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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaaccgcttatcgtacttttattaaacatgactgtaacatacagcctcatttacttggtgggttttgtcttctctcaacatag

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA02G06710.1 (Glycine max), 5'ss of exon 6
GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaacc----gcttatcgtacttttat-taaacatgactgtaacatacagcctcatttacttggtgggttttgtcttctctcaacatag--------------------------------------------
 ||||| ||||| |||||||||||||| ||||| ||||| |||||||||||||| |   |  | ||||| |  ||||      ||| ||  | ||| ||  ||| |  |||          |  |||  ||   | |  ||| | |  |    |||  ||                                             
ATTGCTCTGGAAAGGAAATTGGTTCATACAAGAGAAAAGTTGTAAGATCCTTGCTTTAGTTGTTAGgtaatacaaacacgagacttttcacattttaatacaaaaaaaacttctcagatttgaatcaaataacagatctgttgtatacttgtacaagttattaccttcccagttattgcaaaatttcaccattttctgattatag

upper sequence: AT3G42050.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G25740.1 (Glycine max), 5'ss of exon 6
GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaac----cgcttatcgtacttttat-taaacatgactgtaacatacagcctcatttacttggtgggttttgtcttctctcaacatag------------------------------------------
 ||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| || |  ||  | ||||| |  ||||       || ||  | ||| ||  ||| |  | | |   ||      |||  ||   | |  ||| | |  |    |||  ||                                           
ATTGCTCTGGAAAGGAAATTGGTTCATACAAGAGAAAAGTTGTAAGATCCTCGCTTTAATTGTTAGgtaatacaaacacaagaattttcacattttaatacaaaaaaaattctcggatttgaa-tcaaataacagatctgttgtatacttgtacaagttaaccttcccagttattgcaaaatttcaccgtttactgattatag
















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|116433606|gb|EG476198.1|EG476198
EST:     AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
genomic: AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
EST: gi|116433595|gb|EG476187.1|EG476187
EST:     AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
genomic: AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
EST: gi|125048740|gb|EL121009.1|EL121009
EST:     AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGA
genomic: AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGA
EST: gi|86031307|gb|DR327060.1|DR327060
EST:     AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
genomic: AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
EST: gi|86031303|gb|DR327056.1|DR327056
EST:     AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGAT
genomic: AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGAT
EST: gi|124855633|gb|EH940070.1|EH940070
EST:     TTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
genomic: TTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
EST: gi|86031311|gb|DR327064.1|DR327064
EST:     ATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAA
genomic: ATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGG-ATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAA
EST: gi|125209970|gb|EL224924.1|EL224924
EST:     CTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
genomic: CTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
EST: gi|86031304|gb|DR327057.1|DR327057
EST:     AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
genomic: AATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGATGATGT
EST: gi|125292222|gb|EL306307.1|EL306307
EST:     ATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAAG                         TGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGA
genomic: ATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAA-Ggtattcaaaa ... ctcaacatagTGCTAGGCCAAAAGCTGGTAATGCTGTTATTGGTAATGGAATTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAGgtattcaaaaccgcttatcgtacttttattaaacatgactgtaacatacagcctcatttacttggtgggttttgtcttctctcaacatag

- - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - AAGCTG