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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttcttcttcaccgtttacacgtatcaaacaagttaatgattctccctctcaatgtcagttcctgaattttgtgatctttgtcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACAGCTGAATAATCTGTGTTACATTTATGCTCTTTATCTCCTCCACAAACAT

Basic information

species Arabidopsis thaliana
transcript AT4G16760.2
intron # 12
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|124852870|gb|EH937307.1|EH937307
EST:     GAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAA
genomic: GAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAA
EST: gi|124732296|gb|EH823698.1|EH823698
EST:     TTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
genomic: TTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
EST: gi|116448278|gb|EG490870.1|EG490870
EST:     GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
genomic: GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
EST: gi|124775812|gb|EH865939.1|EH865939
EST:     GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAA
genomic: GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAA
EST: gi|124726612|gb|EH818014.1|EH818014
EST:     GTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTG
genomic: GTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTG
EST: gi|116448274|gb|EG490866.1|EG490866
EST:     GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
genomic: GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
EST: gi|116441440|gb|EG484032.1|EG484032
EST:     GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAAC
genomic: GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAAC
EST: gi|116448277|gb|EG490869.1|EG490869
EST:     GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
genomic: GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
EST: gi|116479261|gb|EG521853.1|EG521853
EST:     GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA                         GTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA
genomic: GATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAAgtaatcttct ... tcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattctccctctcaatgtcagttcctgaattttgtgatctttgtcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACAGCTGAATAATCTGTGTTACATTTATGCTCTTTATCTCCTCCACAAACAT
 agttaat  putative branch site (score: 4)
                                       tctttgtctt  putative PPT
                           tgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttcttcttcaccgtttacacgtatcaaacaagttaatgattctccctctcaatgtcagttcctgaattttgtgatctttgtcttggttagGTTCATAGCGAAACTGGAGCAAGACATAGGTGGCAAAGGAGTGAAGAAACAGCTGAATAATCTGTGTTACATTTATGCTCTTTATCTCCTCCACAAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC