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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtgggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA

Basic information

species Arabidopsis thaliana
transcript AT1G08200.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
gtaagtatacaggcttagtc-caatgacctgagttcttctcatggctgcagc---ttaacttttttgtttaactttttggt----gggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
|||||| | |  | ||  |    | || |    |  |  | ||   |||| |   || | | || |    |  |    |||      |  ||| |||||||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||||||  |||||||||| |||||||||||||||||  |  ||||||
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 5
---------gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtggg----tattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
          ||  | | |        |    |||  |  |||  | |  | || | || ||      |||||| || ||||  ||       | | | ||||||||||| ||| | ||||| |||||||||||||| |||||  | || |||||||||||||| ||||| ||||||||||| ||||||||| | |||||||
gtcagttacttacttttgctattgctttttgttgaagtttgttgatattttagccggagttttgaaaatttgttcaaattttctgttttcctttgtctgcagAATCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 5
gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttt------tttgtttaa--ctttttggtg---ggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
|| ||| |||   |||  | | |||   |||  | ||   |||  |  |||   | |||      |||||| ||   ||| || |      | | | |||||||||||  || | ||||| |||||||||||||| |||||  | || |||||||||||  | ||||| ||||||||||| ||||||||| |  ||||||
gtcagt-tacttacttt-tgctatg--ttgaagtttttagatgattttagccagagttttgaaaatttgttcaaaattttctgttttcctttgtctgcagAATCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 5
----------gtaagtatacaggcttagtccaa--tgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtgggtatttt-cagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
           |    ||  || ||| ||  ||  |    |   |  | |||     |   |  |||   || |   ||  || |   |   | || |  ||||||| || ||  | ||||| ||||||||||||||||||||  |||| ||||| || ||  | || || || |||||||| ||||||||| | |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatatgttactcgatatttttggataatgattctaaatattttctccattccttttctgtagAATCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtgggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
|| ||| | ||   |  |||  |  |  |       | |  |  ||    ||||    |  | ||   ||||||       | |   |||| ||||| || |  ||||| ||||||||||||||||||||  |||| |||||||||||  | ||||| || |||||||| ||||| ||| | |||||||
gttagttt-caacatctgtcataacatttagtagtattttttttctttttcttactactgatcttgctctttttctcccacaat---agAACCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtgggtattttc------agAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
|| ||| | ||   |  |||  || || ||  || ||     |  |     | |  |||||||| |    | ||| |   | | | |      |||| ||||| || || ||||| ||||||||||||||||||||  |||| |||||||||||  | || || || |||||||| ||||| ||| | |||||||
gttagttt-caacatctgtc--ataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

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|116471821|gb|EG514413.1|EG514413
EST:     TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAAC                         AATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAG
genomic: TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatac ... gtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAG
EST: gi|125215097|gb|EL229287.1|EL229287
EST:     TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAAC                         AATCTTCTGCGACGGGAGCCTCTCAAG
genomic: TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatac ... gtattttcagAATCTTCTGCGACGGGAGCCTCTCAAG
EST: gi|124831662|gb|EH916101.1|EH916101
EST:     TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAAC                         AATCTTCTGCGAAACGGGAGCCTCTCAAGCTTGTGGATGGT
genomic: TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatac ... gtattttcagAATCTTCTGCGA--CGGGAGCCTCTCAAGCTTGTGGATGGT
EST: gi|124910914|gb|EH984994.1|EH984994
EST:     TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAAC                         AATCTTCTGCGACGGGAG
genomic: TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatac ... gtattttcagAATCTTCTGCGACGGGAG
EST: gi|164158197|gb|ES022170.1|ES022170
EST:     TTGATGGTCCCAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAAC                         AACCTTCTGCGACGGGAGCCTC
genomic: TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatac ... gtattttcagAATCTTCTGCGACGGGAGCCTC
EST: gi|124888220|gb|EH967122.1|EH967122
EST:     TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAAC                         AATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTG
genomic: TTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatac ... gtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcatggctgcagcttaacttttttgtttaactttttggtgggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA
                            gtttaac  putative branch site (score: 3)
                                              tattttc  putative PPT
                 ttaacttttttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtgggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG