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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttgatcttttgctttgatggaagtgtttcctataagttttagacttaattttaccttaatttattgatccatctcttccttttcaatcttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTATAATT

Basic information

species Arabidopsis thaliana
transcript AT3G02780.1
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|47828035|gb|CK117719.1|CK117719
EST:     AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGA                         ATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
genomic: AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGAgtaagtcttt ... ttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
EST: gi|124831234|gb|EH915673.1|EH915673
EST:     TGTTTGAGGATGA                         ATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
genomic: TGTTTGAGGATGAgtaagtcttt ... ttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
EST: gi|116477195|gb|EG519787.1|EG519787
EST:     AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGA                         ATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
genomic: AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGAgtaagtcttt ... ttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
EST: gi|125064251|gb|EL131940.1|EL131940
EST:     AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGA                         ATGCATTCTTG
genomic: AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGAgtaagtcttt ... ttgcttgcagATGCATTCTTG
EST: gi|116477196|gb|EG519788.1|EG519788
EST:     AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGA                         ATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA
genomic: AAAGATGCTGGTATGGATGCTGTTCAGAGACGTCTCATGTTTGAGGATGAgtaagtcttt ... ttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattttaccttaatttattgatccatctcttccttttcaatcttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTATAATT
                  tattgat  putative branch site (score: 3)
                        tccatctcttcctttt  CT-rich tract
     ttttaccttaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttgatcttttgctttgatggaagtgtttcctataagttttagacttaattttaccttaatttattgatccatctcttccttttcaatcttgcttgcagATGCATTCTTGTTGATGAAACTGATCGTGTTGTGGGGCATGACAGCAAGTATAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - -gttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - accttaa