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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaatttacaccctttattattgtgtttgctcaatttaatgccctttgttgtcacaaacttgctaatatgaataaacctttttattatctatctatggtttatgtgtttgataatctggttttcctttctgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACAAAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G04600.1
intron # 2
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|86067155|gb|DR362912.1|DR362912
EST:     GCTATACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAG                         CTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA
genomic: GCTATACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAGgtataaattt ... tgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA
EST: gi|86067156|gb|DR362913.1|DR362913
EST:     GCTATACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAG                         CTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA
genomic: GCTATACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAGgtataaattt ... tgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA
EST: gi|86074844|gb|DR370601.1|DR370601
EST:     ACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAHG                         CTTTCTTCTCGCAGTTTGGWACAGTTAAGAGAGTTAGAGTCGCCAGAWACA
genomic: ACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAGgtataaattt ... tgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA
EST: gi|86067154|gb|DR362911.1|DR362911
EST:     GCTATACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAG                         CTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA
genomic: GCTATACATCGGTAGAATCCCTCATGGCTTCTATGAGACTGAGATTGAAGgtataaattt ... tgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctatctatggtttatgtgtttgataatctggttttcctttctgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACAAAAAG
                     gtttgat  putative branch site (score: 5)
                              tctggttttcctttct  putative PPT
                      tttgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaatttacaccctttattattgtgtttgctcaatttaatgccctttgttgtcacaaacttgctaatatgaataaacctttttattatctatctatggtttatgtgtttgataatctggttttcctttctgggttatagCTTTCTTCTCGCAGTTTGGAACAGTTAAGAGAGTTAGAGTCGCCAGAAACAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA