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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcttaatatccttccccaatgtattgttgtagcatcaatacagctgtttgcgttgtacttatatatctctcgcttggattgatctgcagCGCAATTGGTAATGAGAGGATTGAATCATTGATTCAAGAGGATCAGAACGTCAAAAGACGAAGAGACCGTTACCAGAAACAGTCCTCTCTTCTCTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G59610.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 20
--------gtttcttaatatccttccccaatgtattgttgtagcatcaatacagctgtttgcgttgtacttatatatctctcgcttggattgatctgcagCGCAATTGGTAATGAGAGGATTGAATCATTGATTCAAGAGGATCAGAACGTCAAAAGACGAAGAGACCGTTACCAGAAACAGTCCTCTCTTCTCTCAAAG
              ||   |  ||   ||||   || |  |  | |   |  |  | ||| | ||  |   ||     |      |  |||| |   ||| ||     | |  |  |||||||||  | |  |||| ||||||||||| || ||| || | || || ||| ||||||||||||||||||||||  |||||
tgacacctaaacactaccttaattattcaataccttctcttttcctgtctgaattttttttcattaaaaaaattgcaattgtttatacattggttctcagTGCCCAAAGCACCGCAAGGATTGAAGAACTACTTCAGGAGGATCAGAATGTGAAACGAAGGAGGGAGCGTAACCAGAAACAGTCCTCTCTTCTTGCAAAG
















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|125014775|gb|EL087044.1|EL087044
EST:     CTGAATCAGCTATACAGCTCTATCAG                         CGCAATTGGTAATGAGAGGATTGAATC
genomic: CTGAATCAGCTATACAGCTCTATCAGgtttcttaat ... tgatctgcagCGCAATTGGTAATGAGAGGATTGAATC
EST: gi|86084079|gb|DR379838.1|DR379838
EST:     GTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG                         CGCAATTGGTAATGAGAGGATTGAATCATTGATTCAAGAGGATCAGAACGT
genomic: GTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAGgtttcttaat ... tgatctgcagCGCAATTGGTAATGAGAGGATTGAATCATTGATTCAAGAGGATCAGAACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatacagctgtttgcgttgtacttatatatctctcgcttggattgatctgcagCGCAATTGGTAATGAGAGGATTGAATCATTGATTCAAGAGGATCAGAACGTCAAAAGACGAAGAGACCGTTACCAGAAACAGTCCTCTCTTCTCTCAAAG
                                          gattgat  putative branch site (score: 4)
                  ttgtacttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcttaatatccttccccaatgtattgttgtagcatcaatacagctgtttgcgttgtacttatatatctctcgcttggattgatctgcagCGCAATTGGTAATGAGAGGATTGAATCATTGATTCAAGAGGATCAGAACGTCAAAAGACGAAGAGACCGTTACCAGAAACAGTCCTCTCTTCTCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA