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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgatgacaacatgtcaacaatacacacctttatttcgaagagagcagcttctcaaaaccatatatatcacctatgagtgaatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGACTGGTCAATGCCACAAGCTTGTGCTGACTCATACCAAAAAACACTCAAG

Basic information

species Arabidopsis thaliana
transcript AT2G33470.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33470.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G34980.1 (Glycine max), 3'ss of exon 5
--------gtaaacgatgacaacatgtcaacaatacacacctttatttcgaagagagcagcttctcaaaaccatatatatcacctatgagtgaatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGACTGGTCAATGCCACAAGCTTGTGCTGACTCATACCAAAAAACACTCAAG
           |  ||   ||| |  |    | ||    | |||| |||    |    |  || |   |  ||| ||| || |  | | |  ||  ||||||||||||||||||||||||||   | |||| ||||||  | |  |||  ||| ||||||||| ||||||| ||| | || || ||  | || || || |||
attttgtgaccagagacctcaagaaatggttagtagttgcatttaattctcgtattttaatttat--gattcatttatttctctaacgtgcaaaattttcagAGCAATGGATTTCTTAGTGGCATTATTCCAAAACTTAATTGAGCATGCAGATTGGTCAATGTCACAAGCCTGTACAGATTCCTATAACAAGACTCTAAAG

upper sequence: AT2G33470.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G00690.2 (Glycine max), 3'ss of exon 3
-----gtaaacgatgacaacatgtcaacaatacacacctttatttcgaagagagcagcttctcaaaac-catatatatcacctatgagtgaatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGACTGGTCAATGCCACAAGCTTGTGCTGACTCATACCAAAAAACACTCAAG
     || |  ||    | |   | |  | |     || |  ||    |   |  |   | | |  |  ||| ||| |  |  |   || ||   |||||||||||||||||||| ||||   |||||||||||||  | |  ||| |||| ||| ||||| ||||||| ||| | || || ||  | || || || |||
tggtggtcagagaccctagctaatgattatttgttgccatatttgttcatgcaatattattttatgatacatttatttttctaacatgtaaaatcttcagAGCAATGGATTTCTTGGTGGCTTTGTTCCGAAACTTAATCGAGCATGAAGATTGGCCAATGTCACAAGCATGTACAGATTCGTATAACAAGACTCTGAAG

upper sequence: AT2G33470.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G00670.1 (Glycine max), 3'ss of exon 4
--------gtaaacgatgacaacatgtcaacaatacacacctttatttcgaagagagcagcttctcaaaaccatatatatcacctatgagtgaatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGACTGGTCAATGCCACAAGCTTGTGCTGACTCATACCAAAAAACACTCAAG
         ||   | ||   | |   |     ||   |   || ||||    |       || | | |  ||| ||| || |  |   || ||   |||||||||||||||||||| ||||   |||||||||||||  | |  ||| |||| ||| ||||| ||||||| ||| | || || ||  | || || || |||
gatcatttttatttggtggtcagagaccctagctaatgattattttttcatgcaatattatttatgata--catttatttctctaacatgtaaaatcttcagAGCAATGGATTTCTTGGTGGCTTTGTTCCGAAACTTAATCGAGCATGAAGATTGGCCAATGTCACAAGCATGTACAGATTCGTATAACAAGACTCTGAAG

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|86080333|gb|DR376090.1|DR376090
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
EST: gi|124769981|gb|EH860111.1|EH860111
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAG
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAG
EST: gi|116453283|gb|EG495875.1|EG495875
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
EST: gi|116448815|gb|EG491407.1|EG491407
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGGCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAGCTGTTCCGAAAC
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAAC
EST: gi|125097729|gb|EL154096.1|EL154096
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAG
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAG
EST: gi|86077274|gb|DR373031.1|DR373031
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
EST: gi|164210527|gb|ES045189.1|ES045189
EST:     ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTGGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
genomic: ATAGCAAAAGGATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
EST: gi|124711228|gb|EH802630.1|EH802630
EST:     ATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAG                         AGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA
genomic: ATCGTCTAGCTGTACAAACGGTCTTCTCTGGTTAACCAGgtaaacgatg ... aatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaagagagcagcttctcaaaaccatatatatcacctatgagtgaatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGACTGGTCAATGCCACAAGCTTGTGCTGACTCATACCAAAAAACACTCAAG
                                               tctttc  CT-rich tract
                   aaaaccatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacgatgacaacatgtcaacaatacacacctttatttcgaagagagcagcttctcaaaaccatatatatcacctatgagtgaatctttcagAGCAATGGATTTCTTAGTGGAGCTGTTCCGAAACTTGGTAGCACATCAAGACTGGTCAATGCCACAAGCTTGTGCTGACTCATACCAAAAAACACTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT