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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaccgattttcgacatggaacttctgattaaatctttacaggaaccttgatacttttgaaatataaactgtgtgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTACAGCTGCAGTGTCCTATACGAGTGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G06580.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G458549_T01 (Zea mays), 3'ss of exon 10
------------------------------gtgagaccgattttcgacatggaacttctgat-taaatctttacag---gaaccttgatact-tttgaaatataaactgtg----tgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTACAGCTGCAGTGTCCTATACGAGTGCAG
                                 ||   |  | ||  ||  | || |  ||  | | || | | |    |  | |||  |     | |   |||     |     |||||||| ||||  ||| | ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||| |||||
gtgggcccactattcgtaatctgcattttctctaggttgtgtatcctcacagtacattggaagttagtcgtaaaaatgtgtgctttgtcataacataacgcatacgacatactgctgcagTGAGGAAGGCAAGCTTAAGAAACTTGGTGATCTTATGAACGAGAGCCATTACAGCTGCAGCGTGCTATACGAATGCAG
















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|116456853|gb|EG499445.1|EG499445
EST:     GAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG                         TGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTA
genomic: GAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAGgtgagaccga ... ctgtgtgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTA
EST: gi|116456852|gb|EG499444.1|EG499444
EST:     GAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG                         TGACGAAGAGAAGTTAAAGAAACTTGGTGATTTCATGAATGAAAGCCATTA
genomic: GAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAGgtgagaccga ... ctgtgtgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTA
EST: gi|164140895|gb|ES028829.1|ES028829
EST:     CCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG                         TGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTA
genomic: CCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAGgtgagaccga ... ctgtgtgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgattaaatctttacaggaaccttgatacttttgaaatataaactgtgtgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTACAGCTGCAGTGTCCTATACGAGTGCAG
                        ttgatacttttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaccgattttcgacatggaacttctgattaaatctttacaggaaccttgatacttttgaaatataaactgtgtgcagTGACGAAGAGAAGTTAAAGAAACTTGGTGATCTCATGAATGAAAGCCATTACAGCTGCAGTGTCCTATACGAGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG