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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag

Basic information

species Arabidopsis thaliana
transcript AT2G31610.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G26790.1 (Glycine max), 5'ss of exon 1
CGAGCTTACCGATTCTCTTCG-TCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtgatttcattttttg-ttttcagtggacttctctagctgtatcgtattgg--aactgatctggttactgtgtttgtag-------------------
 | | ||| ||   | |  |  ||  | |  |     | |  |   || ||    | ||  |||  | |  |||||||| ||||| ||||||||||||||||||| |      |||||       |  ||  |   |   |  |  |  | |  ||     ||    | |  || |  | ||| | |                   
-GGGTTTAGCGCCACACCCCAATCGTAGCCGTCGCACTCTGTGTTTTCAGCGCCGTCTCCGATCTCCGACAATGGCGACCCAAATGAGCAAGAAGAGAAAGgtgactcactcattcataccacaatcatccttcaccaattgaaattaaacctcatcaattaataactataatttcaatttttatcgtgtgtttctgtgtgcgcag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 1
CGAGCTTACCGATTCTCTTCG-TCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag-----------------------------
 | | ||| ||   | || |  ||  | |  |     | |  |   || ||    | ||  |||  | |  |||||||| ||||| ||||||||||||||||||| |      |||||       |       | |||| | |  || |    |     |   || |  | ||| || ||  |                              
-GGGTTTAGCGCCACACTCCAATCGTAGCCGTCGCACTCTGTGTTTTCTGCGCCGTCTCCGATCTCCGACAATGGCGACCCAAATGAGCAAGAAGAGAAAGgtgactcactcattcataccacaatc-----agccttcaccaattgaaattaaacctcatcaat-taataactatgatttcaattttttatcgtgtgtttctgtgtgcgcag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgat-ctggttactgtgtttgtag----------------------
            |    || |    | |||  ||     | ||| || | |     ||| | |  |||  |||||||||||||| |||||||||||||||||   |  | || |  | |||| |||||  | |  ||||  ||||  | |     | || | ||  | ||||  || |  |||                       
----------ATTAGGGTTTGCAAAAGCATAGAGAAACCC-GAGCTCAGAT----CTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtc--tgatcatatgttcttttattttcctttgttttctg-agct--accaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 1
CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaatt--gtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag
                                       | | |        |     |  ||       |||||||| || ||||||||||||||||||||   ||  |  ||  |  |   |  ||        || ||||   |  ||  |    |                          
--------------------------------------ACGGCGTGGCATGAAACCCTAGCTCTCTGGCAATGGCGACGCAGATCAGCAAGAAGAGAAAGgtctgttcagcaatgccgctccctcctt--------ctcctctgatttgattcttccag--------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ31296 (Selaginella moellendorffii), 5'ss of exon 1
CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTA-TGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaatt--gtgatttcattttttgttt-tcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag
                                         |  || |  |||    |     | |  | | ||||||| || ||||||||||||||||||||   ||  |  ||  |  | |    || ||    ||  |||||  | |                                     
-----------------------------------------GGCATGGCATGAAACCCTAGCTCTCTGGCAATGGCGACGCAGATCAGCAAGAAGAGAAAGgtttgttcagcaatgccgctctccccttctcctctgatctctcttccag-------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 1
CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaatt--gtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag
                                                      |    | |   |  | ||||||||||| ||||||||||||||||||||   |   |  ||  |  |   |   |    |   ||  || ||                                        
----------------------------------------------------GCTAGGGCTTTGGCG-GCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgtcaagcaatgccgctccct-cctctgattctctcttccag----------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 1
CGAGCTTACCGATTCTC--TTCGTCTCAACATTTAGG-GTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtg--------aattgtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag
   || ||| |  |     || |||  ||    |||  |   |  |  | ||  |  |    | |   |  | ||||||||||| ||||||||||||||||||||         |||   | | ||   || || | | | | || |  || ||                                        
--GGCATACTGCATAATAATTTGTCAAAAGCCCTAGAAGAGCCCTAATTAGGACGGCTAGGGCTTTGGCG-GCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcagcaatgccgctctccccttctgctctgatttgattcttccag----------------------------------------

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|116442865|gb|EG485457.1|EG485457
EST:     TGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAG                         TTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGA
genomic: TGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtg ... gtgtttgtagTTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGA
EST: gi|164096781|gb|ES047202.1|ES047202
EST:     TCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAG                         TTTGTAGCGGATGGTGTATTCTGCGCTGAATTGAATGAGGTTCTCACAAGA
genomic: TCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtg ... gtgtttgtagTTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGA
EST: gi|152035868|gb|BP863417.2|BP863417
EST:     TGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAG                         TTTGTAGGGGATGGTGTATCCTACGCTGAATTGAATGAGGTTCTAACAAGA
genomic: TGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtg ... gtgtttgtagTTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGA
EST: gi|124856950|gb|EH941387.1|EH941387
EST:     GCAAGAAGAGAAAG                         TTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGA
genomic: GCAAGAAGAGAAAGgtgaattgtg ... gtgtttgtagTTTGTAGCGGATGGTGTATTCTACGCTGAATTGAATGAGGTTCTCACAAGA
EST: gi|124855270|gb|EH939707.1|EH939707
EST:     TGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAG                         TTTGTAGCGGATG
genomic: TGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtg ... gtgtttgtagTTTGTAGCGGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgatctggttactgtgtttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA