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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaaacaacaaacttgttctgttttgctttagaaaactggtaacaatcgctttggtttgcctctgtcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACGGTATTCTCGCTCTACTCCACTGCTCTTGTTGGACGTTTAGTCGGTTTAG

Basic information

species Arabidopsis thaliana
transcript AT1G32080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G01340.1 (Glycine max), 3'ss of exon 4
----gtaaaacaaacaacaa-acttgt-tctgttttgctttagaaaac------tggtaacaatcgctttggtt--------tgcctctgtcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACGGTATTCTCGCTCTACTCCACTGCTCTTGTTGGACGTTTAGTCGGTTTAG
     | |||||  |      |||||| | | |  |  ||||   |||      |||  | | ||  |||   |        | | |||    | ||||||| || || ||||| ||||||||||| ||||| ||||| ||| |||| ||  |||||||  | ||||| |||||||||||||||||| |||| | |||||
caatatgaaacatgctttgttacttgtctttctcatcttttaatcaacatttaatggctaaattccatttaagtattaatgattcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G34440.1 (Glycine max), 3'ss of exon 4
----gtaa-aacaaacaacaaacttgtt-ctgttttgctttag-aaaactggtaacaatcgcttt----ggtttgcc---------tctgtcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACGGTATTCTCGCTCTACTCCACTGCTCTTGTTGGACGTTTAGTCGGTTTAG
     | | ||     | |||     || || ||  || | |  |||||| | |  | || | ||    | ||  |          |||    | ||||||| ||  | ||||| ||||||||||| ||||| ||||| ||| ||||  |  |||||||  | ||||| |||||||||||||||||| | || | |||||
tatgatgacaatccttatcaagtgaatttcttttcagcatcatcaaaacttgcatgattcacattaaaagattaactaatgatttatctactgttttcagCTTGTACAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTTCCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTGGTTGCTTTAG

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtaaaacaaacaacaaacttgttctgttttgctttagaaaactggtaa-caatcgctttggt-ttgcctctgtc-ttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACGGTATTCTCGCTCTACTCCACTGCTCTTGTTGGACGTTTAGTCGGTTTAG
                  | ||   |    |       |  ||   |  | | | || |  |||| |  || ||||  |  |  |||| |  || ||||||| || |||||||| ||||||||||| ||||||||| | ||  | |||||  |||||||  | || || |||||| || |||||||  |  | || ||||
tgtaaagagcatttatcatcaagagatgtccttcaccatagtgcgctagtcttgcaatcgagtaaactctctctttcctactttctctatgatttttcagCTTGTAAAGAGGCATGCAGCTGAGATTTTCACATCTATCATTATCTCAACAATATTCTCCTTGTATTCAACTGCTTTTATTGGACGCATTCTGGGGTTAG

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|125214754|gb|EL229062.1|EL229062
EST:     CGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
genomic: CGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
EST: gi|125282554|gb|EL296639.1|EL296639
EST:     TCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAGAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAG
genomic: TCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAG
EST: gi|125192503|gb|EL207457.1|EL207457
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTT
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTT
EST: gi|47830990|gb|CK120674.1|CK120674
EST:     CTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
genomic: CTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
EST: gi|124955714|gb|EL030704.1|EL030704
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAG
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAG
EST: gi|124991035|gb|EL063304.1|EL063304
EST:     TGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATAGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACAT
genomic: TGGCTCTGTCATTCTCTCTTTCGCTTTCTCCAT-GTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACAT
EST: gi|125021035|gb|EL093304.1|EL093304
EST:     TTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGTCTGAGATCTTCACATCTGTGATAGTTTCAAC
genomic: TTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAG-CTGAGATCTTCACATCTGTGATAGTTTCAAC
EST: gi|125083006|gb|EL143723.1|EL143723
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGA
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGA
EST: gi|124993217|gb|EL065486.1|EL065486
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAG
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgctttagaaaactggtaacaatcgctttggtttgcctctgtcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACGGTATTCTCGCTCTACTCCACTGCTCTTGTTGGACGTTTAGTCGGTTTAG
                 tggtaac  putative branch site (score: 2)
                                   tttgcctctgtcttct  putative PPT
       tttagaaaa  TA-rich tract