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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G54840.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 2
ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttga--ttgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
   ||| ||      |  ||  | | || | |    |  |     |   |   |  || | ||  |  |  |  |||| | |  || |  ||||  ||| |||| ||  |  | || ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||||||  | || || |||
--gtttactgcacattttgccctttattactaca-ataatgcctctatatc--atgttac-tagcagctttctttaacgtgtccatccttttgatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 2
--------ttattttcttgt-tgctcagcagtattttgccaagtgtggt----ataattggtttcaactttgcgtaaga----------cataccactaacttttggattcacttgat-tgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
        ||| |  || || |  |||  | | ||||   |  | |  |    ||  |||   | || ||    |   |          ||| ||  |   ||||   ||  | |  | || |||| ||  |  | ||||| || |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||| | || || |||
gtttggacttactcactagtgtcttcataattcttttaatatttctcatctccattgttgacattaagttgaattggaatgaaaaggttcatgcccttcgtttttattttaccctattctgtagTTGGTATTGCTTGGAGATTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGCTTTGTCCGTGGTCAGTTTGACCCCACTTCAAAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 3
ttattttcttgttgc-tcagcagta-ttttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttg-attgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
 ||| ||   |   | | |  |||   | ||     | | ||| ||   |  |  || |     | ||| |      |  ||||  |    ||    ||  |||| ||  |  | |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||  |||| || |||
-tatgttagggcatcattaatagtggctgtgatttatctagtaaaacctgaat--acctgattaacgacttttgttaatgttttcaaccttctcatgttatagTTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
ttattttc-----ttgttgctcagcagt-attttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
||| |  |     ||  || | | | || ||  |||||    |  | |  ||| |||   ||||     | ||  |  |||||  |||| ||     ||    ||| | ||||| ||||| || ||||||||||||||||| |||||||| || |||||||| ||||||||||||||  | |||||||||
ttaatcacaacagtttctgtttatctgttatactgcca----ttattttcttg-tttagcctttaaaggaaac-cataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
--ttattttct-----tgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
  ||| |  |      |  ||||   | ||||  |||||    |  | |  |||  || ||| |||   |  |   |  |||||| ||     |||||| |   ||| | ||||| ||||| || ||||||||||| ||||| |||||||| || |||||||| ||||||||||||||  | |||||||||
aattaatcacaacaaattctgcttgtctgtatactgcca----ttattttcttg--tttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaa-acagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
------ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
        | | || |  |    |  | |   | | ||| | | |    ||||  |   |       |||   ||  ||      || |       |||  ||||| | ||| | || || || ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||||||| ||||||| |||
ctgcaagaaatatcattatagaaattaattgatgggcaaatatag---gattgaataagaaccc---taaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG

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|164230211|gb|ES103894.1|ES103894
EST:     TGCCAAAAATCTACGTGTGAAG                         TTAGCTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
genomic: TGCCAAAAATCTACGTGTGAAGgttttttttt ... ttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
EST: gi|19875441|gb|AU236272.1|AU236272
EST:     GCAATTCAGAGAATGCTGTTCCAGCTGATGCCAAAAATCTACGTGTGAAG                         TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
genomic: GCAATTCAGAGAATGCTGTTCCAGCTGATGCCAAAAATCTACGTGTGAAGgttttttttt ... ttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
                                        ttcactt  CT-rich tract
                             taactttt  TA-rich tract