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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT

Basic information

species Arabidopsis thaliana
transcript AT1G79000.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
              ||    | | ||   |||   ||   | |      | | | || |  || ||   |        ||| || |      | || |    | || | |||||| || |||||||||||  |||| || || |||||||| |||||  || | || || |||||||  |||||||||||||| ||||| |||||||| |||
-----------gtgtgttggtgcttctcacttttgttcc-gtcaccttgcct-tgtgcttgatctggaataacaccc-tgaccacttacggaaactata---cactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 16
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
||    | |  ||| | | |  ||| |  ||    || || ||        |||||  |      |||||||  |  || |  | |||    || |  || |      |||| ||  |||| || ||||| || ||| | ||||| || || ||||||||||| ||||| |||||||||||||||||||| || ||||| |||||||| |||
gtttgtaga--tcaggcattgccattattctcgtgtt-aacac--------tattttata-----gattttgcatgtattaatactgtt--tatttgggttta---aatcagAGATTTAAAAGAACATCTAAGGAGACTTCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTAATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
           |  | | || |       |  | |||   ||  | |  | | |||       | |||||||| |  || | || |||       | | |   |    |||| ||  ||||||| ||||| || ||  | ||||| || || ||||||||||| ||||| ||||| |||||||||||||| || ||||| |||||||| |||
---------gtttgt-agatcaggcattgccaatattctcgagttaactctttttta------tagattttgtatgtattaacactgt------ttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
                    |   |    |   |||   || | |   |  || ||    || | | || | | ||     |   |   |   ||| | |   |    |||| ||  |||| || ||  | || || || ||||| || || |||||| | || ||||| ||||||||||| |||||||| || |||||||||||||| || 
-------------------gtttgtgggtcaggcat---aggcattgcaattacttaagtcact-gtttatatattttgcgtgtataacattttctttttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
              || | ||   ||||| |    |  | | | |   | |||||  ||| ||   || |    |  || |   || |     | | | |       ||||| || || ||||||||| |||| ||  | |||||||| || |||||  |||| ||||| ||||| ||||| ||||||||||| ||||||||||| || |||
-----------gtttgtagttg--tcaacttgtggtcaatgccatcttaaatatt--gtctatg-aatatcacat--ataaatcttata---ctttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
               tgttgat  putative branch site (score: 4)
                                    tctctgtctctctgtt  putative PPT
     tttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT