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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgaattagaagtaaatattttcatttccataccccgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG

Basic information

species Arabidopsis thaliana
transcript AT2G45950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39480.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtttgtttgaattagaagtaaatattttcatttccataccc-cgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG
                                            |||||    ||| |    |  ||||     |  | | |   |||  |    | | | |       | |||   | | |||||||||||  |||||||||| | ||||||  | |||||||||||| |||| ||||||||||| ||||| || |||||  | ||| | || || |||||||
gttctactacctgttttacctctctctttaatgtttatacattgttgttatctttatacaagataatttatggctgaacaacaatgtcaagatgatcttacttgggggttattct--tgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG

upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G46780.1 (Glycine max), 3'ss of exon 2
----------------------------------------------gtttgtttgaattaga-agtaaatattttcatttccataccccgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG
                                               | | |||  |  ||| | |  ||   |  |   | ||     |||  |    | | | |       || | |  | | |||||||||||  |||||||||| | ||||||  | |||||||||||| |||| ||||||||||| ||||| || |||||  | ||| |||| || |||||||
gttctactacctgtttgcctctctctttaatgtttttacattgttattatctttatacaagataatttatggctgaacaacaatgtat-gtcaagatgatcttact-tgggggttattctttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG

upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0046g02450.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------gtttgtttgaattagaagtaaatattttcatttccataccccgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG
                            || ||   |||||| ||   | |  |  |||  ||| |    ||    | |  | ||    | |||||     |  ||||| || ||| ||| |||||| |  |||||  ||||||| ||||||||||| ||||||||||| ||||| ||||||||  | ||  |||| ||||||||||
gtttgcacatatctaacttatcattttctttttctgattagatgttcttttgctagtttgaatagcaaagcta-tgtttgaccttttggccattttttgggc-atagGAGCGGAAATCTTTTGATGAGAAGTTCATTAGAATGGATACAAAGAGGCTATGTGAGTTGACATCTGCTGCTGACAGCCTCCAATTGAAGCCTTTGGTTG

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|86086982|gb|DR382741.1|DR382741
EST:     TGATTCTTGATTACTGCAGATTTCATCAACTGCCAGGACGTTCAAATAAG                         GAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTC
genomic: TGATTCTTGATTACTGCAGATTTCATCAACTGCCAGGACGTTCAAATAAGgtttgtttga ... cactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttccataccccgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG
                                    tctattttccactct  CT-rich tract
                              attacatctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttgaattagaagtaaatattttcatttccataccccgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA