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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacttgtgaaggatcaaattttttagagtcttgtttgtttctgtcaaggtcctaatattatatgtgatataaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAATCTAAGGCCGAGGAGACCAAATCAGTAGATAGCGAGGAAACCTCTGAGA

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 11
splice site 3'
intron type U2

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|164141912|gb|ES037629.1|ES037629
EST:     GGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
genomic: GGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
EST: gi|124974075|gb|EL047659.1|EL047659
EST:     GAATCCAAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGA
genomic: GAATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGA
EST: gi|164004691|gb|ES155932.1|ES155932
EST:     GAATCCAAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAG
genomic: GAATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAG
EST: gi|125106564|gb|EL159953.1|EL159953
EST:     AATCCAAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGAATTCCGATTCTGA
genomic: AATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGA-TTCCGATTCTGA
EST: gi|125110644|gb|EL162502.1|EL162502
EST:     AAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
genomic: AAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
EST: gi|164161777|gb|EL967738.1|EL967738
EST:     GAGGAATCCAAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
genomic: GAGGAATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
EST: gi|116412926|gb|EG455518.1|EG455518
EST:     GAATCCAAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
genomic: GAATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
EST: gi|86078431|gb|DR374188.1|DR374188
EST:     GAATCCAAGGACGCAC-TGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
genomic: GAATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
EST: gi|116412928|gb|EG455520.1|EG455520
EST:     GAATCCAAGGACGCACCTGCGGAATCTGAT                         GCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA
genomic: GAATCCAAGGACGCACCTGCGGAATCTGATgtaagcactt ... taaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtcttgtttgtttctgtcaaggtcctaatattatatgtgatataaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAATCTAAGGCCGAGGAGACCAAATCAGTAGATAGCGAGGAAACCTCTGAGA
                         tcctaat  putative branch site (score: 2)
                            taatattatatgtgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacttgtgaaggatcaaattttttagagtcttgtttgtttctgtcaaggtcctaatattatatgtgatataaattccagGCTGAAGACGAACCAGAGGATGATGAAGGAGGAGATGATTCCGATTCTGAATCTAAGGCCGAGGAGACCAAATCAGTAGATAGCGAGGAAACCTCTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA