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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacatctatacagcttagtaaccttcttttgtacctcttgtgttggaatggatcgtgttgttcttttatgatgtgttttttgagtgctgcttcagctaattccaggccaggtactcaaaaatgagaccattccttggttgctgtatgattttatgttttatgtatatatctttactttgttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGATCTCCTGCTTCTACAGAACATCGCAAGCTACTTGCTTCTTGCTTGTGGT

Basic information

species Arabidopsis thaliana
transcript AT4G33625.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G33625.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0017g00540.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtacatctatacagcttagtaaccttcttttgtacctcttgtgttggaatggatcgtgttgttcttttatgatgtgttttttgagtgctgcttcagctaattccaggccaggtac-tcaaaaatgagaccattccttggttgctgtatgattttatgttttatgtatatatctttactttgttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGATCTCCTGCTTCTACAGAACATCGCAAGCTACTTGCTTCTTGCTTGTGGT
                                                                                       |||     || |   ||      | |||   | |   |      | ||  |          ||||  || | || ||  |  |   ||  || || |      ||||||||||| ||||||||||||||||| ||| |  |    | | |  ||||||||||| | ||||| || ||||| || |||||  |||| ||||| ||||||
--------------------------------------------------------------------------------------tagtagccttttatagaagcttttgtcagaagcattgcatgcacaaacacacacaaaa----gtattcttatttggttcttacagtaatgattgctct-----cttcagTGTTGCAGTGATGACAAGAGCTTTTCCTAATGAATCTAGTAAGCAGAAGGATCTCGTTCTTCTTCAAAACATAGCTAGCTATATGCTCCTTGCCTGTGGT
















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|124810608|gb|EH895474.1|EH895474
EST:     GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTT                         TGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGA
genomic: GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTTgtaagtacat ... ttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGA
EST: gi|124776068|gb|EH866195.1|EH866195
EST:     TTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTT                         TGTTGCTGTGATGACAAGAGCTTTCCCTGACTATAGGACTCAAAAGAAGGA
genomic: TTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTTgtaagtacat ... ttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGA
EST: gi|19878218|gb|AU239049.1|AU239049
EST:     GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTT                         TGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGA
genomic: GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTTgtaagtacat ... ttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGA
EST: gi|124874069|gb|EH955714.1|EH955714
EST:     GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTT                         TTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGG
genomic: GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTTgtaagtacat ... ttcatttcagT-GTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGG
EST: gi|164089862|gb|ES022520.1|ES022520
EST:     GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTT                         TTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAA
genomic: GTTCTTGAATACTGGGCTGGTAGAGGAATGCTTCAAATTTTgtaagtacat ... ttcatttcagT-GTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgctgtatgattttatgttttatgtatatatctttactttgttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGATCTCCTGCTTCTACAGAACATCGCAAGCTACTTGCTTCTTGCTTGTGGT
                                  tctttactttgttc  CT-rich tract
         tatgattttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacatctatacagcttagtaaccttcttttgtacctcttgtgttggaatggatcgtgttgttcttttatgatgtgttttttgagtgctgcttcagctaattccaggccaggtactcaaaaatgagaccattccttggttgctgtatgattttatgttttatgtatatatctttactttgttcatttcagTGTTGCTGTGATGACAAGAGCTTTCCCTGACTATATGACTCAAAAGAAGGATCTCCTGCTTCTACAGAACATCGCAAGCTACTTGCTTCTTGCTTGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT