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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaatgttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag

Basic information

species Arabidopsis thaliana
transcript AT1G25350.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G25350.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA10G41920.1 (Glycine max), 5'ss of exon 11
GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaat-gttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag-------
|||||||||||||||||| || ||||||||| ||||||||||| |||| ||||||||||||||| |||||||||||||| |||| |||||||||| ||   | |||||| |  |     |   |  | | ||| ||     | || |  |  |  ||||| ||   || |  |           
GTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAGgtatgttggtttgttttgtagcacctcttgcctcatgtgattgttccaacttaactatttaggtgtttaacagctttgtgataatatttgcag

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA20G25120.2 (Glycine max), 5'ss of exon 11
------GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaat-gttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag-------
      ||||||||||   ||||| || || ||| ||   ||||||||| |||||||||||||||| ||  |||||||||||||| |||| || ||||||| ||   | |||||| |  |     |   |  | | ||| ||     | |        || | ||| || | || |  |           
TTCCCGGTATGATGATTACAATCCTGAAGCGGAACAGACGGAGTATATTGATCATATTGAAGAAAT-GTCCAGTGGATGGGTTGGAAACCATTTAAGGTATgttggtttgttttgtagcacctcttggctcatgtgattgttccaacttagcgatggagatgcttaacagttttgtgataatatttgcag

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 5'ss of exon 11
GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgt---attttcaatgttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag
||||||||| ||||| || || || |||||| |||| |||||| |||||||||| ||||||||   |||||||||||||||||| ||||||||   ||||||| |  ||      | | |  || | | |     |||||    ||   ||| |||  ||| ||||  | |        
GTATGATGACACAAACCCTGAAGCTGAAAAGAAAGAATATATTGATCATATTGACGAAATTGTCCGGTGGATGGGTTGGGAACCTTTCAAGgtgccattttcagtcctt------attggtgcactatga-----attgt-caagacaacatttgatatttctcaaattgtgcag----

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 5'ss of exon 11
GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaatgttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag
|| ||| || ||||| ||||| || |||||| ||||||||||| |||||||||||||||| ||  | ||||||||||||||||| ||||||||||  |  ||| | |  |   | |  |||| | |  |    || | || |    ||| |||  | |||     ||||       
GTTTGACGACACAAACCCAGAAGCTGAAAAGAAAGAGTATATTGATCATATTGAAGAAATCGTCCAATGGATGGGTTGGGAACCTTTCAAGgtataatttatgatctagattta-atgtcataggttgtgcctttct-ttgggcaacatttgatatctattggcattttgcag---

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ20630 (Selaginella moellendorffii), 5'ss of exon 10
GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaatgttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag
|| ||| ||||| |||||||| || ||||| ||||| |||||| | || ||  |||| |||||  |||||||||||||| |||| ||||||||  ||| ||  |||      |||  || || |   || |||  ||   |   | ||                            
GTTTGACGATACGAATCCAGATGCCGAAAAAGAAGAATATATTGAACACATAAAAGAGATTGTAGAGTGGATGGGTTGGAAACCGTTCAAGgt-ctttaaacattt------aattcctgataggagtttttaacgtcggttcttgcag---------------------------

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ32802 (Selaginella moellendorffii), 5'ss of exon 10
GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaatgttttgcacgaatagctcattgttattattattg-tgtttgaattcatctgacgtttatcaatctttttttttag
|| ||||||||| |||||||| || ||||| ||||| |||||| | || ||  |||| |||||  |||||||||||||| |||| ||||||||  ||| ||  |||    |     | | |  ||| ||| | | | |  ||| |                                
GTTTGATGATACGAATCCAGATGCCGAAAAAGAAGAATATATTGAACACATAAAAGAGATTGTAGAGTGGATGGGTTGGAAACCGTTCAAGgt-ctttaaacatttaattc---ctgataagagtttttaatgtcggttcttgcag-------------------------------

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|164146358|gb|ES046433.1|ES046433
EST:     TAATCATATTGTAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG                         ATTACATACACCAGTGATTATTTCCAGGAACTGTATGATTTGGC
genomic: TAATCATATTG-AAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaa ... ttttttttagATTACATACACCAGTGATTATTTCCAGGAACTGTATGATTTGGC
EST: gi|164112940|gb|ES083384.1|ES083384
EST:     TTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG                         ATTACATACACCAGTGATTATTTCCAGGAACTGTATGATTTGGC
genomic: TTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaa ... ttttttttagATTACATACACCAGTGATTATTTCCAGGAACTGTATGATTTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAGgtattttcaatgttttgcacgaatagctcattgttattattattgtgtttgaattcatctgacgtttatcaatctttttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA