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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG

Basic information

species Vitis vinifera
transcript Vv09s0002g00340.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 7
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctct-tatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
                     ||      |||  |||  ||||  |||||  | ||   | |  ||||| |     ||    |  | ||| |   | | ||    ||| | ||||||| |||| | | |||| || ||||||||||||||||||||||| |  ||||| ||||| ||||| || || |||||||| || ||||||||||| || || |||| ||| ||||
---------------------gtaggaactttaccttctttttaaatctt--actggacattttttgaataaacagga----agcagttcgaatctcattat--gatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G088064_T03 (Zea mays), 3'ss of exon 7
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
                     || |   |||||   |||| ||  |  | |    ||||  |   |||| |    |||| | |     | |||  | |       |  || |||| ||| |||||  ||||||| ||||||||||| |||||||| || |  ||||| ||||| ||||| || || ||||||||||||||||||||||| || || || | ||| ||||
---------------------gtgtgcatttttaacttctctttcaattgtcctggacatttt-ctgaataaacatgatatca----ctgaagtctcatc--ttgaccttattcttcct-tctta--agGTCCACATGATGATGCAATTACTGATTAGGAATGAGAAAGATGGCATTCTGTGCCCAATTCCTCAGTACCCTTTGTACTCAGCCTCCATAGCTCTTCATG

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G01630.2 (Glycine max), 3'ss of exon 5
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
       |   | |||  | |   ||  || |||| |  ||       |||||| ||  | |  |  | | |||||    ||  || ||  |   ||||   ||       |  |  || | || |||||||||||  |||||||| ||||| || ||| | || || ||||| ||||| ||||||||||| ||||||||| ||||||| || |||||||  || ||||
------gtatgtctctactctaccttagttatttcctatttgg-----ttttaaggatga-tggtgtagactttgtttcatttgaaatttgaatttaaaagcca-------tcatttctatgttttcagGTCCATAATATGATGCAATTACTCATTAGATCAGAAAATGATGGTATTCTGTGTCCCATTCCACAGTACCCTCTGTACTCAGCCTCAATTGACCTCCATG

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G05130.1 (Glycine max), 3'ss of exon 7
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
       |   | |||  | |   |||  | |||| |  ||       |||||| ||  | |  |  | | |||||    || ||| ||  |   ||||   ||       |  |  || | || |||||||||||  |||||||| ||||| || ||| | || || ||||| ||||| ||||||||||| ||||||||| ||||||| || |||||||  || ||||
------gtatgtctctactctacctttgatatttcctatttgg-----ttttaaagatga-tggtgtagactttgtttcatttaaaatttgaatttaaaggcca-------tcatttctatgttttcagGTCCATAATATGATGCAATTACTCATTAGATCAGAAAATGATGGTATTCTGTGTCCCATTCCACAGTACCCTCTGTACTCAGCCTCAATTGCCCTCCATG

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
                                        |  | ||  |  ||  | | ||  | | || |    || | |  ||   |  |  |  | |    |   |  | | |||||| |   |||| ||||||||||||||  | || ||||   | ||||| |||||||| |||||||| ||||||||||| || |||||||| ||||||||||  || || |
---------------------------------------gtaaggattatcaaacta-atcttctcgtaactcgtagaatctggaacaccttgttttga-agttgacagtgatgttcctctccttctagGTTCATATGATGATGCAACTTCTCATAACTTCAGAGAAAGATGGAATCCTTTGTCCTATTCCTCAGTATCCATTGTACTCAGCTTCAATTGCCCTTCACG

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttt---tctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
                                                                          || | ||     ||| ||| ||  ||   || ||||||   | |   |  ||    |||| || |||||||||||  | ||  | ||  | ||||| ||||| |||||||  || ||||||||||| || |||||||| ||||||||||  || ||||
--------------------------------------------------------------------------gtaagttct---tttaaaggattcatgctaagtgtttttggtgttttttactctatagGTTCACATGATGATGCAACTTCTCTTGAGCTCAGAGAAAGATGGTATTCTTTCCCCGATTCCTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATG

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G72330.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgttttt---ctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
                                   |  |  |   | |    || |  | || || ||      || | ||     ||| ||| ||  ||   || |||||||    |   |  ||    |||| || |||||||||||  | ||  | ||  | ||||| ||||| |||||||  || ||||||||||| || |||||||| ||||||||||  || ||||
----------------------------------gtaacaatcaaaacgaa-aacgttatctcatagagttagagtaagttct---tttaaaggattcatgctaagtgtttttggtgttttttactctatagGTTCACATGATGATGCAACTTCTCTTGAGCTCAGAGAAAGATGGTATTCTTTCCCCGATTCCTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATG

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|161710855|gb|FC058161.1|FC058161
EST:     TTCCTTCTAATCCGAATGACATTTTCTTGACTGATGGTGCAAGCCCAGCA                         GTCCATATGATGATGCAGTTACTGATAAGAAC-----AGGATGGAATTCTT
genomic: TTCCTTCTAATCCAAATGACATTTTCTTGACTGATGGTGCAAGCCCAGCAgtaaatttca ... ctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTT
EST: gi|161710403|gb|FC059015.1|FC059015
EST:     TTCCTTCTAATCCGAATGACATTTTCTTGACTGATGGTGCAAGCCCAGCA                         GTCCATATGATGATGCAGTTACTGATAAGAACAGAGAAGGATGGAATTCTT
genomic: TTCCTTCTAATCCAAATGACATTTTCTTGACTGATGGTGCAAGCCCAGCAgtaaatttca ... ctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTT
EST: gi|161717648|gb|FC066273.1|FC066273
EST:     TTCCTTCTAATCCGAATGACATTTTCTTGACTGATGGTGCAAGCCCAGCA                         GTCCATATGATGATGCAGTTACTGATAAGAACAGAGAAGGATGGAATTCTT
genomic: TTCCTTCTAATCCAAATGACATTTTCTTGACTGATGGTGCAAGCCCAGCAgtaaatttca ... ctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattttaaaatttcaagcataaataacaaatgtttttctccctctcttatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG
                      aaataac  putative branch site (score: 2)
                                tgtttttctccctctc  putative PPT
     tttaaaatttcaagca  TA-rich tract