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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGACGAGAAGGTCGACCTATTGGAGCATTTGAGCTTGCGAAAGCGGTTGAAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaaaacttcaatctttgaattagtttcatgtctgaaaatttggaccacctttacacacgatgagaactaaatatgatccacgaaaaacaaaaa...

Basic information

species Arabidopsis thaliana
transcript AT4G26900.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26900.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 5'ss of exon 15
GGAGGACGAGAAGGTCGACCTATTGGAGCATTTGAGCTTGCGAAAGCGGTTGAAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaaaacttcaatc--tttgaattagtttcatgtctgaaa---atttggaccacctttacacacgatgagaactaaatatgatccacgaaaaacaaaaa
|| || || ||  | || ||||| ||||||| ||| || || ||||| ||||||||||| ||||| || ||||||||  | || ||||| || ||||||||||   |||    ||  | |  ||  |  |  |    || ||||     ||||   | |  |||  | |   |  |  |||| ||  | | | |   |||     
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatttttatttacgcaatatttgtagattttctg--ctaagtaatagcaaagtggaaccc---

upper sequence: AT4G26900.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: PP1S43_232V6.1 (Physcomitrella patens), 5'ss of exon 16
GGAGGACGAGAAGGTCGACCTATTGGAGCATTTGAGCTTGCGAAAGCGGTTGAAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaaaacttcaatctttgaattagtttcatgtctgaaaatttggac-cacctttacacacga-tgagaactaaatatga--tccacgaaaaacaaaaa
|| || || ||  |  ||||||| ||||||| ||||||||| ||||| ||| ||||  | ||||| || ||||| || |||||||||||  | ||||| |||||        ||  | |||||  || ||  |  | | ||    |||     |  ||||     | | |  | ||   ||   |  || |   |||       
GGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATTGTGACGgtacgggtttg-ctctactctttttatcagacttgtttttgtggctttcattacgtctttgtgtgccagtatgcacggcatgcaaagtcaatacaaagtgt---
















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|124925446|gb|EL003433.1|EL003433
EST:     AGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATG                         GTCAAGGGAAAGGATTCGACATA
genomic: AGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaa ... cgagtttcagGTCAAGGGAAAGGATTCGACATA
EST: gi|125249752|gb|EL263837.1|EL263837
EST:     AAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATG                         GTCAAGGGAAAGGATTCGACATA
genomic: AAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaa ... cgagtttcagGTCAAGGGAAAGGATTCGACATA
EST: gi|125313199|gb|EL327284.1|EL327284
EST:     AGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATG                         GTCAAGGGAAAGGATTCGACATA
genomic: AGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaa ... cgagtttcagGTCAAGGGAAAGGATTCGACATA
EST: gi|164157258|gb|ES023376.1|ES023376
EST:     CTATTGAACTGCATAGACTGTGATG                         GTCAAGGGAAAGGATTCGACATAGACTTAGTAAAGCTCATCTCAGATTCAG
genomic: CTATTGAACTGCATAGACTGTGATGgtacactcaa ... cgagtttcagGTCAAGGGAAAGGATTCGACATAGACTTAGTAAAGCTCATCTCAGATTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGACGAGAAGGTCGACCTATTGGAGCATTTGAGCTTGCGAAAGCGGTTGAAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaaaacttcaatctttgaattagtttcatgtctgaaaatttggaccacctttacacacgatgagaactaaatatgatccacgaaaaacaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa