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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG

Basic information

species Arabidopsis thaliana
transcript AT5G18620.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
 |||  |  |||  |||   |   |  |||    | |  ||||| | |   | |      | || || || |  |   | ||  | ||| |   | ||||  || |   |||||| || ||||| || || |||||||| || |||||||||||||| ||  | || ||||| || ||||| ||||||||||||||  | || ||||||| 
-ttataacattttaattaaaagcaactgtttgcaatt--ttgca-tactgaagatcaaacttttcatactga-cagattttgtgttttgat---cattgttcaact---agATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
   | ||  |||   || || | ||||   ||    |||||||| | |   | |      | |  || || | |    | ||  | || ||   | ||||| ||     |||||| || ||||| || || |||||||| || ||||||||||| || ||  | || ||||| || ||||| |||||||||||||| || || ||||||| 
accattatatttt--ttttttaataaaagcaac---tgtttgca-tactgaagatcaaactttccatactga-tggattgtgtatgtt-ttgatcattgtacaacc---agATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagct--ctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
          ||| | | | |||     || ||| |||||     ||| | |  | | ||  |  |   |||     ||  |||  |  |||  |    | ||    |||||||||| || ||||| || || || ||||| |||||||| |||||||| ||  |||||||||| |||||||||||||||||||||||  |||| ||||||||
----------ttaaaatatcaag--ggtttgatgtgtgttgatt-tgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 21
gttagtaactttagattgttaagtaaag-ttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgt----agATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
                 ||    ||| | ||  | | |   |    |  || |    |   | ||||   |    | | |||||||  | | | | |||  ||  |||||    |||||| |||||||| || || || ||||| || ||||| |||||||| ||| |||||||||| ||||||||||||||||| |||||  |||| ||||||| 
----------------agtgggataaggctttgttattaactttttttggaaattactttctgtttagaatgtcaaggttctgcctaatttgtgcattttgaatcattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAAGCTATTGGAAAGAAGTTGGACCGCTACAA

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
-gttagta-actttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
  ||  |     ||   |||  || | ||| |  ||| | || |   | |   ||  |         |||    ||  | ||||  |  |||  |    | ||    ||| |||||| || ||||| || || || ||||| |||||||| |||||||| ||  |||||||||| |||||||||||||||||||||||  |||| ||||||| 
gtttgatgtgtgttgatttgccaaatgaagct--tgaat-ttagttttccattaagat---------atcaagggtctg-tctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
gttagtaactttagattgttaagtaaagttaatgag---tgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
           || ||||| |  |  |  | |  |      ||||   | |  |||| | ||  |||| | |         ||||| | |     |    |  ||    |  |||||| || || ||||||||||| ||||| ||||| || || ||||| |||||||||||||| ||||||||||| |||||||||||  |||||||||||| 
-----ggttgatatattgtcagatgcatcttacaacatccatttgtttttcatcaaaat-ggtgattttttcg--------tctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 21
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctc--tgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
                                                      ||  | | ||  |  | |  || |    ||  |    | ||    ||    |||| |||| |||||||||||  |       |||||  | ||||| ||  | ||| | || |||||||||||||||| | ||||||||||||| ||||| || |||| 
------------------------------------------------------gtaagcttttccttgtcaagaaacatattgtttaagctgttttgctgctgtaatt-tagACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 21
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctc--tgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
                                                      ||  | | ||  |  | |  || |    ||  |    | |||   |     |||| |||| |||||||||||  |       |||||  | ||||| ||  | ||| | || |||||||||||||||| | ||||||||||||| ||||| || |||| 
------------------------------------------------------gtaagcttttccttgtcaagaaacatattgtttaagctgttctgctactgtaatt-tagACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA

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|163993867|gb|ES200109.1|ES200109
EST:     GATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATG                         ATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTA
genomic: GATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaact ... aaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
                                       tttgtaaaaattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA