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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA

Basic information

species Arabidopsis thaliana
transcript AT5G56500.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 12
--gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
     |||    ||  ||| ||||    | | ||      |  | ||   ||  |  | || |    | ||   ||  |||||||| ||||  || |||   ||   |||||||||||||||||||||  | ||||| ||| | |||||||| || |||||||| || || || 
gttagatcttgttcactaacagaaaatca-tatgttcacatgtacatctgaataacataaaagatgatgtt---ttaccagGTTCTCTCTAACGATAACTTCAAGTTTGGTTACAATGCTGCAACTGGACAGTACGAGGATTTGATGGCTGCTGGTATCATTGACCCCACTAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 12
--gtaatcaatctccttaaaagaatgcaa--gtttgagtcttttgatatagaaac--taagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
   ||||||||    ||  | ||   | |   | |  || |  |||| || |     | |   |||||    |||       ||||| || || |||||||| || ||| |||| | |||||||||||| || ||||| |||||||| |||||||| ||||| ||||| || || || 
gtataatcaatgagtttccaggaggtccatgatctctgtttcatgatgtatatgtgttgaccaaatgggagctttt-----tcagGTGCTCTCCAGTGACAATCCAAAATATGGGTTCAATGCTGCAACAGGAAAATATGAAGATCTAATGGCTGCTGGAATAATTGACCCTACTAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 11
gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttg---acagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
                              | || ||||  |  |      |   |  |    |   | | | ||    ||||| ||| |    || |||  ||| || ||||| |||||||| |||||   ||  ||  |||||||||| ||||||||||||||||||||||| 
-----------------------------gtaagactttctacctgcggcttggcttgagttttgactgccggtgtgtgcagGTCCTTGCCGACGATAACTTTAACCACGGTTATAATGCTGCGACTGGTGCATTTGAGAATCTCATGGCGGCAGGAATCATTGATCCAACCAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 11
gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
                      |   | ||||   ||   | |        | |||   || ||      |  || ||||| ||| |    || |||  ||| || ||||| |||||||| |||||   ||  ||  |||||||||| ||||||||||||||||||||||| 
---------------------gtaagactttgtacctgcggctt---ggcttgagttt-tgactgccggtgtgtg-cagGTCCTTGCCGACGATAACTTTAACCACGGTTATAATGCTGCGACTGGTGCATTTGAGAATCTCATGGCGGCAGGAATCATTGATCCAACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
            ttttgat  putative branch site (score: 4)
                                      cttttttc  putative PPT
            ttttgatatagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG