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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatactttgttctctggcattgttttagcggttagtactaactttatttggtgctaatcttacaagttttctgtttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGATGCACTTGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTG

Basic information

species Arabidopsis thaliana
transcript AT2G40290.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 3
gtatatactttgttctctggcattgttttagcggttagtactaactttatttggtgctaa-tcttacaagttttctgtttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGATGCACTTGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTG
||| ||| |||  | || |        | | |   |  | | |   || |||    |||| | ||      ||   | |  |||||||||||||| || || |||||  | ||||||||||| ||| | ||||||||||| ||||| ||  ||||||| || |||||  |||||||  |||| |
gtaaatatttt--tatcagagtaaaactgaccacatcttgcaagtcttgtttatgactaaatgtttttttattgtcgctcatagGTGACTAAGGTGGTGCCAGCTGTATCAGAAGAAGTGAAGGATTCTCTTGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAG

upper sequence: AT2G40290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g07100.t01 (Vitis vinifera), 3'ss of exon 3
---------gtatatactttgttctc-tggcattgttttagcggttagtact---aactttatttggtgctaat-----cttacaagttttctgt-ttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGATGCACTTGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTG
         || |||   ||||  |    ||| |   || ||  | | ||||   |||  ||| |  |  |||      |||   | ||    || ||  ||||||| || ||  | |||||| |  | || || ||||| ||| |  |  | ||||||||||| ||| ||||||||||||||||| | |||||||| ||||
gtaatggtggtgtatctgttgtctttactgcactacgttggca-taaatactgaaaaccatatctcatattaaaggccacttgtcatttactcgtattacagGTGACCAAAGTGATCCCTGCTATGTCAGAGGAGGTGAAGGATTCTTTGATCAAGAACATTAGAAGGCGAATGACACCACAACCATTAAAAATCCGTGCTG

upper sequence: AT2G40290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ25833 (Selaginella moellendorffii), 3'ss of exon 4
gtatatactttgttctctggcattgttttagcggttagtactaactttatttggtgctaatcttacaagttttctgtttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGATGCACTTGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTG
                        ||  ||     | ||  |  |||| | |  |  |  |  | |    || |  |||  |||| || |||   || || || || ||||||||||| |||||||| |||||||||||| |  ||||| ||||||| || || ||| |||| ||| | || |
------------------------gtactaaaaactggtcatt-ctttctcttttatt--ttctgctctattgcctttttcagGTTACGAAGACGGTTCCAGCAGTGACGGAAGAAGTCAAAGATGCTCTTGTGAAGAACGTCCGGAGGCGAATGACGCCCCAGCCACTGAAGATCAGAGCCG

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|163993717|gb|EL996594.1|EL996594
EST:     TGGGTCCTCTCACCCGTGAGATCAAAGAAGTTGGGCCTGATGGGCAAGAG                         GTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGA
genomic: TGGGTCCTCTCACCCGTGAGATCAAAGAAGTTGGGCCTGATGGGCAAGAGgtatatactt ... ctgtttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcggttagtactaactttatttggtgctaatcttacaagttttctgtttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGATGCACTTGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTG
                                         ttttctgttt  CT-rich tract
          tactaactttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatactttgttctctggcattgttttagcggttagtactaactttatttggtgctaatcttacaagttttctgtttgtagGTGACTAAGGTTGTACCTGCTGTTACGGAAGAAGTGAAAGATGCACTTGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA