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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaagtcttcttttttggttttcatttatccccagagtaagttttttatacgtttgagctttgttaacagCTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAGCTTGAAAAACAG

Basic information

species Arabidopsis thaliana
transcript AT5G13260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0244g00070.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------gtagaaagtcttcttttttggttttcatttatccccagagta-agttttttatacgt-ttgagctttgtta-acagCTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAGCTTGAAAAACAG
                                                   | |   | ||  |  |       | |   ||       || ||  | | | | || |||   | ||||  |||||| || |||||||| |||| ||||||||| ||||| || || || ||||||||||| ||||||
gtctattgccttccccacccgcccccacccccttttttttcttttcccgaaaaagcatttttgtcatcaaaacacgtcattcatttatttatagcatataacatgtgttggattctgttgtacagCTCAGACTTGAGGAAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG
















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|164060338|gb|ES199721.1|ES199721
EST:     CTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAGAG                         CTTAGGCTTGAGGATGAGAAATGCAAGGAAG
genomic: CTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAAAGgtagaaagtc ... ttgttaacagCTTAGGCTTGAGGATGAGAAATGCAAGGAAG
EST: gi|86066754|gb|DR362511.1|DR362511
EST:     CTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAAAG                         CTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAG
genomic: CTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAAAGgtagaaagtc ... ttgttaacagCTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAG
EST: gi|86066755|gb|DR362512.1|DR362512
EST:     CTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAAAG                         CTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAG
genomic: CTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAAAGgtagaaagtc ... ttgttaacagCTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttcatttatccccagagtaagttttttatacgtttgagctttgttaacagCTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAGCTTGAAAAACAG
                                           ctttgtt  CT-rich tract
                    agtaagttttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaagtcttcttttttggttttcatttatccccagagtaagttttttatacgtttgagctttgttaacagCTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAGCTTGAAAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT