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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcttaaacaaaactctactttcttgttctgtctctctatttcttttgaggaaacttatggcttatatgaggcttcttgtgtactttgtgaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG

Basic information

species Arabidopsis thaliana
transcript AT1G43190.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G36770.1 (Glycine max), 3'ss of exon 2
--------------gtctcttaaacaaaactctactttcttgttctgtctctctatttcttttgaggaaacttatggcttatatgaggcttcttgtgtactttgtgaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG
              | || |||||||| |||  ||| | |   |  |  |||  |  |  ||| |    | || |   || | ||     ||| |||   |   || |||||||| ||||||||||||||||| |||||||||||| |||| | || |||| | | |||||||||||||  |||||
gttttctttttcatgact-ttaaacaagactg-actgtttgtcttagaatcttaaggttgtttcatttcatttttattttttttgtaaaatct-gtgctatacttgcagGCTCTTATCCAAATGCAAGATGTTCCTTCTGCAGTTAATGCTTTACAATTTTATGCAAATGTTCAGCCAAGCATAAG

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G30820.1 (Glycine max), 3'ss of exon 3
-------------gtctcttaaacaaaactctactttcttgttctgtctctctatttcttttgaggaaacttatggcttatatgaggcttcttgtgtactttgtgaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG
               |  |||||| | |||     ||    ||       |    || |||      |  | |    ||   | |    | |    |||||   | |||||||| ||||||||||||||||| |||||||||||| |||  | || |||| | | |||||||||||||  |||||
gttttttttttcatgcctttaaactagactaattgtttccattagaatcttaaggttatttcatttcatttcagttttttggtaaaatctgtgccatactt---gcagGCTCTTATCCAAATGCAAGATGTTCCTTCTGCAGTTAATGCCTTACAATTTTATGCAAATGTTCAGCCAAGCATAAG

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G27970.1 (Glycine max), 3'ss of exon 1
gtctcttaaacaaaactctactttctt---gttctgtctctcta----tttcttttgaggaaac-ttatggcttatatgaggcttcttgtgtactttgtgaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG
  ||   |||  |   |||  |||| |    ||||     |  |    |  ||| | |  |||  || |   |||| ||     |||  ||  |||   | |||||||||| |||||||||||| || |||||||||||| |||| | || |||| | | ||||| |||||||  |||||
tgcttgcaaattattttctgttttccttagattcttagaattcaaggctgacttattactaaatattttcttttatttgtataatctattgctctt---gcagGCTCTTCTTCAAATGCAAGATATTCCTTCTGCAGTTAATGCTTTACAATTTTATGCAAATGTCCAGCCAAGCATAAG

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G08870.1 (Glycine max), 3'ss of exon 3
gtctcttaaacaaaactctactttcttgttctgtctctctatttct----tttgagga-aacttatggct---tatatgaggcttcttgtgtactttgt-------gaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG
|| |  |  |   |       | | || |  | ||  |  |||  |    ||  |||   | ||||  ||   ||| |     |  |||| || | | |       | |||||||||| |||||||||||| || |||||||||||| |||| | || |||| | | ||||| |||||||  |||||
gttttcttcatgcattcaatgtattttctgttttccttagattcttagaattcaaggctgaattattactaaatattttcttttatttgtataatctattgctcttgcagGCTCTTCTTCAAATGCAAGATATTCCTTCTGCAGTTAATGCTTTACAATTTTATGCAAATGTCCAGCCAAGCATAAG

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|125084603|gb|EL144754.1|EL144754
EST:     AACCATTTGGTGTTATAACTAAGCTTGTGATGCTCAGGGCAAAGAATCAG                         GCTCTTCTCCAAATGCAAGAT
genomic: AACCATTTGGTGTTATAACTAAGCTTGTGATGCTCAGGGCAAAGAATCAGgtctcttaaa ... ctttgtgaagGCTCTTCTCCAAATGCAAGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttttgaggaaacttatggcttatatgaggcttcttgtgtactttgtgaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG
             aaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcttaaacaaaactctactttcttgttctgtctctctatttcttttgaggaaacttatggcttatatgaggcttcttgtgtactttgtgaagGCTCTTCTCCAAATGCAAGATGTTTCTTCTGCAGTTAGTGCTCTTCAGTTTTTTACTAATGTTCAGCCAACTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG