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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgctaaaaaagttcgagtaatggagattttgttctgtttgtgtgtgtgatgtgtttgattctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G05820.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g17740.1 (Oryza sativa), 3'ss of exon 1
ttatgctaaaaaagttcgagtaa-tggagattttgt--tctgttt--gtgtgtgtgatgtgtttg--attctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG
          ||  |  | |||  |     |||  |  |||| ||  | || |    ||  | ||  ||    |  || ||||   | |    |   |   |  ||||| ||||| |||||||| |||||||||||| | ||||||||||  || || ||||| || ||| | ||  | ||| | ||||||||  | ||||| || |
-------gggaagctctgtgtaccttcttgtttaattatctgcttaagggtatacattgcttctgtcatcaactaattaatatggatcatgcaaactgaacttacagGGAGAGCCTAGCTTTCATCTGTTTGGATTCATCATGTGCATTGGGGCCACTGCTGCAAGGGCATTGAAGACGGTGTTGCAAGGAATCCTCCTTTCATCCG

upper sequence: AT5G05820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G443265_T01 (Zea mays), 3'ss of exon 2
---ttatgctaaaaaagttcgagtaatggagattttgttctgtttgtgtgtgtgatgtgtttgattctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG
    |       | |  || || |      |   |    ||| |  ||    | | || | | || || | || |||||  |       |   |   |  ||||| ||||| |||||||| |||||||||||| | |||||||| | |||||| || || || ||  | ||  ||||  | ||||||||| | || ||||| |
caagtggaacctagagctttgattgcatacggactaaagctgctgttggacctaa-gtttctaatact-tact-gatatggtgcttgcaaatcgaacttacagGGCGAGCCTAGCTTTCATCTGTTTGGATTCATCATGTGCATAGGAGCAACTGCAGCAAGGGCGTTGAAGACAGTATTGCAAGGAATTCTTCTGTCTTCCG

upper sequence: AT5G05820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G447617_T02 (Zea mays), 3'ss of exon 1
ttatgctaaaaaagttcgagtaatggag--attttgttctgtttgtgtgtgtgatgtgtttgattctatgcttgatattctttaatttatgggt---gttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG
      |  | ||  | |||   || |   ||  ||    |      |||  ||  | |  | |   || |||  |  | |  |||||     |    ||  ||||| ||||| |||||||| |||||||||||| | |||||||| | |||||| || || || ||  | ||  |||| || ||||||||| | || |||||||
-----gtggagaacgtagagctttgaatgcatactggctagagctgttgttggacctctaggttctaatacttactgatatagaatttgcaaatcgaatttacagGGCGAGCCTAGCTTTCATCTGTTTGGATTCATCATGTGCATAGGAGCAACTGCAGCAAGGGCGTTGAAGACAGTACTGCAAGGAATTCTTCTGTCTTCTG

upper sequence: AT5G05820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G03510.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------ttatgctaaaaaagttcga-gtaatggagattttgttctgtttgtgtgtgtgatgtgtttgattctatgcttg-atattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG-
                                                                         | ||   | |   |||  | ||||     |  || || | |    |  | |||| ||  || || | ||  ||    |   ||  | |||  | |   | |||| || || || || || |||||||||||  |||| ||  |||| || |||||||| || || || ||||||||||| ||||| |||||||||||||||| 
tatgtatgtcacacaacataacacccttttgattcttttaaatgtttttgttaatttgggtttgtttctgatgtgatttcagattggtttaacgtaaaaataacatttttttttaatggcttctgatatggatg-ttttgtgtgtgtgcgtgtcttcttctatatg-gccattaggGGGAACCGAGTTTCCATCTGTTTGGATTTATTATATGTGTTGCGGCTACAGCTGCAAGGGCTCTGAAATCAGTGCTACAAGGGATTTTGCTTTCTTCTGA

upper sequence: AT5G05820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G34800.1 (Glycine max), 3'ss of exon 2
-----ttatgctaaaaaagttcgagtaatggagattttgttctgtttgtgtgtgtgatgtgtttgattctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG
     | ||   | |   |||| |   ||  | ||    || | |||   ||  |  ||     | |  | ||  || | |||||  ||||  || | || | |||| || || || ||||| |||||||||||  |||| ||  |||| || || ||||| || || |||||||||||||| ||||| ||||||||| |||| |
tgatgtgatttcagattggttcaat--ataaaaataacattttttttaaatggcttctgatacgggtgttgtgtgtg-tcttcttctattt--ggctattattagGGGGAACCGAGTTTTCATCTGTTTGGATTTATTATATGTGTTGCGGCTACGGCTGCAAGGGCTCTTAAATCAGTGCTACAAGGGATTTTGCTTGCTTCCG

upper sequence: AT5G05820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g03270.t01 (Vitis vinifera), 3'ss of exon 1
ttatgctaaaaaagttcgagtaatggagatt--ttgttctgtttgtgtgtgtgatgtgtttgattctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG
|||    |   |  || |  | ||  |   |  |||   | |||            |  ||  |   |  |||| ||| |||  |||| |  |||     ||||||| ||||| ||||| || ||||| ||  | ||||| ||||  || || ||||| || ||||||||||||||||||||||| ||| ||||||||||||
ttagttaatggatttttgcattattcatggtggttgaattatttcccatcaaaccataattattctgagtcttgttatcctt--atttttatgtggaaatagGGTGAACCAAGTTTTCATCTATTTGGGTTTTTAATGTGTATTGGTGCTACTGCTGCAAGGGCACTTAAATCAGTGCTTCAAGGGATTCTGCTTTCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgatgtgtttgattctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG
                                ctttaat  putative branch site (score: 4)
                        ttgatattctttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgctaaaaaagttcgagtaatggagattttgttctgtttgtgtgtgtgatgtgtttgattctatgcttgatattctttaatttatgggtgttgtcagGGTGAGCCAAGCTTTCACCTGTTTGGATTCCTTATGTGCATTGCAGCAACAGCTGCGAGAGCACTTAAATCAGTGCTTCAAGGAATTTTGCTTTCTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - taaaaaa
- - - - - - - - - - - - - -gattttg
- - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga