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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtacttttattggctgctttacttgatttaagtcggtatctatattctcaacgtttcattttcttgggaaaag

Basic information

species Arabidopsis thaliana
transcript AT4G14710.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14710.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv05s0020g04080.t01 (Vitis vinifera), 5'ss of exon 4
TGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaag--------tacttttattggctgctttacttgatttaagtcggtatctatattctcaacgtttcattttcttgggaaaag
||||| ||||| || ||||| ||||||| |||  | |||| |||||| ||||| ||| | ||||||||||| ||||| || ||||| || |||||||| |||| |         | |||| | |  |    | |    | ||  |    | | |   | || |  ||| | ||| | | |||   
TGCCCAGAAAAACTGCCAAATTATGAAGAGAAGATCAAGAACTTTTTTGAAGAGCATCTTCACACTGATGAGGAGATTCGCTACTGTGTGGCAGGAAGTGgtaggatgagttgcagttttgtagtttttagttcccactctacctattaacccaggctttctaatttttactttatggtgaag--
















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|124885991|gb|EH964893.1|EH964893
EST:     AACATTTGCACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAAGCG                         GTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGG
genomic: AACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtactt ... ttgggaaaagGTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGG
EST: gi|86080820|gb|DR376577.1|DR376577
EST:     AGAACATTTGCACACTGATGAAGAGATCCGTTA-YGCGTTGCAGGAAGCG                         GTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
genomic: AGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtactt ... ttgggaaaagGTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
EST: gi|86074670|gb|DR370427.1|DR370427
EST:     AGAACATTTGCACACTGATGAAGAGATCCGTTA-TGCGTTGCAGGAAGCG                         GTTACTTTGATGTTAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
genomic: AGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtactt ... ttgggaaaagGTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
EST: gi|86082287|gb|DR378046.1|DR378046
EST:     AGAACATTTGCACACTGATGAAGAGATCCGTTA-TGCGTTGCAGGAAGCG                         GTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
genomic: AGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtactt ... ttgggaaaagGTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
EST: gi|164191639|gb|ES133728.1|ES133728
EST:     TTGCAGGAAGCG                         GTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
genomic: TTGCAGGAAGCGgtaagtactt ... ttgggaaaagGTTACTTTGATGTGAGGGATCGCAATGAAGCTTGGATTAGAGTATGGGTAA
EST: gi|125049106|gb|EL121375.1|EL121375
EST:     AGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCG                         GTTACTTTGATGTGAGGGATCGCAAT
genomic: AGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtactt ... ttgggaaaagGTTACTTTGATGTGAGGGATCGCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACTGCGTTGCAGGAAGCGgtaagtacttttattggctgctttacttgatttaagtcggtatctatattctcaacgtttcattttcttgggaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC