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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacttcacttgattgaattaatcctttcgctttttgagacctctaaagcttaattactgatgtgtctgtcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAG

Basic information

species Arabidopsis thaliana
transcript AT4G17050.1
intron # 9
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|124750049|gb|EH840179.1|EH840179
EST:     AACTGCGGAAACTTCTTCCGATGTCCGTTGCTTATGACTTCAACATCCAT                         ACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGT
genomic: AACTGCGGAAACTTCTTCCGATGTCCGTTGCTTATGACTTCAACATCCATgtaagcactt ... tcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGT
EST: gi|164054788|gb|ES112215.1|ES112215
EST:     TCCGATGTCCGTTGCTTATGAC-TCAACATCCAT                         ACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAGGAAGTTCA
genomic: TCCGATGTCCGTTGCTTATGACTTCAACATCCATgtaagcactt ... tcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAGGAAGTTCA
EST: gi|124810172|gb|EH895348.1|EH895348
EST:     AACTGCGGAAACTTCTTCCGATGTCCGTTGCTTATGACTTCAACATCCAT                         ACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAGG
genomic: AACTGCGGAAACTTCTTCCGATGTCCGTTGCTTATGACTTCAACATCCATgtaagcactt ... tcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAGG
EST: gi|86084005|gb|DR379764.1|DR379764
EST:     AACTGCGGAAACTTCTTCCGATGTCCGTTGCTTATGACTTCAACATCCAT                         ATTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAG
genomic: AACTGCGGAAACTTCTTCCGATGTCCGTTGCTTATGACTTCAACATCCATgtaagcactt ... tcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgctttttgagacctctaaagcttaattactgatgtgtctgtcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAG
                               tactgat  putative branch site (score: 2)
 ttaattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacttcacttgattgaattaatcctttcgctttttgagacctctaaagcttaattactgatgtgtctgtcatctgcagACTATGGATTTTCAGCCTGGAGAGTTTCTGAATGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA