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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattaaatcacataaccttggttgattctcacaacatgaaaccaatgtgactcagagagttgactaaaagcttttaacaattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAAGCAGCGTGTATGCTTCTAAGGATCGATGATATAGTGAGTGGAATCAAGA

Basic information

species Arabidopsis thaliana
transcript AT5G26360.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 13
gtaaggattaaatcacataaccttggttgattctcacaacatgaaaccaatgtgactcagagagttgactaaaagctt-ttaacaat--tttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAAGCAGCGTGTATGCTTCTAAGGATCGATGATATAGTGAGTGGAATCAAGA
                       |   |    | | |    |    |   || |  |  |         | ||| ||  ||| | ||  ||| ||||| ||||| ||||||| ||| |||||||| || |||||||| ||||| || || || || ||||| || |||||||||||||| || ||||| |||||||
--------------------gtctctctccccccctcgtgcttgtgcttttgcgtgtttgcattcatcttgaaacctcattatctatccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAGGCTGCCTGCATGCTCCTGAGGATCGATGATATTGTCAGTGGCATCAAGA

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggattaaatcacataaccttggttgattctca-caacatga-----aaccaatgtgactcagagagttgactaaaagcttttaa--caattttc---cagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAAGCAGCGTGTATGCTTCTAAGGATCGATGATATAGTGAGTGGAATCAAGA
     |||   ||    | |  |   || |   | |   | |||      |   |||   |  | | |||||| |||  |     | |  |||| |     ||||| |||||| | |||||||| ||||| || || || ||||| || || ||||| || || ||||| || ||||||||||| |||||||| || |||||||
----tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
















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|125128520|gb|EL172799.1|EL172799
EST:     CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAG                         ATATGGGATTCG
genomic: CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCG
EST: gi|124967817|gb|EL041825.1|EL041825
EST:     CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAG                         ATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTA
genomic: CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTA
EST: gi|125275375|gb|EL289460.1|EL289460
EST:     ATATGAAAGAGAGCCAAG                         ATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGA
genomic: ATATGAAAGAGAG-CAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGA
EST: gi|164157255|gb|ES023373.1|ES023373
EST:     CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAG                         ATATGGGATTCGTACAATGTGAAGGCG
genomic: CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCG
EST: gi|124760671|gb|EH850801.1|EH850801
EST:     GATATGAAAGAGAGCAAG                         ATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAA
genomic: GATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAA
EST: gi|124809148|gb|EH894900.1|EH894900
EST:     CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAG                         ATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAG
genomic: CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAG
EST: gi|125013313|gb|EL085582.1|EL085582
EST:     CTGGTACTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAG                         ATATGGGATTCGTA
genomic: CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCGTA
EST: gi|86059716|gb|DR355473.1|DR355473
EST:     CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAG                         ATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAA
genomic: CTGGTATTGACGGGAACACTGGTGCAATAGCTGATATGAAAGAGAGCAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAA
EST: gi|124915520|gb|EH989394.1|EH989394
EST:     GGTGCAATAGCTGATATGAAAGAGTAGCAAG                         ATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGA
genomic: GGTGCAATAGCTGATATGAAAGAG-AGCAAGgtaaggatta ... aattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgaaaccaatgtgactcagagagttgactaaaagcttttaacaattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAAGCAGCGTGTATGCTTCTAAGGATCGATGATATAGTGAGTGGAATCAAGA
                                      ttttaac  putative branch site (score: 2)
                                               ttttcc  putative PPT
                                      ttttaacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggattaaatcacataaccttggttgattctcacaacatgaaaccaatgtgactcagagagttgactaaaagcttttaacaattttccagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAAGCAGCGTGTATGCTTCTAAGGATCGATGATATAGTGAGTGGAATCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA