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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGGGAGTACTTAGCTGGAGACTTGATGCTGATAACTATGAAACCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtctttatttatttactatcccactagacttgaatggtagatgtttatttttgtccaagtcttattttaactctctaggggttttctcaatcttggtttgatgattaaaaagtgttcaaaatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G14716.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14716.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0020g04080.t01 (Vitis vinifera), 5'ss of exon 3
AGCTGGGAGTACTTAGCTGGAGACTTGATGCTGATAACTATGAAACCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtctttatttatttactatcccactagacttgaatggtagat-gtttatttttgtccaagtcttattttaactctctaggggttttctcaatcttggtttgatgattaaaaagtgttcaaaatgcag-------
| || ||||| || |||||| || | |||||||||||||||||||| |||||||| ||||| ||||| |||||| | ||||| ||||| ||||||||||||   ||   ||  |||  |    ||  | |    ||| ||       || |||  ||    | |||   || |  |  |||    |   | | |||   |   || | |  |||  | |  |||            
AACTTGGAGTGCTCAGCTGGCGATTAGATGCTGATAACTATGAAACAGATGAGGAATTGAAGAAGATTCGTGAAGCCCGTGGATACTCCTACATGgtttgtcacctaacttacttttttcattcagaaaaaggaaattgttctccaattctttcagtttgtgccttgaatttataccatagcctatagttaagtctgtataatataagtggaaatggatgtaaacattttctccag
















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|19878312|gb|AU239143.1|AU239143
EST:     CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|125245147|gb|EL259232.1|EL259232
EST:     CTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|125284364|gb|EL298449.1|EL298449
EST:     GAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: GAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|163988125|gb|EL994873.1|EL994873
EST:     CGATGAGGATTTGAAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCC
genomic: CGATGAGGATTTG-AAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCC
EST: gi|164228522|gb|EL998400.1|EL998400
EST:     CCGATGAGGATTTG-AAAAGATCCGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAA-GCTTCCAAACTA
genomic: CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTA
EST: gi|19874934|gb|AU235765.1|AU235765
EST:     CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|164133995|gb|ES128313.1|ES128313
EST:     CGATGAGGATTTGAAAAAGTATCCGCGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAA
genomic: CGATGAGGATTTGAAAAAG-ATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAA
EST: gi|152035832|gb|BP862940.2|BP862940
EST:     CCGATGAGGATTTGAAAAAGATACGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCC-GGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|125212665|gb|EL227619.1|EL227619
EST:     CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGA
genomic: CCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGA
EST: gi|124807070|gb|EH893545.1|EH893545
EST:     ATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: ATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|125099472|gb|EL155270.1|EL155270
EST:     CTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CTCGTGGTTACTCTTACATGgtttgtggtc ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGGGAGTACTTAGCTGGAGACTTGATGCTGATAACTATGAAACCGATGAGGATTTGAAAAAGATCCGTGAATCTCGTGGTTACTCTTACATGgtttgtggtctttatttatttactatcccactagacttgaatggtagatgtttatttttgtccaagtcttattttaactctctaggggttttctcaatcttggtttgatgattaaaaagtgttcaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT