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 5'  3'   
2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGTTCATTACCTCAAGAAGAAAGCAGATTCTGTTCCACTTCCAGTCTCAATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatatttcctaatttatgctttaatgatatgattaaaatgtacgatttaattttactatgaccactgtaatctagccactatttaaatttggtatatatagtaactatcttgtggataataatattttgaatggtttag

Basic information

species Arabidopsis thaliana
transcript AT1G61110.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G61110.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv00s0375g00040.t01 (Vitis vinifera), 5'ss of exon 1
GTAGTTCATTACCTCAAGAAGAAAGCAGATTCTGTTCCACTTCCAGTCTCAATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgta-tttatatttcctaatttatgctttaatgatatgattaaaatgtacg-atttaattttactatgaccactgtaatctagccactatttaaatttggtatatatagtaactatcttgtggataataatattttgaatggtttag
||||| || ||||| |||| ||| || | || || ||||| || || | ||||| ||||| | |||||||||||||||||||| |||||||| ||||||| || ||| | | ||| ||| | | || | | | | | || | | | | || || ||
GTAGTCCACTACCTGAAGAGGAAGGCGGCCTCCGTGCCACTACCTGTGACCATCATAGCAGACGTGGATCTTTACAAGTTTGATCCATGGGAGCTACCAAgtaattcatactcaattgttttgtttttcgttttttgttcgttgttttagtacttgttgatgcatgggtttttgaaaattatag--------------------------------------------------------------
















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|86046307|gb|DR342062.1|DR342062
EST:     ATCATCGCAGAGATTTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: ATCATCGCAGAGATT-GATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046299|gb|DR342054.1|DR342054
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046300|gb|DR342055.1|DR342055
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCTAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046304|gb|DR342059.1|DR342059
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046315|gb|DR342070.1|DR342070
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046318|gb|DR342073.1|DR342073
EST:     AATCATCGSAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046319|gb|DR342074.1|DR342074
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046302|gb|DR342057.1|DR342057
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046309|gb|DR342064.1|DR342064
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046320|gb|DR342075.1|DR342075
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046308|gb|DR342063.1|DR342063
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046316|gb|DR342071.1|DR342071
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046301|gb|DR342056.1|DR342056
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGYGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046306|gb|DR342061.1|DR342061
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046312|gb|DR342067.1|DR342067
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046311|gb|DR342066.1|DR342066
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046313|gb|DR342068.1|DR342068
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046321|gb|DR342076.1|DR342076
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046297|gb|DR342052.1|DR342052
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046303|gb|DR342058.1|DR342058
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046317|gb|DR342072.1|DR342072
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
EST: gi|86046310|gb|DR342065.1|DR342065
EST:     AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAA                         GCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC
genomic: AATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatat ... aatggtttagGCAAGGCGAGTTTTGGAGAGCACGAGTGGTACTTCTTTAGTCCTCGGGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGTTCATTACCTCAAGAAGAAAGCAGATTCTGTTCCACTTCCAGTCTCAATCATCGCAGAGATTGATCTTTACAAGTTTGATCCTTGGGAGCTTCCAAgtatttatatttcctaatttatgctttaatgatatgattaaaatgtacgatttaattttactatgaccactgtaatctagccactatttaaatttggtatatatagtaactatcttgtggataataatattttgaatggtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT