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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaatctttagattgcttcaagaaaaaaagttttaaagactttaagagattcttagatacatagaatttgaagatcttgtattggtttttgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGATTCCAGATGCTCTTGGTTTAATCTTTAGCCACTTACCTCTTCAAGAAGT

Basic information

species Arabidopsis thaliana
transcript AT4G08980.1
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|86056941|gb|DR352698.1|DR352698
EST:     CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056935|gb|DR352692.1|DR352692
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056928|gb|DR352685.1|DR352685
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056918|gb|DR352675.1|DR352675
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056937|gb|DR352694.1|DR352694
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056921|gb|DR352678.1|DR352678
EST:     CCTTACTCAGCTTTTGTGGKGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056930|gb|DR352687.1|DR352687
EST:     CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056922|gb|DR352679.1|DR352679
EST:     CTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: CTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056925|gb|DR352682.1|DR352682
EST:     TCTCTTTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATT
genomic: TCTCTTTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATT
EST: gi|125172724|gb|EL194753.1|EL194753
EST:     AATATTGAAGAAAGTTTCTCTG                         ATTATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTG
genomic: AATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagA-TATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTG
EST: gi|86056939|gb|DR352696.1|DR352696
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056934|gb|DR352691.1|DR352691
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056924|gb|DR352681.1|DR352681
EST:     CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: CCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056943|gb|DR352700.1|DR352700
EST:     TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|86056945|gb|DR352702.1|DR352702
EST:     TCTCTTTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: TCTCTTTCCTTACTCAGCTTTTGTGGTGAATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
EST: gi|125036308|gb|EL108577.1|EL108577
EST:     AATATTGAAGAAAGTTTCTCTG                         ATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA
genomic: AATATTGAAGAAAGTTTCTCTGgtgaataaga ... tgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagattcttagatacatagaatttgaagatcttgtattggtttttgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGATTCCAGATGCTCTTGGTTTAATCTTTAGCCACTTACCTCTTCAAGAAGT
                                         tttttgt  CT-rich tract
                atagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaatctttagattgcttcaagaaaaaaagttttaaagactttaagagattcttagatacatagaatttgaagatcttgtattggtttttgtgaaacagATATTTGTTAGATGGAAGAAGATTGCGAGTTTCGACATTGGGATGAGTTGATTCCAGATGCTCTTGGTTTAATCTTTAGCCACTTACCTCTTCAAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT