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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC

Basic information

species Arabidopsis thaliana
transcript AT4G39080.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                |  |      |     | | |||     ||    || | ||  ||   ||     |||  || | ||      |   | ||| ||||     || | | |||         | |||  | ||||| ||||| ||||| || || ||||||||||| ||||| || || || ||| | || ||||| |||||||| |||||||| |||||||| |||
----------------aattagcattgactcctgaaaaatcaataa--agagcttgctgtttgtttgggccaaatggtttagttaggaactgctaact-ttgt----attacatctga---------tacagGATAGCCAAATATCAAGAAGCAAACCCTGGTGTATTCACTATTGTCACTTTTCCTTTCTTATTTGCTGTCATGTTTGGAGATTGGGGACATGGAATTTGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                      | |     | |||  || |     |     ||| | |||||  | | |   |||    ||||   ||  |   | |  |      || | | |||   |        |||||| ||||||||||| ||||| ||||| || |||||||||||||| || ||||| ||| | || ||||| ||||||||||||||||| |||||||| |||
---------------------cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatac--tgtaaggtggata--agtgctaatgatgtgttccatgtggt-------acagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                    |||   | | || |||||  ||  |||| | |  |      |  |      | | |||   || || |  || ||  |  |||    ||| | | ||          | |||||| ||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || || || || || ||||||||||||||||| ||||| || |||
----------------cttattttttgtaattaaagaagtgg--aattaatgtcatttgaggtttggctcaagactgtaaggtgga-taagtgttgatgctgt----gttccatgtgg---------tacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttg-tagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                      |   | | ||||     |    | ||  |  |||  | | | ||        || | ||| ||  |||| | | ||||   | |  |||       ||   ||||   |||  | |||||||| |||||||| ||||| ||||||| ||| ||||| || || || |||||||| ||||| ||||||||||| ||||||||||| ||||||
--------------------actagtggattttatatccct---atttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactcaaataatcgtt-------aa---tacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttg-tagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                       |   ||  ||     |  |||  ||  |  |   | || | ||        || | ||| ||  |||  |   ||||   | |  | | |          ||||   |||  | |||||||| |||||||| ||||| ||||||| |||  |||| || || || |||||||| || || ||||||||||| ||||||||||| ||||||
-----------------------ggtacaacttgtactagtggattttatatgttttcgtttagttgcttcttgatttattgataatctgtctgaaactcaaataatcgctac----------tacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAGTTGTCACGTTTCCATTCCTTTTTGCCGTAATGTTTGGTGACTGGGGGCATGGCATATGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                                ||| ||      || |      |   ||||  || ||     || | || |        | | | |||| | ||     | | |  |||  ||  | ||| || || ||||||||||| || |||||   ||| |  ||  | |||||||| || || ||||| ||||| ||||||||||||||||||||||||||||| 
------------------------------cctaacaatttaagaacttgtttcattatttgttttttacttttattttttatttgaaatatatcaatcttat-acttcaacttttatacta-acatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGT

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                   | || ||  | ||||||||   |    |||    |    ||| | || ||          || |  | |   |   | |||| | ||  |  | | |  |||  |   | ||| || || ||||||||||| || |||||   ||| |  ||  | |||||||| || || ||||| ||||| ||||||||||||||||| ||||||||||| 
---------------ttattcttaac--aatttaagaacttgtt--ttgctattttttttttacttttat---------ttttgaaatatatc--aatcttat-actttaacttttatacta-atatttcagGGTTGCTAAGTATCAGGAGGCAAATCCGACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGTCATGGAATATGT

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                      |     | |||||   |   ||  ||      |   |    || |||  ||| |       ||| |  ||||  ||| |   | | ||   |     |  |    ||||| |||||||||||||| || || ||||| ||||||||||| |||||||| || || || ||||| ||||| ||||||||||||||||| |||||| |||||
----------------------tattttactttaacctatttgatttt-----cattttgctgatgatatcaaatta----acagaat-tgtttgcctcatactaaaattatgtgattccatttaattgcagGGTGGCCAAGTATCAAGAGGCAAATCCTGGTGTATTCACTATTGTTACATTTCCATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                               ||   |      |||| | |     |  | ||| ||   |   |  |||| ||    || |  | |  | ||     |   |||        |   | ||| |||||||||||||||||||  ||||| ||||||| |   ||| |||| ||||| |||||||| ||||| ||||||||||||||||| ||||||||||||
-------------------------------ttgttatttttcaaatggtattgccctatagaagtacttggctaaatgtt-taagtggcatcatccaatagtagagatcaactaattcaataatatttcagGGTGGCCAAGTATCAGGAAGTGAATCCTGGTGTATACGTGATTATTACATTCCCTTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcc--tttgaattataagaaaatgtgttgtagactgcgttttactcttgtcaca-gtttcctatgaactctac-tctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
||| ||||  |  |     |  | | |  |    |||| | ||    |||   | ||   ||| || | | |    |    |||| | |    |||| ||  | ||||| | | |  || |  |  || | | ||| ||||    ||||||||| || ||||| |||   || |||||  | || || || ||||| |||||||||||||||||||| ||||| |||||||| |||
gtaggtgtggtgatcagtataattatgtcgag-gagaagctggtctgtgatttttgctatttttaactgtcaagcga----ttgtggtcatatttttgcttctttcacacggtactgatcatttaaacatgtacagAGTGGGGCGGTATCAGGAGGCAAATCCTGGTTGTTTTACCATAATAACATTTCCATTCCTGTTCGCTGTTATGTTTGGTGACTGGGGCCATGGAATCTGC

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcc--tttgaatta-taagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactct----actctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
||||||||     |  |   | | |||  |  |   ||  |||   |||| ||| ||   ||| || |  ||||  | |||| |   |  ||  ||    ||||        |||  || |  | |    | | ||||||||||    |||||||||||| ||||| ||    || |||||  | || ||||| ||||| |||||||||||||||||||| ||||| |||||||| || 
gtaagtgtgcagatcaacgatattacgacgcgttgaaactgggttgttgatgatcgctgttttcaactgctaagggattgtggtaatggttgttttcctttctttcattcagttctgatcagatgttgtgaatatgcagTGTGGGACGGTATCAGGAAGCAAATCCTGGATGTTTTACCATAATAACTTTCCCTTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGT

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S6_159V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtgtctttctggagcttttgacgcagt-ttaagaaacgggaaattgaa-gatagcc-tttgaatt--ataagaaaatgtgttgtagactgcgttttactcttgt---cacagtttcctatgaactct----actctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
|| ||||||  |       | |       |  |  |||||| | |   |  | |||  |  ||  ||    ||||| ||   |  |   |  ||| |||   |||  |   |||| ||  | | |   | |    | |  |||||||||    ||||||||| || ||||| ||    || || || || || ||||||||||| ||||||||||||||||||||||||||||| || || |||
gtcagtgtccatacacctatgtaactttggcatctagaaactgaattctatatgatgtctattccaagcggataaggaatctttgtaccgtgtgcttttcgttctcctatgcacaattgacaaggggttgttgaaaatgcgcagTGTGGGGCGGTATCAGGAGGCAAATCCTGGATGTTTTACTATCGTAACGTTCCCCTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
                                          ctctactct  CT-rich tract
              ttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA