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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCTCCGAAAGGGATTAAAACGAATTGGATTATGCACGAGTATCGTCTCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagcttttctgatttttaatttctgggttttttttcgatttttgtgatgatgatgaattgatgatgattaatgggttttttttggttgaaattttgcag

Basic information

species Arabidopsis thaliana
transcript AT5G63790.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G63790.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G38560.1 (Glycine max), 5'ss of exon 2
AAAAGCTCCGAAAGGGATTAAAACGAATTGGATTATGCACGAGTATCGTCTCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctt----ttctgattt--ttaatttctgggtt--ttttttcgatttttgtgatgatgatgaattgatgatgattaatgggttttttttggttgaaattttgcag
|||||| || |||||  | ||||| ||||||||||||||||| ||||| ||||| ||||| || |||||||| || |  || || || |||||||| || ||| |       ||   ||||   |||  ||| | ||  |||  |  | | || |       |  ||  |    |     ||      |||| | ||  |||       
AAAAGCCCCCAAAGGTGTGAAAACCAATTGGATTATGCACGAATATCGCCTCGCCAATGTTGACCGATCTGCCTCCAAGAAAAAAAACAACAACTTGAGGgtatgtcccaaattggaatttcactaaaatctagattagtttgcttaagtgttttttaatcaaccaagcgggtctagc--ataaaaagttttcgtttttaat-------

upper sequence: AT5G63790.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 5'ss of exon 2
------AAAAGCTCCGAAAGGGATTAAAACGAATTGGATTATGCACGAGTATCGTCTCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt--ctgatttttaatttctgggttttttttcgatttttgtgatgatgatgaattga-tgatgatta-----atgggttttttttggttgaaattttgcag
       |||||||| | |||  | ||||| |||||||| |||||||||||||| ||||| ||||| |||||||| ||      |  |||||| ||||||||||| ||| | || |   |   |  ||  ||   | | ||| ||   | |||   |  |  |  ||  || ||||| ||      || | | | | ||  |    | |||||||
TGCCGGCAAAGCTCCCAGAGGTGTCAAAACCAATTGGATCATGCACGAGTATCGCCTCGCCAATGTTGATCGATCCGC------CGGCAAGAAAAACAACTTAAGGgtacgattgtaattctatactacattaaagatatttatttattatttaaaaaaaaaagaaaaagagtgatggttctttttattgatatatattattattgactttgcag
















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|116415196|gb|EG457788.1|EG457788
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
EST: gi|116442855|gb|EG485447.1|EG485447
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
EST: gi|125023149|gb|EL095418.1|EL095418
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGGACATACAATAAGAAAGGAACAATGGA
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGA
EST: gi|116445706|gb|EG488298.1|EG488298
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
EST: gi|116445702|gb|EG488294.1|EG488294
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
EST: gi|116474563|gb|EG517155.1|EG517155
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
EST: gi|124706906|gb|EH798308.1|EH798308
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGGGTTTTGTGTCGG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGG
EST: gi|116411311|gb|EG453903.1|EG453903
EST:     TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGA                         CTTGATGATTGAGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG
genomic: TCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagctttt ... aattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGCTCCGAAAGGGATTAAAACGAATTGGATTATGCACGAGTATCGTCTCGCTAATGTCGATCGATCTGCTTCTACCAACAAGAAGAACAACTTAAGAgtaagcttttctgatttttaatttctgggttttttttcgatttttgtgatgatgatgaattgatgatgattaatgggttttttttggttgaaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC