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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccattgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC

Basic information

species Arabidopsis thaliana
transcript AT2G35795.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G35795.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g09450.1 (Oryza sativa), 3'ss of exon 2
gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccattgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC
                                    |   || |  ||||| | | |    ||    |||||||    |   |||  | |   || | || |  ||  |||       ||            |  | ||||        |||||| |  |      | || ||||| || || || || | |||||| ||||| || ||||||||||||||||| |||||||||| ||| || || ||||||
------------------------------------ttaattcaacagttttt-atttggtaacttgcaatttgagatt--tatttacgtttctttctttcattaagttgttgttcctttcc----------tcctttgatccc---tgcagGGAAAACGCCCATCCTGAGAAGGTAAAAGAGGCGCATAAGAAGGTCATGGTTGCTAACCATCCAGATGCAGGCGGTAGCCATTACCTTGCTTCAAAGATC

upper sequence: AT2G35795.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G16850.1 (Glycine max), 3'ss of exon 2
gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccattgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC
                                         ||| ||| || |      |   |  || |   |  |  |   ||    | || |   |         |  | | ||  |  |  | |   |||   ||||| |     |||||| | || | | || || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| ||||| || ||||  || || || || || 
---------------------------------------tattactaggttgtgtgctttagcttctccaa--gactggaatgttgatcttgtctttgtca-------tcaagcttttctgaatttatattgttccatgattcat----cagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA

upper sequence: AT2G35795.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccat-tgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC
                                  ||  ||  | ||  |||   | || |  |   ||| ||  |||   || ||    |  || | || ||||  ||||  ||  ||||||     |||||  ||||           | ||||||| ||   | || || ||||||||||||||||| |||| ||| ||||| ||||||||||| |||||||||||||| |||| ||| || || || |||
-------------------------------caactaatgcct-gtcattttgaagtcatgta---tcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgttt-----gtggg--tttg-----------atagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC

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|164050491|gb|EL996771.1|EL996771
EST:     TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGG
genomic: TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGG
EST: gi|164001647|gb|ES198569.1|ES198569
EST:     TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGGAA
genomic: TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAA
EST: gi|19743034|gb|AU228387.1|AU228387
EST:     TTCCAGCCTACGATGACGAAAAGTGAATCTGCTCTCATTCTTTGCGTCA-                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGGAACCACACAGGAAGGTAATGGT
genomic: TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
EST: gi|164146882|gb|ES196502.1|ES196502
EST:     CGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
genomic: CGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
EST: gi|86081560|gb|DR377317.1|DR377317
EST:     TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
genomic: TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
EST: gi|86031884|gb|DR327637.1|DR327637
EST:     TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGCCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
genomic: TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
EST: gi|86083806|gb|DR379565.1|DR379565
EST:     TACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
genomic: TACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
EST: gi|19876514|gb|AU237345.1|AU237345
EST:     TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAG                         GGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT
genomic: TTCCAGCCTACGATGACGAAAAGGGAAGCTGCTCTCATTCTTGGCGTCAGgtgaaggaaa ... gaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC
          gtgtaac  putative branch site (score: 3)
                     tttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccattgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG