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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagaaattccgatattattgttgcgtttaccattacttgtagctattttatactgtatttgtcagcatgcatagactaacagttttctcctgtgcagACAAAGAGCTGCTAGTAAAGCCCAAGGGGATGGTGCAAGGAAGAATCGGCACAGAGATCGTTCAAATCGAGCTCTTCCAGCTCCTGAAGCTAATGCAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G54610.1
intron # 6
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|164103720|gb|ES168230.1|ES168230
EST:     GCGACGAGATGAAGAAACTCGGAG                         ACAAAGAGCTGCTAGTAAAGCCCAAGGGGATGGTGCAAGGAAGAATCGGCA
genomic: GCGACGAGATGAAGAAACTCGGAGgtttgtaaca ... tcctgtgcagACAAAGAGCTGCTAGTAAAGCCCAAGGGGATGGTGCAAGGAAGAATCGGCA
EST: gi|164223100|gb|ES160643.1|ES160643
EST:     CCCCCGAGCAAAGAAATTGATGCAAAGCGACGAGATGAAGAAACTCGGAG                         ACAAAGAGCTGCTAGTAAAGCCCAAGGG
genomic: CCCCCGAGCAAAGAAATTGATGCAAAGCGACGAGATGAAGAAACTCGGAGgtttgtaaca ... tcctgtgcagACAAAGAGCTGCTAGTAAAGCCCAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattttatactgtatttgtcagcatgcatagactaacagttttctcctgtgcagACAAAGAGCTGCTAGTAAAGCCCAAGGGGATGGTGCAAGGAAGAATCGGCACAGAGATCGTTCAAATCGAGCTCTTCCAGCTCCTGAAGCTAATGCAGAA
                               gactaac  putative branch site (score: 1)
                                        ttttctcctgt  putative PPT
     ttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagaaattccgatattattgttgcgtttaccattacttgtagctattttatactgtatttgtcagcatgcatagactaacagttttctcctgtgcagACAAAGAGCTGCTAGTAAAGCCCAAGGGGATGGTGCAAGGAAGAATCGGCACAGAGATCGTTCAAATCGAGCTCTTCCAGCTCCTGAAGCTAATGCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC