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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC

Basic information

species Vitis vinifera
transcript Vv05s0029g00240.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 5
gtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactc--cctaatttactt---atga-agGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
               || | ||   || ||| | |        |||||  |||   |||||| |  | |||||    ||      |      | ||   ||  |   | |   | || |   |||| ||||||| |||||  |||||||| |||| ||||  ||||||||||| ||||| |||||    || |||||||||||| | |||||||| ||||| || ||||
---------------gtttgtccataactccat-gccaatgttcttgctattttc-ttgtataaagccctatttgtccaatttgtttagttgtttactctccttatgcttgcatgacatgacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAAATGCCAGGACTGATAACTGATTTTGTTATCTCTCTGGATGATCGCTATC

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G180331_T01 (Zea mays), 3'ss of exon 1
gtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattt--tgaattgtattagtctctattaaggcatgacaatccacaatata-taatcactccctaatt---tacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
                           | |  | ||  ||| ||  | || |    || | |  || |    | || |||  ||   |  ||| | || | |  || |  | | |   ||||| || ||||||| || ||  |||||||| ||||||| |  ||||||||||| || || | |||     | |||||||||||| | |||||||| |||||||||||||
--------------------------gtgctctggtaagaatccgcgtatctatcaaaattttctactaataaatagggctgga--gttgacattttagttagaaccctatgactgtgtactt-tgtagGTTGCTATCTCCATAAAACCATTGAAGGTTCGCAACTGGATTCTGCCAGAAACGCCAGGATTGATAACTGATTTTGTTATCTCTCTTGATGACCGTTATC

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 5
gtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
                    | ||||    | || | | ||    |     | |  ||     ||  || |  ||||||| |  ||| | ||||     | ||   |||   |   | || |||||||||||||||| |||||| |||| |||||||||||||||||||| || |||||    |||||||||||||||||||| ||||||||||| || | ||
-------------------atattcatactcattttgtaaagtagtctggctagtgtttgtgcagcttcaaccaaggcataatgatcaataatac----ttacagactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCAGGGCTTATAACTGATTTTCTGATATCTCTCGATGATCGGTTTC

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 5
gtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaa-tttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
               || | ||   |     |||  |    |   ||  ||    | | |||     || |  ||||  |    ||  |  |   ||| | |    ||||  |||||| || ||||||| |||||||| |||||| |||| ||||||||||||||||||||||| |||||    |||||||||||||||||||| ||||| ||||| || | ||
---------------gtatatcaaaaggatatttaatatctattctgttttggtcagtatatgtacttcaaccaaggtgtatgtatatatcaatgatacttatagactaagcttacttttgcagGTTGCCATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCTGAAATGCCTGGGCTTATAACTGATTTTCTGATTTCTCTTGATGATCGGTTTC

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
gtatgcggataatatgtgtttcttcaattcctttgt-ttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
                  | ||   | |   ||||| |||  | || | ||      ||||   ||  || |  |||| || |  ||| | ||||     | || | |||   |   | || |||||||||||||||| |||||| |||| |||||||||||||||||||| || |||||    |||||||||||||||||||| ||||| ||||| || | ||
-----------------atatccatactcattttgtattgtcatctggtatgc--gtttgtgc-agcttcaaccaaggtataatgatcaataatac----ttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G36670.1 (Glycine max), 3'ss of exon 5
gtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
                               | | |   |     |  | | |  |||       | | || |     ||    ||| |  |||  ||   |||    || |||||| || ||||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||||    ||||||||||||||| |||| ||||| ||||| || | ||
------------------------------gtatatcaaaggatatttaatatctattcagc--atatgtacttgtatatatatatcaatgatacttacagacta---aacttactt-tgcagGTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAAATGCCTGGGCTTATAACTGATTTTTTGATTTCTCTTGATGATCGGTTTC

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|26257072|gb|CA808135.1|CA808135
EST:     GCAATATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAG                         GTTGCAGCATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGAA
genomic: GCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggat ... acttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGAC
EST: gi|110378930|gb|EC944090.1|EC944090
EST:     GCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAG                         GTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGAC
genomic: GCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggat ... acttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGAC
EST: gi|33401496|gb|CF207123.1|CF207123
EST:     GCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAG                         GTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGAC
genomic: GCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggat ... acttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC
                                    ccctaat  putative branch site (score: 3)
                                          tttactt  CT-rich tract
                                       taatttacttatgaa  TA-rich tract