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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacctctgaactaattgttggttgctaaacaactcgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 18
gtattacctctgaactaattgttggttgctaaacaact--cgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG
|| |    ||| || | ||  || |||||    | | |     ||     | || |  || |  | | | |  | |   ||||| ||||| ||||| ||||| |||||||| || ||||||||  ||||||||||||| || || ||| ||||||| || ||||| || ||||| ||  | |
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtccat-ttacaccatt--attgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
gtattacctctgaactaattgttggttgctaaacaact--cgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG
|| |    ||| || | ||  || |||||    | | |     ||     | || |  || |  | | | |  | |   ||||| ||||| ||||| ||||| |||||||| || ||||||||  ||||||||||||| || || ||| ||||||| || ||||| || ||||| ||  | |
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctat-ttacaccatt--attgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 17
-----------gtattacctctgaactaattgttggttgctaaacaactcgatgttcaagttgctgaat-atccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG
             ||| | | |  | |  || |   |||  | |  |  | |  || ||  | || | | ||   ||   ||    |||||| | || || || |||||||||||||| ||  | || |||||| | |||||||||||||||||  || ||||||| || ||||||||||| ||||| || |
gtttgtgtgttccattgcttttataat--ttatctattgtaacatcatgctagttttaaaatacttagtcattgttcggttc----ttgcagTCACTCGTTGAATTTTTTGGTACTCTGTCACGAGAATGGGCATTAGAGTGCATGAAAGATCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 17
-----------gtattacctctgaactaattgttggttgctaaacaactc-gatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG
             ||| | | |  | |  || |   |||  | |  |  |   | || || ||  |    ||   || | ||    |||||| | || || || |||||||||||||| || || || |||||| | ||||| |||||||| ||  || ||||||| || ||||||||||| ||||| || |
gtttgtgtgatccattgcttttataat--ttatctattgtaacattatgctagtttttaaattcttagtcattgttcaattc----ttgcagTCACTCGTTGAATTTTTTGGTACTCTGTCAAGAGAATGGGCATTAGAGTGTATGAAAGACCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
-gtattacctctgaactaattgttggttgctaaacaactcgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG
  | |||    | ||||   ||||  ||| |  || |   | |  | || |||||    |   |     ||   | | ||||| ||||| ||||| |||||||| |||||  | || |||||  ||||||||||||| || || ||  ||||||| || |||||||||||||||||||| |
gtttttatacttcaactg--tgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttc---tcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctaaacaactcgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG
 tgctaaa  putative branch site (score: 2)
                                           tcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattacctctgaactaattgttggttgctaaacaactcgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG