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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGACATTGGAAGCCGACATTGTGATAGTTGGGGTTGGTGCAAAACCATTGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatctgctgcctgtgcgtctcttcttcttcttatcccgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacag

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
GAGGACATTGGAAGCCGACATTGTGATAGTTGGGGTTGGTGCAAAACCATTGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgt----atttatctgctgcctgt-gcgtctcttcttcttcttatcc-cgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacag
 |||    ||||||| ||||||||  | ||||| ||||||| || |||  | ||| | |||||||| |||||||| || || || |||||||||||||||||    |  ||| |||  |   | | | ||| | || ||||| |     |   ||| |   |      || || | |  ||  || | | | |    || 
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagatatatgcatcagatagagcctcctgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa
















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|124931203|gb|EL008581.1|EL008581
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAG
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAG
EST: gi|47828341|gb|CK118025.1|CK118025
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|164238115|gb|ES059181.1|ES059181
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTC
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTC
EST: gi|47828077|gb|CK117761.1|CK117761
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|125017288|gb|EL089557.1|EL089557
EST:     TCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGA
genomic: TCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGA
EST: gi|125125613|gb|EL171048.1|EL171048
EST:     AAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: AAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|47830852|gb|CK120536.1|CK120536
EST:     GTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: GTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|125286687|gb|EL300772.1|EL300772
EST:     GTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: GTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGACATTGGAAGCCGACATTGTGATAGTTGGGGTTGGTGCAAAACCATTGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatctgctgcctgtgcgtctcttcttcttcttatcccgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA