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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaagaataggtattgatcttagtaactgggttcttggatggatttcatatatttgttttgtttgtttcagATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTAATGATGTCATGGCAATTTTGGTTCAG

Basic information

species Vitis vinifera
transcript Vv15s0046g02200.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 9
----------gtttgaagaatag-gtattgatcttagtaactggg-----ttcttggatggatttcatatatttgttttgtttgtttcagATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTAATGATGTCATGGCAATTTTGGTTCAG
          |||||| || ||  || |  |  ||  ||  |        | | |  || |   ||  | | |  |  || | | ||||||||||||| | | ||||||| | ||||||||||||||||| || ||||| ||||| |||||| ||||| | || |||
gtagtgaaaagtttgatgattattgtttacaagttgatagttcaaagatatacatttatagtaatctgacaatcatactgct-gcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAAATGAGGTCATGTCAATTCTTGTGCAG

upper sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G316815_T01 (Zea mays), 3'ss of exon 1
----gtttgaagaataggtattg--atcttagtaactgggtt---cttggatggatttcatat-----------atttgttttgtttgt-ttcagATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTAATGATGTCATGGCAATTTTGGTTCAG
     | |||     |    |||  || || ||  ||    |   ||| ||||  |||||  |           || | |  |  |||| ||||||||||||| | ||||| ||||| ||||||| |||||| || || ||||| ||||| |||||||||||| | || |||
gtatttatgagctgcactctttgcaatttttgtttctaaactatactttgatgattttcaattttggcactctgatatatcatacttgtcttcagATACTGTGAGGAAAGAGGCAGCTACAATAACGGCTGTCTTTCCTTCTCCGAATGAGGTCATGGCAATTCTTGTCCAG
















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|161709184|gb|FC057959.1|FC057959
EST:     TCCTAGCAATGTTGCCCGTGGACTTTCTTCTTTGTACAAAGAAATCACAG                         ATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTA
genomic: TCCTAGCAATGTTGCCCGTGGACTTTCTTCTTTGTACAAAGAAATCACAGgtttgaagaa ... tttgtttcagATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTA
EST: gi|161711843|gb|FC058756.1|FC058756
EST:     TCCTAGCAATGTTGCCCGTGGACTTTCTTCTTTGTACAAAGAAATCACAG                         ATACTGTGCGAAAAGAAGCAGCCAC
genomic: TCCTAGCAATGTTGCCCGTGGACTTTCTTCTTTGTACAAAGAAATCACAGgtttgaagaa ... tttgtttcagATACTGTGCGAAAAGAAGCAGCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttagtaactgggttcttggatggatttcatatatttgttttgtttgtttcagATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTAATGATGTCATGGCAATTTTGGTTCAG
    tagtaac  putative branch site (score: 1)
                                        ttttgttt  putative PPT
                          atttcatatatttgtt  TA-rich tract