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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcctagataactgtctctcctttttattttccttgatggctacttcattgaaatagccactgttgtttctgaaacggtgcatttggatagcgtg...

Basic information

species Arabidopsis thaliana
transcript AT4G32760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 5'ss of exon 2
GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcctagataactgtctctcctttttattttccttgat--ggctacttcattgaaatagccactgttgtttctgaaacggtgcatttggatagcgtg
||||||||| ||||| || |||||||| ||||| || ||||| || | ||||||||||| ||| ||||||||  | || || |||||    | ||||   |||| || ||   |   |  ||  |   | |   ||||  |    | |  ||||| |    |  ||||  |||      | 
GCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACGgtaagctctacaaaaacttaatctctttcttgactatgtaaatttgatgaatgggttgattttcaaatttctgttt-tactgctctgcaaatggccttaat-
















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|47828022|gb|CK117706.1|CK117706
EST:     AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
genomic: AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
EST: gi|86063775|gb|DR359532.1|DR359532
EST:     TAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
genomic: TAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
EST: gi|86063774|gb|DR359531.1|DR359531
EST:     AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
genomic: AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
EST: gi|86063771|gb|DR359528.1|DR359528
EST:     AAAAACGGATTGGTAGCAGGAWTCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
genomic: AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
EST: gi|86063772|gb|DR359529.1|DR359529
EST:     AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
genomic: AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
EST: gi|86063777|gb|DR359534.1|DR359534
EST:     AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATAAG
genomic: AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
EST: gi|86063778|gb|DR359535.1|DR359535
EST:     AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT                         CTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG
genomic: AAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcct ... tatgttctagCTGCTTGAGACAATAGTGAAGAACTGTGGTGACATGGTTCATATGCATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACTgtgagctcctagataactgtctctcctttttattttccttgatggctacttcattgaaatagccactgttgtttctgaaacggtgcatttggatagcgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT