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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCAGATGCGCAACAAAGAGGGAGATAGAAAGCGAGCTTTCTTAACCTTGGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgattcaattctctggttttgagacaaggactagtaaagttttggtctaatttgtgttttattcttgttttcag

Basic information

species Arabidopsis thaliana
transcript AT2G07340.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G07340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv11s0065g00480.t01 (Vitis vinifera), 5'ss of exon 3
AATCAGATGCGCAACAAAGAGGGAGATAGAAAGCGAGCTTTCTTAACCTTGGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgattcaattctctggttttga--gacaaggactagtaaagttttggtc------taatttgtgttttattcttgttttcag-------------
|| |||||||| |||||||| ||||| |  ||||| ||||||||||||||||| || ||| | | |||| |||| || |||||||| |||||||| ||||| | || | | ||  |      |   |  ||||  || |  | | ||| | |||      || | |||||||  ||     | || |             
AACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGTCTATAGgtatgtaaatgaaaccataatctcatattgacagagaattttcatgttattgtcacatattagtgtgtgtttagtttaatatatctgttttatctaagaa
















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|86036312|gb|DR332065.1|DR332065
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86079502|gb|DR375259.1|DR375259
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GAAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036311|gb|DR332064.1|DR332064
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036314|gb|DR332067.1|DR332067
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036302|gb|DR332055.1|DR332055
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|164135115|gb|ES011716.1|ES011716
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036303|gb|DR332056.1|DR332056
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036310|gb|DR332063.1|DR332063
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036301|gb|DR332054.1|DR332054
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GAAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036305|gb|DR332058.1|DR332058
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GAAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036306|gb|DR332059.1|DR332059
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GAAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036307|gb|DR332060.1|DR332060
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036309|gb|DR332062.1|DR332062
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GAAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036308|gb|DR332061.1|DR332061
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GAAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC
EST: gi|86036313|gb|DR332066.1|DR332066
EST:     GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAG                         GCAGAAC
genomic: GGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgatt ... ttgttttcagGAAGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCAGATGCGCAACAAAGAGGGAGATAGAAAGCGAGCTTTCTTAACCTTGGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGTCAATAGgcaagtgattcaattctctggttttgagacaaggactagtaaagttttggtctaatttgtgttttattcttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA