagcatttccctcctgattgcagAAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAG

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 12
gttcgtaactgtgctcgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
                  |||    |||| | | ||| |   |||| |      |    || |||     |  ||  ||||||||| || ||| |||||||||||||||||||||||||| | ||||||||||||||||| || || || ||||| || ||||||
---------------gtcggtgcgctagttttagttt-tcgcgatttt------actgagttttct--actgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

upper sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
gttcgtaactgtgctcgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
                     |   |   |||| |||  |||  | | |     |    || |||     |  ||  ||||||||| || ||| |||||||||||||||||||||||||| | ||||||||||||||||| || || || ||||| || ||||||
--------------------gtcggtgcgctcattttagttt--tcgcgattttactgagttttct--actgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG
                  ttttgat  putative branch site (score: 4)
                                        tcttcgt  putative PPT
            aatttcttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtaactgtgctcgaggttttatagtctcaatttcttttgattgtgtaaggatcaggtcttcgtggttttagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG