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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgctgaactagtcagaatgcccatgccaatgtttttgaaagcagcttcacccttaccaactttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT

Basic information

species Vitis vinifera
transcript Vv02s0012g00910.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
gtatgtatgctgaa--ctagt-cagaatgcccatgcca-atgtttttgaaagcagc-ttcacccttaccaactttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT
||| ||     |||  ||| |  ||||      |  || ||       |   |||   |||   | |    | |  | ||||| |||||||||||||| ||||| |||||||||||||| ||||| || || |  || || |||||||| || ||||| ||| | ||   ||   ||    
gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------------gtatgtatgctgaactagtcagaatgcccatgccaatgtttttgaaagcagc-ttcaccct-----taccaactttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT-
                      |   | |||| |  |    |   |     |    | | |    |  | |    ||||| |     ||   | ||| |  |||| |||||||| || || ||||  || ||||| ||||||||||| || || | |||||||||||| |||||| ||||||| | |||  | ||       | 
gtccgttctctacccctgcctctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACAAGAGCCGGTTCATACGAAATTCGGTGCTA-ATTTGGAACATTTGCCCATG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------gtatgt---atgctgaac--tagtcagaatg---cccatgccaat--gtttttgaaagcagcttcaccct-----taccaactt---tctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT
               ||||||   ||   | |   |||    ||||   | |||||  |   | ||||| ||| | |||   | |     || |  |||   | | ||||| ||||||||||| || ||||| || ||||| ||||||||||| || || |  |||||||| ||||||||  ||||||                     
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------

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|110687469|gb|EE064917.1|EE064917
EST:     GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG                         GTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
genomic: GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAGgtatgtatgc ... ctttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
EST: gi|110387207|gb|EC951857.1|EC951857
EST:     GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG                         GTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
genomic: GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAGgtatgtatgc ... ctttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
EST: gi|29782813|gb|CB348455.2|CB348455
EST:     GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGATTTCG-ATC                         GATCTGGGAGAAGAGCGGGTACAATACCCGTTGAGTGGGTGCGCTATATTA
genomic: GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAGgtatgtatgc ... ctttctacagG-TCTGGGAGAAGAGCGGGTACAATACC-GTTGAGTGGGTGCGCTATATTA
EST: gi|32457429|gb|CD798603.1|CD798603
EST:     GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG                         GTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
genomic: GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAGgtatgtatgc ... ctttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
EST: gi|27582169|gb|CB004864.1|CB004864
EST:     GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG                         GTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
genomic: GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAGgtatgtatgc ... ctttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
EST: gi|28969506|gb|CB348539.1|CB348539
EST:     GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG                         GTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC
genomic: GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAGgtatgtatgc ... ctttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgcccatgccaatgtttttgaaagcagcttcacccttaccaactttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT
                                   cccttac  putative branch site (score: 3)
                                             ctttctac  putative PPT
             aatgttttt  TA-rich tract