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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattcatatgaaaattctgttctgtaaaatggtatttagtgtcctgaaaatatgcttaaagcaaccggttgggttgggtcttcactgacattgattgttgtatcttcagGTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAAACAAGTAGTGGTGAAGGAGTGTTGAGTCATGTTGTAGCCGCCAAACAGA

Basic information

species Arabidopsis thaliana
transcript AT1G55960.1
intron # 5
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|125223774|gb|EL237859.1|EL237859
EST:     CCTTAATGAAAGAG                         GTTCCATCAGAGTTAGAAACT-GGACAGATAATGTCACAGGCTCCATGGAA
genomic: CCTTAATGAAAGAGgtgagattca ... gtatcttcagGTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAA
EST: gi|86088157|gb|DR383916.1|DR383916
EST:     GTCATAGAACCCAAGGACGCATTCTATCTGCTGTCACCTTAATGAAAGAG                         GTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAA
genomic: GTCATAGAACCCAAGGACCCATTCTATCTGCTGTCACCTTAATGAAAGAGgtgagattca ... gtatcttcagGTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAA
EST: gi|47828193|gb|CK117877.1|CK117877
EST:     GTCATAGAACCCAAGGACCCATTCTATCTGCTGTCACCTTAATGAAAGAG                         GTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAA
genomic: GTCATAGAACCCAAGGACCCATTCTATCTGCTGTCACCTTAATGAAAGAGgtgagattca ... gtatcttcagGTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaagcaaccggttgggttgggtcttcactgacattgattgttgtatcttcagGTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAAACAAGTAGTGGTGAAGGAGTGTTGAGTCATGTTGTAGCCGCCAAACAGA
                                              tatcttc  CT-rich tract
 attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattcatatgaaaattctgttctgtaaaatggtatttagtgtcctgaaaatatgcttaaagcaaccggttgggttgggtcttcactgacattgattgttgtatcttcagGTTCCATCAGAGTTAGAAACTGGGACAGATAATGTCACAGGCTCCATGGAAACAAGTAGTGGTGAAGGAGTGTTGAGTCATGTTGTAGCCGCCAAACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG