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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATAACAAAGCAGCTGTGGCATTAGAGAGGTCTAGAGAATTAAGCAATGGTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatataccaaagtaatcattatatatttgattcatcaagaaagtatatatagtgaatgttagtttcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G29200.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29200.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G30070.1 (Glycine max), 5'ss of exon 3
TAATAACAAAGCAGCTGTGGCATTAGAGAGGTCTAGAGAATTAAGCAATGGTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatataccaaagtaatcattatatatttgattcatcaagaaagtatatatagtgaatgttagttt---cttgcag--------------------------
                           || | ||    ||   |  ||||| |||||| | || |||||||||||||| ||||||||||| || || ||||||||||         | | | | |  ||||    | |  ||   || |||  | | || |  ||| ||      | ||                           
--------------------------GGAAGCCTGTGCAA---AATAATGGCTACATCTTAGTCAGTGCAAATGGAGGTCTTAATCAACAACGAGTTGCTgtaagta------gtggcagttaattcatatcatttccgacattcaaatatcaacattgcacattacttgaagaatacaaatacaaataatccataatcgtggaat

upper sequence: AT1G29200.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G09080.1 (Glycine max), 5'ss of exon 3
TAATAACAAAGCAGCTGTGGCATTAGAGAGGTCTAGAGAATTAAGCAATGGTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatataccaaagtaatcattatatatttgattcatcaagaaagtatatatagtg---aatgttagtttcttgcag--------------------------
                           || | ||  | ||   |  ||||| |||||| | || |||||||||||||| ||||||||||| || || ||||||||||       | | | | | |  ||||    | |  ||   || |||  | | ||   | |  |||     | ||                           
--------------------------GGAAGCCTGTACAA---AATAATGGCTACATCTTAGTCAGTGCAAATGGAGGTCTTAATCAACAACGAGTTGCTgtaagta------gaggcagttaattcatatcatttccgacattcaaatatcaacattgcacattactagaagaatacaaatacaataatccataatcgtggaata
















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|116409042|gb|EG451634.1|EG451634
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
EST: gi|116408812|gb|EG451404.1|EG451404
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGTGGTTGCTGCTCTGCTC
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTC
EST: gi|116408813|gb|EG451405.1|EG451405
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGTGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
EST: gi|116409036|gb|EG451628.1|EG451628
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
EST: gi|116408811|gb|EG451403.1|EG451403
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
EST: gi|116409043|gb|EG451635.1|EG451635
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
EST: gi|116408810|gb|EG451402.1|EG451402
EST:     GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCT                         ATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT
genomic: GTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatat ... tttcttgcagATCTGTAACGCTGTTGCGGTTGCTGCTCTGCTCAACGCGACTCTAGTTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATAACAAAGCAGCTGTGGCATTAGAGAGGTCTAGAGAATTAAGCAATGGTTACATCATGGTTAGTGCAAATGGAGGCCTTAATCAACAGCGCGTGGCTgtaagtatataccaaagtaatcattatatatttgattcatcaagaaagtatatatagtgaatgttagtttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG