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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatccttctctctatatgtcccttattattaccctattttgtaactcggttcatgacaaagtgtttgtttctttttgtgtag

Basic information

species Arabidopsis thaliana
transcript AT2G42680.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42680.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G42900.1 (Glycine max), 5'ss of exon 3
ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatccttctctctatatgtcccttattattac----cctattttgtaactcggttcatgacaaagtgtttgtttctttttgtgtag--------------
||||    || || ||||| || ||||| ||||| |||||||| ||||  |||||||| || || ||||| || |||||||||||||  ||  || |  ||  ||      || ||| ||      | || |  | | |    | || |  || |     ||     |   ||                
ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtat--tactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcag
















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|86081161|gb|DR376918.1|DR376918
EST:     TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA                         ATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
genomic: TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
EST: gi|47829297|gb|CK118981.1|CK118981
EST:     TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA                         ATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
genomic: TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
EST: gi|125122000|gb|EL168867.1|EL168867
EST:     AACTTGCTCAA                         ATCATCAATGAGTAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGC
genomic: AACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAG-AAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGC
EST: gi|86086850|gb|DR382609.1|DR382609
EST:     TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA                         ATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
genomic: TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
EST: gi|116455455|gb|EG498047.1|EG498047
EST:     TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA                         ATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
genomic: TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
EST: gi|164121656|gb|ES036196.1|ES036196
EST:     TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA                         ATCATCAATGAGAAGCCACAAGTGATTCA
genomic: TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCA
EST: gi|116455456|gb|EG498048.1|EG498048
EST:     TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAA                         ATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT
genomic: TTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatc ... ttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAACGTGTGCCTACTGAGCTAAAGAAAGCCATTATGCAAGCCAGGACAGACAAGAAGCTAACCCAGTCCCAACTTGCTCAAgtatattatccttctctctatatgtcccttattattaccctattttgtaactcggttcatgacaaagtgtttgtttctttttgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC