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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccaactggctgtaaatacattttattgattcctcttcaatggtaaattgatgtcccttttaatggatatatgtttttttggtgtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTCCACATTGCACTGGATGATGTGTCCATCACAGGCTTGACATTCGGAAAGG

Basic information

species Arabidopsis thaliana
transcript AT2G20530.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20530.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
----------------------------gttagccaactggctgtaa--atacattttattgattcctcttcaatggtaaattgatgtcccttttaat-------------ggatatatgtt--tttttggtgtttt--tcaa----gTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTCCACATTGCACTGGATGATGTGTCCATCACAGGCTTGACATTCGGAAAGG
                              || | ||   | |   |   ||   | |  |  ||      | |   ||    ||| |    |||||              ||||||||| |  |  ||  |  |||   |||    | | ||||| || || || ||||| ||||| ||    || ||    |||||| ||||||| ||||||||||||||||||||| |  | |  || ||||| |
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG

upper sequence: AT2G20530.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 3
------------------------------gttagccaactggctgtaa--atacattttattgattcct---cttcaatggtaaattgatgtcccttttaat-------------ggatatatg-------tttttttggtgtttttca-agTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTCCACATTGCACTGGATGATGTGTCCATCACAGGCTTGACATTCGGAAAGG
                                || | ||   | |   |   ||   | |  |  ||      ||   || |||   |||| |    |||||              |||||||||       || ||    | |    || || | ||||| || || || ||||| ||||| ||    || ||    |||||| ||||||| ||||||||||||||||||||| |  | |  || ||||| |
gtactgtcttatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtagtatgatatttagtttaagagctaatatagtaggatatatggtaataattattcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
















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|164203023|gb|ES087334.1|ES087334
EST:     AAGCTGTGGTTGCTCAGTACAACGCAAGCCAACTTATTACTCAGAGAGAG                         TCGGTGAGTAGAGAAATCAGGAAA-TCCTAAC
genomic: AAGCTGTGGTTGCTCAGTACAACGCAAGCCAACTTATTACTCAGAGAGAGgttagccaac ... gtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAAC
EST: gi|164204457|gb|ES026722.1|ES026722
EST:     GTACAACGCAAGCCAACTTATTACTCAGAGAGAG                         TCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC
genomic: GTACAACGCAAGCCAACTTATTACTCAGAGAGAGgttagccaac ... gtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC
EST: gi|86075231|gb|DR370988.1|DR370988
EST:     TACTCAGAGAGAG                         TCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC
genomic: TACTCAGAGAGAGgttagccaac ... gtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC
EST: gi|86075189|gb|DR370946.1|DR370946
EST:     TGCTCAGTACAACGCAAGCCAACTTATTACTCAGAGAGAG                         TCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC
genomic: TGCTCAGTACAACGCAAGCCAACTTATTACTCAGAGAGAGgttagccaac ... gtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC
EST: gi|47828978|gb|CK118662.1|CK118662
EST:     AAGCTGTGGTTGCTCAGTACAACGCAAGCCAACTTATTACTCAGAGAGAG                         TCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCANACTTC
genomic: AAGCTGTGGTTGCTCAGTACAACGCAAGCCAACTTATTACTCAGAGAGAGgttagccaac ... gtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggtaaattgatgtcccttttaatggatatatgtttttttggtgtttttcaagTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTCCACATTGCACTGGATGATGTGTCCATCACAGGCTTGACATTCGGAAAGG
                   ttttaat  putative branch site (score: 3)
                                            tgtttttc  putative PPT
                   ttttaatggatatatg  TA-rich tract