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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctcccttttctctcagattttttttagtagctgaattagggtttttgttccgttttcgctattgcttcttccgcatcttataaagggtttaatgttatacttctctgatgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG

Basic information

species Arabidopsis thaliana
transcript AT5G27720.1
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|86050911|gb|DR346666.1|DR346666
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|86050917|gb|DR346672.1|DR346672
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|164072209|gb|ES175279.1|ES175279
EST:     TTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|47831834|gb|CK121518.1|CK121518
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|164192751|gb|ES169742.1|ES169742
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATC
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATC
EST: gi|47832106|gb|CK121790.1|CK121790
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|116449433|gb|EG492025.1|EG492025
EST:     TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|86050907|gb|DR346662.1|DR346662
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|86050915|gb|DR346670.1|DR346670
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|86050918|gb|DR346673.1|DR346673
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|116480858|gb|EG523450.1|EG523450
EST:     GTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: GTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|86050914|gb|DR346669.1|DR346669
EST:     TCATATTTGAATCGTTCACCTTCTCGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|116480849|gb|EG523441.1|EG523441
EST:     TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: TCATATTTGAATCGTTCACCTTCTTGCCGATCTTCGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
EST: gi|86050916|gb|DR346671.1|DR346671
EST:     CATATTTGAATCGTTCACCTTCTCGCCGATCTTGCGGAGTATATTACAAG                         GTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
genomic: CATATTTGAATCGTTCACCTTCTTGCCGATCTT-CGGAGTATATTACAAGgtttctccct ... atgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcttccgcatcttataaagggtttaatgttatacttctctgatgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG
                                        ctctgat  putative branch site (score: 4)
                         tttaatgttatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctcccttttctctcagattttttttagtagctgaattagggtttttgttccgttttcgctattgcttcttccgcatcttataaagggtttaatgttatacttctctgatgtcatcagGTTCTTAACGGATCTCTAAATCTTCTGATTTAAGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG