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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgattcttttccttgtcatagccaaaatttatgcgtggcatggtgagaattttgttatctgatgcggtttttttatctattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGA

Basic information

species Arabidopsis thaliana
transcript AT2G45540.2
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: LOC_Os04g46894.1 (Oryza sativa), 3'ss of exon 24
gtattgtgattcttttccttgtcatagccaaaatttatgcgtggcatggtgagaattttgttatctgatgcggtttttttatctattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGA
     ||  || | || |   |  |    ||||||||         | || | |     ||||| | |  | |    |  ||  |   ||| |||||||  | |||||||||||  |  |||| || |||||||| || || || || | |||||||||||| |||||||| |||||||||||||||||
-----gtacttgtatttcagcttgtg--taaaatttacagtacaattcgtaaaagcagagttatgtaaccccgaacataaatgca---gATTCTGTAAATTTGCCTCCTTGGGCTGAGGACCCTGTTGATTTTGTCCATAAACACCGGAAGGCTCTTGAGAGTGAGCATGTTTCTGCTCATTTGCATGA

upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM2G044143_T01 (Zea mays), 3'ss of exon 24
gtattgtgattcttttccttgtcatagccaaaatttatgcgtggcatggtgagaattttgttatctgatgcggtttttttatc-tattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGA
     || |||   || |   | ||  |||  ||  | ||   | | | | | ||   |        ||||  ||    || | |   |||| | ||| || | ||||| |||||  |||| |  ||||||||||| || || || || | |||||||||||| ||||| || |||||||||||||||||
-----gtaattgcatttcaacttatgtccactatgca-gctgagta-gataaaaacagta-------atgcaattccggtaccattgcagATTCCGTAGAATTGCCTCCCTGGGCTGAAAATCATGTGGATTTTGTCCATAAACATCGGAAGGCTCTTGAGAGTGAGCACGTCTCTGCTCATTTGCATGA

upper sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 25
----gta-ttgtgatt--cttttccttgtcatagccaaa-atttatgcgtggcat--------ggtgagaattttgttatctgatgcggtttttttatctattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGA
    ||| |||| |||   |||| |  |||||| | |||   ||| |  |   ||         ||   || |||  ||| | || |   ||| | ||   | |||| ||||||||||||||||||||||  | |||||||| |||||| | || ||||| || | |||||||||||| |||||||| ||||| |||||||||||
gtatgtacttgtaattaatttttaccagtcatacctaaatgattaagtttcttatcactctgaagttgaaaattttctattttattcaaatttatcatt--tcagATTCTGTAAAACTTCCTCCTTGGGCTGAGAACCCAGTTGATTTTATTCATAAGCACCGGATGGCTCTTGAGAGTGAGCATGTCTCTGCACATTTGCATGA

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|47828319|gb|CK118003.1|CK118003
EST:     CAACGAAAATTCGATTGACTTTGGTACAACACAGTTGGGAGAAAAGCTTG                         ATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACA
genomic: CAACGAAAATTCGATTGACTTTGGTACAACACAGTTGGGAGAAAAGCTTGgtattgtgat ... tatctattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcgtggcatggtgagaattttgttatctgatgcggtttttttatctattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGA
                            atctgat  putative branch site (score: 4)
                                       tttttttatctatt  putative PPT
                                       tttttttatctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtgattcttttccttgtcatagccaaaatttatgcgtggcatggtgagaattttgttatctgatgcggtttttttatctattagATGCTGTAAAACTTCCTCCTTGGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA