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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatagctttgttcttatcagattcaagttggaagatttcaattgttaagactatccatgtttgttatttgctcaagcttacatgcattctatctgcagGTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGACTGGCAGTGCAACTGGTGGCCGGAGGAAGCGGTGTGAAAAACGCGAAAA

Basic information

species Arabidopsis thaliana
transcript AT4G34200.1
intron # 3
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|86054944|gb|DR350701.1|DR350701
EST:     ATGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTCTGCTGAG                         GTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGA
genomic: ATGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTCTGCTGAGgtgagcactc ... ctatctgcagGTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGA
EST: gi|124994102|gb|EL066371.1|EL066371
EST:     ATGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTCTGCTGAG                         GTTCTGACCGAGCTGAAACCATATGTG
genomic: ATGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTCTGCTGAGgtgagcactc ... ctatctgcagGTTCTGACCGAGCTGAAACCATATGTG
EST: gi|116478276|gb|EG520868.1|EG520868
EST:     ATGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTCTGCTGAG                         GTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGA
genomic: ATGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTCTGCTGAGgtgagcactc ... ctatctgcagGTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGA
EST: gi|86054873|gb|DR350630.1|DR350630
EST:     TGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTTTCTGCTGAG                         GTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGA
genomic: TGGAGAGCTTGCTGCTACTGCAGTCAATGCACCTATGGTTT-CTGCTGAGgtgagcactc ... ctatctgcagGTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaagactatccatgtttgttatttgctcaagcttacatgcattctatctgcagGTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGACTGGCAGTGCAACTGGTGGCCGGAGGAAGCGGTGTGAAAAACGCGAAAA
                               agcttac  putative branch site (score: 3)
                                           ttctatct  putative PPT
                tttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatagctttgttcttatcagattcaagttggaagatttcaattgttaagactatccatgtttgttatttgctcaagcttacatgcattctatctgcagGTTCTGACCGAGCTGAAACCATATGTGGTGCTAGCCGAGAAACTAGGAAGACTGGCAGTGCAACTGGTGGCCGGAGGAAGCGGTGTGAAAAACGCGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - aagacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttacat