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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttccacttaaagcagaccctgtttgacttttttttcccccgtttccattgtgtttgtttaatcacaagtctcttttactattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGATCCAAAGTTTGGAAGTTATGCTGACGAGTGGAAGTTATTATGTTTTTGT

Basic information

species Arabidopsis thaliana
transcript AT3G15660.1
intron # 5
splice site 3'
intron type U2

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|86075951|gb|DR371708.1|DR371708
EST:     TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|19874734|gb|AU235565.1|AU235565
EST:     TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|125083005|gb|EL143722.1|EL143722
EST:     GGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: GGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|163996431|gb|ES125283.1|ES125283
EST:     CCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: CCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|86079164|gb|DR374921.1|DR374921
EST:     TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|164165483|gb|EL989282.1|EL989282
EST:     ATTGGCGGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: ATTGGCGGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|86081518|gb|DR377275.1|DR377275
EST:     TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
genomic: TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGA
EST: gi|19740939|gb|AU226292.1|AU226292
EST:     TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAG                         GAAGGTGAAGTTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTG
genomic: TTAAGGGAGAGTTCATTGGCGGCTCAGACATCATCCTTAACATGCACAAGgttagttcca ... actattctagGAAGGTGAA-TTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcccccgtttccattgtgtttgtttaatcacaagtctcttttactattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGATCCAAAGTTTGGAAGTTATGCTGACGAGTGGAAGTTATTATGTTTTTGT
                        gtttaat  putative branch site (score: 4)
                                     tctcttttactattct  putative PPT
                     tttgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttccacttaaagcagaccctgtttgacttttttttcccccgtttccattgtgtttgtttaatcacaagtctcttttactattctagGAAGGTGAATTGGAGCAGAAGCTTAAAGACGTCTCCGGAAACCAAGATTGATCCAAAGTTTGGAAGTTATGCTGACGAGTGGAAGTTATTATGTTTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG