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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA

Basic information

species Arabidopsis thaliana
transcript AT2G25760.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
-------gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
       ||   | |  | | | |  || | ||||||    | |      |  |      || ||  | | | |  ||  | |   |  |||||||||  | |||||||| ||||||||||| |||||||| ||| ||||||| || || || ||||| ||||||||
gtatttagtgc-cagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaa-ataaatatcgtgctttcgaatg-gtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgt-agGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
||  ||| ||    |  | | || |  ||  ||||  |   |    | | ||   |    | || || | |  |    || |   |||||||  | || ||||| ||| ||||||||||||| || || |||||  | || ||||||||||||||||||||
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
gtatgctgtttgtgtttgcaagtttacttgctttcttt-tggttttctgtgatctgtaatgtgattttgatgtgtccacttttg-tagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
           || |||     ||  || |  || ||  | ||  |   |  |   |    |    |  | || |    |  |  ||||| ||  | || ||||| ||| ||||||||||||| || ||||||||  | || ||||||||||||||||||||
-----------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 2
---------gtatgctgtttgtgtttgcaagtttacttgcttt--cttttggttttctgtgatctgtaatgtg-attttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
         | ||    || ||  |    |  ||     | |    |||||||||| | | | |      | | |    |   |     || |  ||||||||  |||||||||||||||| ||||| ||||||||| ||||||| || || ||||| |||  || ||||||
gtaatagaggaatttctttagtactacacaacttggaaacctggaattttggttttgtatcagcaccggagagtaagccgtcttcctttctatcttagGTGGCACTGAAGTTTGAGCATAGGACCAGTAAAGGATGTCACTATGGCCCTCCTTATGAATGGACAGCTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G342407_T01 (Zea mays), 3'ss of exon 4
gtatgctgtttgt-gtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
       ||||||   || ||  |||  |   |||  |    ||||   | |  |  |||     ||  ||| ||    |||||||||| || ||||| || |||||| ||| ||| |||||||| || ||||| || || ||||||||||| ||||| ||
-------gtttgtcacttacacattttatgaatttgatggattttttccttacata-aatcca--ttaaatg-gtaattttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
gtatgctgtttgtgtttgcaagtttactt---gctttcttttggttttctgtgatctgtaatgtgatt-ttgatgtgtccactt-----ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
||||| |||| | || |  |  |||  ||   |  |   |||| ||       ||  |   ||| ||| |||| || |     |     |||||||| || || || ||||||||||||| ||||||||| || || ||||| || || ||||||||||| ||||||||
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 2
gtatgctgttt----gtgtttgcaagtttacttgcttt-----cttttggttttctgtgatctgtaatgtgatt-ttgatgtgtccactt-----ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
||||| ||||     |||| |  |  |||| ||| ||        | || |||      ||  |   |||  || |||| || |     |     |||||||| || || || ||||||||||||| |||||| || || || ||||| || || ||||||||||| ||||||||
gtatggtgttggttagtgtgttgatatttatttggttaaagagtgtatgatttatgcatattggatttgtcgttattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAGGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 2
gtatgctgtttgt--gtttgcaagtt--tacttgctt------tcttttggttttctgtg-atctgtaatgtgattttgatgtgtccactt-----ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
||||| |||| ||  |  ||    ||  || ||| ||      | | || |  |  ||   ||  |  |||| |||   | || |     |     |||||| | || || || ||||||||||||| ||||||||| || || ||||| || ||  |||||||||| ||||||||
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 2
--gtatgctgtttgtgtttgcaagtttacttgct--ttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
   |||  || || | |||     ||    || |  |   |||  |||  | |  |||| ||  |   | |    | |  | |||   |||||||  |||| ||||| || ||||  ||||| || ||||| ||||||||||| || ||||||||||| |||||
gtatattttggttttattttttgattattgtgttgatctgtttcttttctttttttctgaaacatatctatctcctattgatttt---agGTGGCCCTGAAATTTGAACACAGAAGTAGCAAGGGCTGTAATTATGGGCCACCATACGAGTGGCAAGTGTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccactt-----------ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
|| |    ||| ||  |    | |    |   |   | ||||  ||| || |  ||  | |  | || || |||   ||            || ||||| || || || ||||||||||||| ||||||||| || || ||||| ||||| ||||||||||||||||||||
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
|||  ||||| |       |  ||| ||   ||   || | | || | | | | |       |   || |||            |||| |||||||||||||| || |||| ||| |||||||| ||||||||||| |||||||||||||||||||||| 
gtagactgttcga------agatttgctcagttggattggctcttttctcagcggctgatcaaagatgttgt-----------cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
|||  ||||| |       ||| ||      | ||  |||| || || |  |||     |    |   |  |||      |   |||| |||||||||||||| || |||| ||| |||||||| ||||||||||| |||||||||||||||||||||| 
gtagactgttcg-------aagatt-----ttctcagttggattgctcttttctcagcggctgatcaaagatgt------tgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
                                ttttgat  putative branch site (score: 4)
                                          tccactttt  putative PPT
                               attttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG