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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataaaggtttaaactaagttctgctgtcatgaatgattggtttctgttggttagtaagcatggatctggtaagtttaaccactgtgtcctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCACCTCAACGGGAGAGATACTCATATCCGCCAGATCAAAGTTTACGGCCCT

Basic information

species Arabidopsis thaliana
transcript AT2G18290.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18290.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 4
----taataaaggtttaaactaagttctgctgtcatgaatgattggtttctgttggttagtaagcatggatctggtaagtttaaccactgtgtcctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCACCTCAACGGGAGAGATACTCATATCCGCCAGATCAAAGTTTACGGCCCT
     ||| |  || ||   |  |   |  |   |      ||  |||  | ||  ||  | || |    | || |   |||   |           ||  ||||||||||||||| || || |||||||| ||||| || || |||||||||||||| || ||||||||||||||| | ||||||||||||||||| || |||
gaggaaatgattgtctagtttttgactttttacaagtcggcatgtgttaatattccttc-tgagtacaattttgatttatttcttcctcaa---tatttggcagGGAAACTTTTGTGAACACTTTTATGTTGCAAATTGCTATATTGTCAAATCACCTTAATGGGAGAGATACTCATGTGCGCCAGATCAAAGTTTATGGGCCT
















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|116467243|gb|EG509835.1|EG509835
EST:     GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACG                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
genomic: GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
EST: gi|86079120|gb|DR374877.1|DR374877
EST:     GTTAAACCAACTGGTTGGGTTTGCTTATCTCTGTCTGGAACTGATCCACG                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCGAATCA
genomic: GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
EST: gi|124976050|gb|EL049493.1|EL049493
EST:     GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACG                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
genomic: GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
EST: gi|124858488|gb|EH942925.1|EH942925
EST:     GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACG                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
genomic: GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
EST: gi|19798329|gb|AU229791.1|AU229791
EST:     GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCT-GAACCGATCCACC                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
genomic: GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
EST: gi|19877766|gb|AU238597.1|AU238597
EST:     GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACG                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
genomic: GTTAAACCAACTGGTTGGGTTTGCTTATCTTTGTCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
EST: gi|124786034|gb|EH875713.1|EH875713
EST:     TCTGGAACCGATCCACG                         GGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA
genomic: TCTGGAACCGATCCACGgtatgtttgc ... ctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttggttagtaagcatggatctggtaagtttaaccactgtgtcctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCACCTCAACGGGAGAGATACTCATATCCGCCAGATCAAAGTTTACGGCCCT
                             gtttaac  putative branch site (score: 3)
                                      ctgtgtcctcttttc  putative PPT
                          taagtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataaaggtttaaactaagttctgctgtcatgaatgattggtttctgttggttagtaagcatggatctggtaagtttaaccactgtgtcctcttttcagGGAAACTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCACCTCAACGGGAGAGATACTCATATCCGCCAGATCAAAGTTTACGGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
-aataaag
- - - - - - aaactaa
- - - - - - - - - - - ctgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccact