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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG

Basic information

species Vitis vinifera
transcript Vv02s0025g03400.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 10
gtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcattataaattggtc--atgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
                       || |       |||  || | |  | |   | |||| | |  | |  ||      |||    |   |||||  |    || |     ||||| || ||||||||||  | ||   | || ||| | || |||||  | || ||||| || |||||||||||||||||||| | |||||||||||||||||
----------------------gtaggtacag--atgactactttcatactg-tgatgttctgcttctgcaacttgcgaaa----tgctaattgccctagcgtctgctcgtagGTTGCCCGTGGTGATAAGACTGATGAAGACGGTGTGCCCATGCTGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTG

upper sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
gtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
                               | | ||   |  | | |||   || |  |  |  |    |||  |       ||   |  |||||    | |  | |||||| || ||||| || |  |  |   |||||||| | || ||||| || || ||||| || |||||||||||||||||||| ||||| |||||||||||||
----------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG

upper sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 10
gtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcaga-ctttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
||| |||    |   | |    || |  |  |    | |   ||    |||  || | |      || | |  | ||| | | |  ||   ||   |   || |   |  |||| || |||||||| |  | ||   |||||||| | || |||||  | ||||| || || |||||||||||||||||||| ||||| ||||| |||||||
gtatgtatgaatgagtactatgatgt-ttgcaattcgctgtctgctagtcatctagtttcttcttctatgatttgctagatatc--tagctatgcatgtggtctgcttgcagGTTGCACGTGGTGACAAGACTGATGAGGATGGTGTACCCATGCTGTTAAAGATTCCTCGGATGTTTGATCCATGGGGTGGATACAGCATCATAGGCTTTG

upper sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------------------------------------gtaagtactgcttttttcacc-catatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
                                                                                          || |   |  ||||||| | | |      ||| || | ||   ||| |   | |||   ||     | | |||  |  |           |||  | | || |   | |||| ||||| || ||||  |        || |||||||||||||| || ||  | || ||  | ||||||||||||||||| |||||||||||||| ||||
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacga-----------ttgaac-ttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG

upper sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S1_478V6.1 (Physcomitrella patens), 3'ss of exon 10
gtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcatt--ataaattggtcatgtttttat-atagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
        | |  |   || ||     ||   |    |  |||     || | ||      |   ||||| ||  ||||    | |  ||  ||    | | |  | || | |||| || ||||| |||| |||||     || || || || ||| | |||||  | ||  |  ||| |||||| ||||| ||||||||||||||||||||||
------cgtacactccacatcc---ccctgagcttcagaaattaacaatcgagtag-----aaggtttcatatgttaaatcctactccatgtataaaccgtctggtgatgacagGTTGCACGTGGAGATAAAAGTGATGGCGAAGGGATACCAATGTTGCTGAAAGTTCCAAGGTTGTATGATCCTTGGGGAGGTTACAGTATCATTGGCTTTG

upper sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S128_91V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------gtaagtactgcttttttcacccatatgctag--accatggttattgtggttcaaataatgtgcagactttcaaat---actaaaaagcatta-taaattggtcatg---tttttata---tagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
                                               |||| |  |    |    |||  | || ||    ||||  ||  | | |||  |||   | |     |||| |||   |||   | |    |     ||| | | |    || | |     |||| ||||| || ||||  ||       || |||||||||||||| |||||  |||||||  ||| ||| ||||||||||| ||||| ||||| |||||||
gtacgtacattctttgcatttggaatgtttgttgctttatatagctggtaatttataacataccaaccattttgataattgccatcttttctatcgttgtaattgagagagttgtttcgaatgtaactcgtatgtgccaacgttttgataacggagcttgtctgggccagGTTGCTCGGGGAGATAAGAGCAATGGAGAGGGTATTCCTATGCTTCTGAAAGTCCCCCGGTTGTATGACCCATGGGGTGGCTACAGCATCATCGGCTTTG

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|110358368|gb|EC922530.1|EC922530
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
EST: gi|30129909|gb|CB915248.1|CB915248
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
EST: gi|32245741|gb|CD711560.1|CD711560
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGGGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
EST: gi|110362845|gb|EC926402.1|EC926402
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
EST: gi|110716312|gb|EE091183.1|EE091183
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
EST: gi|32246367|gb|CD712186.1|CD712186
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGGGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
EST: gi|110687575|gb|EE065143.1|EE065143
EST:     TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG                         GTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG
genomic: TTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTGgtaagtactg ... ttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcagactttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
                tactaaa  putative branch site (score: 1)
                                          tgttttt  putative PPT
         tttcaaatactaaaaa  TA-rich tract