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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttgttttggttacattggcaacttgagaatgttactagctttgtaaaatcaggtcttgaaaagttgttaactttgtgtgtaaaaatagaatcggtacatgatatgttttggattagccttaacttttaatccatagGTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTACAGGGATGACGATTACCTTATCTTTGATTGTCCAG

Basic information

species Arabidopsis thaliana
transcript AT4G12790.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

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|301501514|gb|HO207054.1|HO207054
EST:     ATGGAGGATCTAAAGCTTGGTCCTAATGGTGCCCTTATGTATTGCATGGA                         GTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTA
genomic: ATGGAGGATCTAAAGCTTGGTCCTAATGGTGCCCTTATGTATTGCATGGAgtatcctttg ... taatccatagGTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTA
EST: gi|164049741|gb|ES043898.1|ES043898
EST:     TGGTGCCCTTATGTATTGCATGGA                         GTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTA
genomic: TGGTGCCCTTATGTATTGCATGGAgtatcctttg ... taatccatagGTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatagaatcggtacatgatatgttttggattagccttaacttttaatccatagGTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTACAGGGATGACGATTACCTTATCTTTGATTGTCCAG
 agccttaac  putative branch site 
                                         ctttt  putative PPT
                                     ttaacttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctttgttttggttacattggcaacttgagaatgttactagctttgtaaaatcaggtcttgaaaagttgttaactttgtgtgtaaaaatagaatcggtacatgatatgttttggattagccttaacttttaatccatagGTATCTTGAGGATAGCTTACATGATTGGGTGGATGAAGAATTGGAGAACTACAGGGATGACGATTACCTTATCTTTGATTGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA