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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttcaaaatgtatttttcatttttaatctttttgttatgagaaatatcttcttttttttttgtatgttatgagaaattttataaactaaaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAACAATCATCAATCCCAAATCTGACACTACGACAACAAGCCTTTGTCGTCA

Basic information

species Arabidopsis thaliana
transcript AT1G71695.1
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|124753223|gb|EH843353.1|EH843353
EST:     CCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGA
genomic: CCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGA
EST: gi|86048096|gb|DR343851.1|DR343851
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|116414392|gb|EG456984.1|EG456984
EST:     GCCGCTGCAATCCTTCGTATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|163986347|gb|EL995982.1|EL995982
EST:     AGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAAG                         GGATGTGAAGCA
genomic: AGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCA-Ggttcgatctt ... aaataaacagGGATGTGAAGCA
EST: gi|86048122|gb|DR343877.1|DR343877
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|125239270|gb|EL253355.1|EL253355
EST:     CTGCCATCCTTCGCATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGAC
genomic: CTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGAC
EST: gi|86048109|gb|DR343864.1|DR343864
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86048130|gb|DR343885.1|DR343885
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86048112|gb|DR343867.1|DR343867
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86048111|gb|DR343866.1|DR343866
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|125232560|gb|EL246645.1|EL246645
EST:     GCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGA
genomic: GCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGA
EST: gi|124857720|gb|EH942157.1|EH942157
EST:     ATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: ATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86056964|gb|DR352721.1|DR352721
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86048118|gb|DR343873.1|DR343873
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86048137|gb|DR343892.1|DR343892
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|125297380|gb|EL311465.1|EL311465
EST:     CCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGA
genomic: CCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGA
EST: gi|125031550|gb|EL103819.1|EL103819
EST:     TTTCCATTGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: TTTCCA-TGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|124750386|gb|EH840516.1|EH840516
EST:     GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTG
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTG
EST: gi|124737867|gb|EH829269.1|EH829269
EST:     GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAG                         GGATGTGAAGCATCAGTG
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTG
EST: gi|86048108|gb|DR343863.1|DR343863
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCAATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCA-TCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGA
EST: gi|86048125|gb|DR343880.1|DR343880
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCCATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
EST: gi|86048131|gb|DR343886.1|DR343886
EST:     GTTTAGCCGCAGCCATCCTTCGTATACATTTCSATGATTGCTTTGTTCAG                         GGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA
genomic: GTTTAGCCGCTGCCATCCTTCGTATACATTTCCATGATTGCTTCGTTCAGgttcgatctt ... aaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcttcttttttttttgtatgttatgagaaattttataaactaaaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAACAATCATCAATCCCAAATCTGACACTACGACAACAAGCCTTTGTCGTCA
                                        aactaaa  putative branch site (score: 2)
        ttttttttttgtatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttcaaaatgtatttttcatttttaatctttttgttatgagaaatatcttcttttttttttgtatgttatgagaaattttataaactaaaataaacagGGATGTGAAGCATCAGTGCTGCTAGCTGGATCAGCCAGTGGACCAGGAGAACAATCATCAATCCCAAATCTGACACTACGACAACAAGCCTTTGTCGTCA

- cttcaaa
- - - - - - - - - - - - - - - - - - - atgagaaa
- - - - - - - - - - - - - - - - - - - - -agaaata