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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGCAAGCGGGTCGGCCCAAGACCATAACCGGTTTCCAGACACACTCCACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttattctttttcctttcttccttgtaccctttatgttgcctacttaggtgtctgattataaaactcggatttgtaactggcaaacag

Basic information

species Arabidopsis thaliana
transcript AT2G20580.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 24
TTGGGCAAGCGGGTCGGCCCAAGACCATAACCGGTTTCCAGACACACTCCACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttattctttttcctttcttccttgtaccctttatgttgcctacttaggtgtctgattataaaactcggatttgtaactggcaaacag
|||| ||||| ||||| || || || || || || || ||||| |||||||| |||||||||||||||||||| || || || || || || ||||| |||||  | |     | | | |||    ||| | |     | |    || ||      || |   ||| ||| || ||| |     |       
TTGGACAAGCAGGTCGTCCGAAAACAATCACTGGCTTTCAGACCCACTCCACCCCTGTTCTCCTGGCTGCTGGGGACAGGGCGGAGCTCGCAACGGAAAAgtaattcacc---tatgccttcaattttgaaactggcttatgatatattt------ctaacactaacact-ggttttttcttcag-------

upper sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 24
TTGGGCAAGCGGGTCGGCCCAAGACCATAACCGGTTTCCAGACACACTCCACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttattctttttcctttcttccttgtaccctttatgttgcctacttaggtgtctgattataaaactcggatttgtaactggcaaacag
|||| ||||| ||||| || || || || || || || ||||| |||||||| |||||||||||||||||||| || || || || || || ||||| |||||  | |  | | | ||||      ||| | |       | || ||  |||   |   | ||  ||    |  ||| |     |       
TTGGACAAGCAGGTCGTCCGAAAACAATCACTGGCTTTCAGACCCACTCCACCCCTGTTCTCCTGGCTGCTGGGGACAGGGCTGAGCTGGCAACGGAAAAgtaattca--cctatgccttaaaattttgaaac-------tggcttatatagtaattctaatactaacaatgattttttcttcag-------

upper sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 24
TTGGGCAAGCGGGTCGGCCCAAGACCATAACCGGTTTCCAGACACACTCCACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttattctttttcctttcttccttgtaccctttatg-ttgcctacttaggtgtctgattataaaactcggatttgtaactggcaaacag
|||| || || |||||||| ||||||||||| ||||||||||||||||| || || |||||||||||||||||||| ||||| ||||| || || || ||||| |  | || |   |||| |    ||| ||  ||   | ||  |   | |   || |     ||| | | |  | |    | |        
TTGGACAGGCTGGTCGGCCAAAGACCATAACTGGTTTCCAGACACACTCAACGCCAGTTCTCCTGGCTGCTGGAGATAGAGCAGAACTTGCTACAGAGAAgtaagaaaatcgtc--ccttccaaagttggacttttggggattatcctttcacaggttttgcactaacagttgcttcttgtgcag--------

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|164193448|gb|ES132201.1|ES132201
EST:     TGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
genomic: TGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
EST: gi|125281089|gb|EL295174.1|EL295174
EST:     ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAGAAGGATT
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAGAAGGATT
EST: gi|116466338|gb|EG508930.1|EG508930
EST:     ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
EST: gi|124908271|gb|EH982351.1|EH982351
EST:     ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAG
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAG
EST: gi|86081058|gb|DR376815.1|DR376815
EST:     ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
EST: gi|164054843|gb|ES115462.1|ES115462
EST:     ACACCTGTTCTCCTGGCTGCTGTAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAGAAGG
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAGAAGG
EST: gi|116466449|gb|EG509041.1|EG509041
EST:     ACACCTGTTTTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAATACTAGAAGGATTCATCATCTTAAAGGAGAA
EST: gi|163971907|gb|ES149429.1|ES149429
EST:     ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAA                         ATACATTCCTCTGTCGCCAA
genomic: ACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttatt ... tggcaaacagATACATTCCTCTGTCGCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGGCAAGCGGGTCGGCCCAAGACCATAACCGGTTTCCAGACACACTCCACACCTGTTCTCCTGGCTGCTGGAGAGAGAGCCGAACTAGCCACGGACAAgtatgttattctttttcctttcttccttgtaccctttatgttgcctacttaggtgtctgattataaaactcggatttgtaactggcaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA