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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATGATGCGGTTGTTTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcatttgggttttctgtcctttatcattctgaatctctggattattgtggttgtttctaattccagggtaattgcag

Basic information

species Arabidopsis thaliana
transcript AT3G13870.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13870.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 7
GTTATGATGCGGTTGTTTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcatttgggttttctgtcctttatcattctgaatctctgg--------attattgtggttgttt-----ctaattccagggtaattgcag----------------------------------------
||||||||||| ||||||||||| || || ||||||||||||||||||||  | ||||||||| |||| ||  |||   | || || | | | | ||  |  |   |  |        | |||| | ||||| |      |  ||  || |  ||   |                                         
GTTATGATGCGATTGTTTAGTCCACGAAAAACAACTTTGATGTTTGTTATTCGTGATAAAACAAGGgtgtgt-tttctctcttgtgccttatttgatgttatagtgcgagggatagctagtattttagttgtatgtttgtttgtttaagtgagatattaaggtgagctgaactttaagtgctgattttttttgtatacag
















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|116444534|gb|EG487126.1|EG487126
EST:     TTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGG                         ACGCCACTGGAAAATTTAGAACCAGTGCTGAGGGAAGACATTCAAAAG
genomic: TTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcattt ... gtaattgcagACGCCACTGGAAAATTTAGAACCAGTGCTGAGGGAAGACATTCAAAAG
EST: gi|124922152|gb|EL000469.1|EL000469
EST:     TTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGG                         ACGCCACTGGAAAATTTAGAA
genomic: TTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcattt ... gtaattgcagACGCCACTGGAAAATTTAGAA
EST: gi|125089604|gb|EL147910.1|EL147910
EST:     CGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGG                         ACGCCACTGGAAAATTTAGAACCAGTGCTGAGGGAAGACATTCAAAAG
genomic: CGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcattt ... gtaattgcagACGCCACTGGAAAATTTAGAACCAGTGCTGAGGGAAGACATTCAAAAG
EST: gi|164220159|gb|ES110093.1|ES110093
EST:     TTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGG                         ACGCCACTGGAAAATTTAGAACCAGTGCTGAGGGAAGACATTC
genomic: TTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcattt ... gtaattgcagACGCCACTGGAAAATTTAGAACCAGTGCTGAGGGAAGACATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATGATGCGGTTGTTTAGTCCGCGGAAGACAACTTTGATGTTTGTTATAAGAGATAAAACACGGgtatgcatttgggttttctgtcctttatcattctgaatctctggattattgtggttgtttctaattccagggtaattgcag

- - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA