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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtatctttgttaaaaatattcacatttggtctaaggagcgtatacgttagcattaacatatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G08650.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 12
atgtatctttgttaaaaatattcacatttggtctaaggagcgt-atacgttagcattaacatatctataggttt---gtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
|  |  |    ||   ||| || |    ||  ||||  ||| |  | | ||    ||  ||| | |     | |   | |   |||  |||||| |   |||||||||| || ||| |||| ||||||||||| |||||||| ||||| || ||| | |||||||| || ||||| |||||||||
agatgccaa-attgccaatgttgattggtga-ctaattagcattgtgcattgcatttctcatctttgcttttctaaaggcagtaacaaggttttcaa--tgcagTTTGAACCAGAATCTTCAAGTGCCATGGGTTTTGGCTTCAGATGTGGATTTCTCGGTCTTCTTCATATGGAGATTGTGCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G003157_T02 (Zea mays), 3'ss of exon 3
---atgtatctttgttaaaaatattcacatttggtctaaggagcgtatacgttagcatta-acatatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
   || | |  |  ||   | | |  |   |||||          ||| | || | |||    ||     |   ||| ||   || |   |     |  |||||||||| || ||| |||| ||||||||||| |||||||| ||||| |||||  | ||||||||||| |||||||| || |||
tgcatctgttctcatttggattctgtaatattggtt---attctttatgcattggtattttgtatgatacttcattt-tctctaaatccatgccattaatgcagTTTGAACCAGAATCTTCTAGTGCCATGGGGTTTGGCTTCAGATGTGGGTTCCTTGGTCTTCTCCATATGGAAATAGTTCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
atgtatctttgttaaaaatattcacatttggtctaag-gagcgtata-cgttagcattaacatatctataggtt--tgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
  || | |||  | ||| ||| ||  |||  |  |    |||  | |  | | |  |||    ||  ||   |    |   |||   |  ||| |    | |||||||| ||||| || ||||||||||||||||||||||||||||| |||||| |||| ||||| || ||||||||||| |||
--gtttttttccttaaa-tatccatgtttcttacagtcaagctgacaatggtggggttagtg-attaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
atgtatctttgttaaaaatattcacatttggtctaa--ggagcgtatacgttagcattaacatatctataggtt--tgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
  || | |||  | ||| ||| ||  |||  | ||     |  |   | | | |  |||    ||  ||   |    |   |||   |  ||| |    | |||||||| ||||| || ||||||||||||||||||||||||| ||| |||||| |||| ||||| || ||||||||||| |||
--gtttttttccttaaa-tatccatgtttcttatagtcaaactgacaatggtggggttagtg-attaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
atgtatctttgttaaaaatattcacatttggtctaag-gagcgtata-cgttagcattaaca--tatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
   | | ||| |   |||||| ||  |||  |  |    |||  | |  | ||| ||||     |   |||  |    |  |||   |  ||| |    | |||||||| ||||| || || |||||||||||||||||||||||||| |||||| |||| ||||| || ||||||||||| |||
---tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatt-tcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 12
atgtatc-tttgttaaaaatattcacatttggtctaaggagcgtatacgttagcattaacatatctataggtttgtcctcaactt-ggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
   |||  |||| |   ||||    | |    |  | ||    |  |  |     |||     |  | |  | ||  | |  |||   | |  ||  |||||||||||||||| || || ||||||||||| ||||||||||| || ||||| |||||||||||||| ||||||||  | |||
--ctattgtttggttgtaataagggcgtagttttaatggtatatgcagatcttggttacttgctaaagaattgtgctcccttcttcaatgtccattttgcagTTTGAGCCTGAGACATCCAGTGCCATGGGCTTTGGCTTTAGGTGTGGGTTCTTGGGTCTTCTCCATATGGAAATCATTCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 12
atgtatctttgttaaaaatattcacatttggtctaaggagcgtatacgttagcattaacatatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
                                       || |  | | ||   |   ||  | |  |    ||    ||   |   |   || ||||||||||| || |||| ||||||||| ||||||||||| ||| |||| || ||| | || ||| | ||||||||||| || |||
----------------------------------gtatggcctcgatgctaa-gtcgccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 12
atgtatctttgttaaaaatattcacatttggtctaaggagcgtatacgttagcattaacatatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
                                       || |  | | ||       ||  | |  |    ||    ||   |   |   || ||||||||||| || |||| ||||||||| ||||||||||| ||| |||| || ||| | || ||| | ||||||||||| || |||
----------------------------------gtatggcctcgatgctaa-gccgccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgttagcattaacatatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
       cattaac  putative branch site (score: 2)
                                         tttttatcct  putative PPT
        attaacatatctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtatctttgttaaaaatattcacatttggtctaaggagcgtatacgttagcattaacatatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - -aaaaata