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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctagtaggctcaagtaatatggcaagttgttggttgtatctggctccttgcattacttgatatgaatgggaatgatgcatagacctttattttcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTAACTAAGCTAGTTGTGGATCCTATGCTTTCATTTGTGACGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G73430.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA17G04990.1 (Glycine max), 3'ss of exon 21
tgctagtaggctcaagtaatatggcaagttgttggttgtatctggctccttgcattacttgatatgaatgggaat--gatgcatagacctttattttcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTAACTAAGCTAGTTGTGGATCCTATGCTTTCATTTGTGACGAAG
|  |  | | ||  ||| ||    |   ||  |  || |||        |||||||   | || |  |     ||     || |    | || ||||  ||||| ||||||||  | |||||  | |||||||||||||||||||||||||| |||||||| |||||||||||| |||||||||| || || |||
ttttcctcgtcttcagtgattcttct--ttaatcattttattccatatgttgcattgtctaatttagaccattatctagcgcctttgacatttttttttcagGAGCTGGAAAAGAGCCTTAAAGCCACTTGTGAGGAGTTCATCATGTCAGTTACTAAGCTTGTTGTGGATCCTTTGCTTTCATTCGTTACAAAG

upper sequence: AT1G73430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 22
-tgctagtaggctcaagtaatatggcaagttgttggttgtatctggctccttgcattacttgatatgaatgggaatgatgcatagacctttattt--tcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTAACTAAGCTAGTTGTGGATCCTATGCTTTCATTTGTGACGAAG
 |  ||| |   |   |||   |   ||||      || | |  | |   ||  ||   |||  ||| |  | ||  |||  |   | ||  |||  | |||||||||||| ||| | || ||  | |||||||||||||| || ||||| || |||||||||||||||||||| |||||||||||||| || |||
atattagaaatttggtgta-cgtatgaagtgcacaatt-tgttggaccaatttgatgtgttgccatgcaatgtaac-atgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
















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|116477892|gb|EG520484.1|EG520484
EST:     CAAGGACCCTGTCACCTCGAGTTTTGGAGAGTCAAATAGATGCCAAAAAG                         GAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTA
genomic: CAAGGACCCTGTCACCTCGAGTTTTGGAGAGTCAAATAGATGCCAAAAAGgttagggatt ... attttcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTA
EST: gi|116477889|gb|EG520481.1|EG520481
EST:     CAAGGACCCTGTCACCTCGAGTTTTGGAGAGTCAAATAGATGCCAAAAAG                         GAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTA
genomic: CAAGGACCCTGTCACCTCGAGTTTTGGAGAGTCAAATAGATGCCAAAAAGgttagggatt ... attttcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTA
EST: gi|125090098|gb|EL148219.1|EL148219
EST:     TGGAGAGTCAAATAGATGCCAAAAAG                         GAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTA
genomic: TGGAGAGTCAAATAGATGCCAAAAAGgttagggatt ... attttcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttgcattacttgatatgaatgggaatgatgcatagacctttattttcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTAACTAAGCTAGTTGTGGATCCTATGCTTTCATTTGTGACGAAG
           acttgat  putative branch site (score: 5)
                                        cctttattttc  putative PPT
                                          tttatttt  TA-rich tract