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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgaaattatttctgttttcttgaaccggaataattgattccggttatcttaaaccggaattgagttagtttacttgattggttatttggttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAAGGAGCAATGGTAATCTACACTTTAGCTGATCCATCAATGGCAGAAGCAA

Basic information

species Arabidopsis thaliana
transcript AT4G21210.1
intron # 1
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|124986152|gb|EL058691.1|EL058691
EST:     TGGTTGTCCCGTTAATACACATCTCTTCTCTAGGG                         ATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGA
genomic: TGGTTGTCCCGTTAATACACATCTCTTCTC-AGGGgtattatcgt ... ttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGA
EST: gi|86070549|gb|DR366306.1|DR366306
EST:     ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGG                         ATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
genomic: ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGGgtattatcgt ... ttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
EST: gi|124963814|gb|EL038124.1|EL038124
EST:     GGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGG                         ATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
genomic: GGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGGgtattatcgt ... ttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
EST: gi|47829804|gb|CK119488.1|CK119488
EST:     ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGG                         ATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
genomic: ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGGgtattatcgt ... ttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
EST: gi|116424173|gb|EG466765.1|EG466765
EST:     ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGG                         ATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
genomic: ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGGgtattatcgt ... ttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
EST: gi|47830494|gb|CK120178.1|CK120178
EST:     ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGG                         ATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA
genomic: ATTGCTTGGTCGACCGTGGTTGTCCCGTTAATACACATCTCTTCTCAGGGgtattatcgt ... ttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttaaaccggaattgagttagtttacttgattggttatttggttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAAGGAGCAATGGTAATCTACACTTTAGCTGATCCATCAATGGCAGAAGCAA
                           acttgat  putative branch site (score: 5)
                                             tttttt  putative PPT
                                     ttatttggtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgaaattatttctgttttcttgaaccggaataattgattccggttatcttaaaccggaattgagttagtttacttgattggttatttggttttttgaagATTGAAGATGGGGAGAAGTTAATGGAGATCATAAAGCAAGCGGCAAGAGAAGGAGCAATGGTAATCTACACTTTAGCTGATCCATCAATGGCAGAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA