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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggtggcttccgttttacaaacatatagtttgatttatcatctcttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G22770.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 10
aaatggtggcttccgttttacaaacatatagtttgatttatca--tctcttggttcttttgcttatggtgtcagattcactattggttgaacttt----cctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
  ||  ||  | || | || ||   ||  |||||| ||| | |  | | ||   ||  ||  || |||| | || | ||  |||   || |  |     | ||||||||| | ||||| ||||||||| | |||||||| |||||||||||  | ||||||||||| || ||||| |||||  |||||
--atactg--taccatatttcagtaattcagtttgttttttgaaatgttttacatccattattt-tggt-taagctgcataattatatgtatatcacaccttgcagTATTAGAAGGCGGGCTCTTGATCTGTTATATGGTATGTGTGATGTTACGAATGCAAAGGAAATTGTCGAGGAGTTATTGCAG

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 11
--aaatggtggcttccgttttacaaacatatagtttgatttatcatctcttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
   | |    | |  |  ||| |     |  | | || ||| |  ||  |    | |    |        | |     |||    ||   | | |  ||||| ||| | ||  | |||||||||||||||||||| |||||||||||  |||| || ||||| || || || |||||| |||||
tgtagtttatgttagctctttgcctctctggattctgttttcttttcaataaactgtgccacaatcacctttattgcaacttcatgtc--attgtattgcagCATTAGGAGAAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAGGAAATTGTGGAGGAGTTGTTGCAG

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 10
aaatggtg-gcttccgttttacaaacatat-agtttgatttatcatctc--ttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
|  || |   | |  | | |       | | | ||   ||| || | ||  |    |       | ||  | || |   |   ||  |||  | | |  ||||| ||| |  || | |||||||||||||||||||| |||||||||||  |||| || || || || || || |||||| |||||
atgtgatttacgttagctctttgcctctgtgaattctgtttttcttttcaataaactgccacattcatattttctgcaacttcat--gtt--attgtattgcagCATTAGACGGAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAAGAAATTGTTGAGGAGTTGTTGCAG

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 10
aaatggtggcttccgttttacaaac-atatagtttga-tttatcatctcttggttcttttgcttat--ggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
 |   |||  ||    |  |      ||| ||    | ||  |    |||   |     |  ||||    | | | |||      ||  |  | || |  |||||||||| ||||||||||| |||||  | ||||| ||||||||||| |||||||||||||||||||| |||||  | ||||||
-agaagtgcattaaaatgcaaggttgatacagagcaaattcctttgttctcaatggcaatttttattaaatctaatatttttacctgcattgatttacaagCAGTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGATGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 10
---aaatggtggcttccgttttacaaacatatagtttgatttatcatctcttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
     ||            || | | | |   |  ||  ||| |  ||  | |  | ||||  | |   |   |  || ||   ||  |  | || | ||||||||||| ||||||||||| |||||  | ||||| |||||||| || |||||||||||||||||||| |||||  | ||||||
agtgcattaaaatgcaaagttgatacaga-gcaaattcctttgttctcaatggaattttttattaaatctagtatttttacc--tgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG

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|125302352|gb|EL316437.1|EL316437
EST:     AAAGACCCTGACATCAG                         TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAA
genomic: AAAGACCCTGACATCAGgttggtttag ... tttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
                                            ctttcctgc  CT-rich tract
      ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatggtggcttccgttttacaaacatatagtttgatttatcatctcttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - -aaacata
- - - - - - - - - - - - - - -agtttga