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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaaattttgatctctaaatttctcctctctctcgattctctatcgttggagatcctagatctttcgtagctgaagatttgcttgttaggatgtgaatgtttataggagtagtgttagcttcataccccaaggttgtgacttgtgataagttttgagggttatggtttgatatggatgcagGTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAGGTGAATTCAAAGGAAACTATTGTCGGCTG

Basic information

species Arabidopsis thaliana
transcript AT2G39990.1
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|164018259|gb|ES116658.1|ES116658
EST:     TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCTTCTGATCAG                         GTTGCTGTGGA
genomic: TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAGgttcgaaatt ... atggatgcagGTTGCTGTGGA
EST: gi|116476016|gb|EG518608.1|EG518608
EST:     TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAG                         GTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAG
genomic: TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAGgttcgaaatt ... atggatgcagGTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAG
EST: gi|116465250|gb|EG507842.1|EG507842
EST:     TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAG                         GTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAG
genomic: TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAGgttcgaaatt ... atggatgcagGTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAG
EST: gi|125145178|gb|EL180375.1|EL180375
EST:     TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAG                         GTTGCTGTGGATATTGATTACCACCACAATATG
genomic: TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAGgttcgaaatt ... atggatgcagGTTGCTGTGGATATTGATTACCACCACAATATG
EST: gi|125320464|gb|EL334549.1|EL334549
EST:     TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAG                         GTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCA
genomic: TCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAGgttcgaaatt ... atggatgcagGTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaaggttgtgacttgtgataagttttgagggttatggtttgatatggatgcagGTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAGGTGAATTCAAAGGAAACTATTGTCGGCTG
                                      gtttgat  putative branch site (score: 5)
                   ataagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaaattttgatctctaaatttctcctctctctcgattctctatcgttggagatcctagatctttcgtagctgaagatttgcttgttaggatgtgaatgtttataggagtagtgttagcttcataccccaaggttgtgacttgtgataagttttgagggttatggtttgatatggatgcagGTTGCTGTGGATATTGATTACCACCACAATATGTTAGCTTCACACCTTAAGGTGAATTCAAAGGAAACTATTGTCGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA