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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaaagaaagggggtattttcttggttttgctttcggaatttgaggtttggtgatttttctgatttgggttttgtttttttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG

Basic information

species Vitis vinifera
transcript Vv07s0005g01360.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G37740.1 (Glycine max), 3'ss of exon 1
------------------------gtaaagaaagaaagggggtattttcttggttttgctttcggaatttgaggtttggtgatttttctgatttgggtttt-----------gtttttttgtctt-tagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
                         |    |    |||    | ||||  || | ||   ||   | |||      |||   ||||| | ||||   || |           |  ||||||| ||  ||||||||||||||||||| |||||||| |||||||| |||||||| || ||||| |||||||| |||||||||
gtaagtaatcacataatacataatttcttaatcttaagcacttgtttttctgttattaactt---atttttcttcctggaattttttttcattttaattctcgtcaataactgcgtttttgttttgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG

upper sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G40340.2 (Glycine max), 3'ss of exon 1
----gtaaagaaagaa-----agggggtattttcttggtttt--gctttcggaattt-gaggtttggtgatttttctgatt--tgggttttgtttt----------------tttgtcttt-------agTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
    ||||| | ||||     | |  | | ||||||  | ||  ||  | |  |||| |   ||  |  ||| || || ||  | | |||| ||||                |  || |||       ||||||||||||||||||| |||||||| |||||||| |||||||| || ||||| |||||||| |||||||||
gtaagtaaacacagaatacataagacgcaatttcttaatcttaagcacttgttattttgttattaagctattattatgcttccttgatttttttttaattctcatcaataactgcgtttttgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG

upper sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G01680.1 (Glycine max), 3'ss of exon 1
gtaaagaaagaaagggggtattttcttggttttgctttcgga-atttgaggtttggtgatttttctgatttgggttttgtttttttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
         | ||      ||| ||||        ||  |   | ||    |||  ||| | || | ||    | || ||||| ||||  | |||||||||| |||||||| || ||||  ||||||||||| ||||| || |||||||||||||| |||||||||
---------gtaaatccacattctcttaacaacttttatgtttactttgtttttcatgaatcttgtcat----gattagttttattgt--tcagTTTGCTCACAGAGATTGCATTCAGACTTGGTGCAATGAGAAAGGAAATACAACTTGTGAAATATGTCTCCAG

upper sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G01630.1 (Glycine max), 3'ss of exon 1
gtaaagaaagaaagggggtattttcttggttttgctttcggaatttgaggtttggtgatttttctgatttgggttttgtttttttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
     | ||  ||      | | ||||        ||  |     |    ||| | || | || | ||     | ||  |||| | |||| |||||||||| |||||||| || ||||  |||||| |||| ||||| || |||||||||||||| |||||||||
-----gtaaataaatccacaatctcttaacaacttttatgtttactttactttagagaatcttgtcatgatcatcttagttttat-tcttcagTTTGCTCACAGAGATTGCATTCAGACATGGTGCGATGAGAAAGGAAATACAACTTGTGAAATATGTCTCCAG

upper sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G02075.1 (Arabidopsis thaliana), 3'ss of exon 1
--------gtaaagaaagaaagggggtattttcttggttttgctttcggaatttgaggtttggtgatttttctgatttgggttttgtttttttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
           ||  |||||| |    |   ||||       || ||  |||||||   |    || ||||         |||||||||| || |  | |||| || |||||| | || |||||  | ||||| ||||||||||| ||||||||||||||||||||||| |||
gtaaaagaaccaaccaagaaaagaaaaaaactcttaa-----ctctcaaaatttgaaactaatggagtttt---------gttttgttttgtt-tgatcagTTCGCACATAGAAACTGCATACAACGTTGGTGTAATGAAAAAGGAAACACAACTTGTGAAATCTGTCTTCAG

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|34544260|gb|CF512492.1|CF512492
EST:     AGAGTTGTAAGACCTTGGAGGCTCCCTGTGCTTGCTCTGGAACCGTTAAG                         TTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACA
genomic: AGAGCTGTAAGACCTTGGAGGCTCCCTGTGCTTGCTCTGGAACCGTTAAGgtaaagaaag ... ttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggaatttgaggtttggtgatttttctgatttgggttttgtttttttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
                       ttctgat  putative branch site (score: 3)
                                   ttttgtttttttgtct  putative PPT
                                   ttttgtttttttgt  TA-rich tract