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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggcttttactactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA

Basic information

species Arabidopsis thaliana
transcript AT4G23920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 3
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttga-gtttgtcttgtttgatctcatta--ttggcttttactactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA
            |  | |      | || | |     |  | |     | |   ||||| | |    |    | | |||| |   || |  |||| |    || |||| |||| || |||||||| ||||| ||||| ||||| ||||| ||||||||||| ||||| || ||||  ||  | || || |  ||||||||||| || || |
----------aacaccttgaagtgtcttgtgaggttgattataccttctacagctttgacgctccattcagctcacctcactgattttgtatttaattgaatgatttc-agCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA

upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggcttt-tactactctgt---tttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA
             ||         || |  |||||    | |||  |||   ||||   | |  |    | ||||    | | ||  ||| || | || ||     || |||||||| || ||||| ||||| ||||| ||||||||||| |||||||| || || || || ||||  ||  | || || || ||||||||||| || || |
------------ttttgaagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA

upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggcttttac-tactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA
         | | ||  | | | |||||   |               | |  ||| || |    |||  | | || ||   | || ||| ||  | |||    || |||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || || || ||||  ||| | | ||| || || |||||||| || || |
---------tcctttattttttgtttttaccacgtttcttgtgatattactgtttatgtgcaactctgttctaatgtctccactgacttctaaattctcaacatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCACTATGTGCAACAAATCCATATGGACGAACTA

upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggctttta-ctactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA
         | | | ||| | | ||    |  ||      |  |   | |  ||| |  |    |||  |   || || | | ||  || ||  | |||  | || |||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || || || ||||  ||  | | |||  | || |||||||| || || |
------agatgcatgccttttttttagcatgtttcttgtgatgt---tactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19878760|gb|AU239591.1|AU239591
EST:     TTGGCACTGTTACTCTTTTGGAGGTTATGGCTCAATACGGCTGCAAAAAT                         CTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCT
genomic: TTGGCACTGTTACTCTTTTGGAGGTTATGGCTCAATACGGCTGCAAAAATgtaatttttt ... tgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgagtttgtcttgtttgatctcattattggcttttactactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA
               gtttgat  putative branch site (score: 5)
                                       ctactctgttttcc  putative PPT
                       tcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggcttttactactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG