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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaatttcatacatttatattacttatgatgctatgtttgtttttccagtttggtttgtctgggtgctgattgaggtttgtgttggctttttggttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTCTCCGCTCAGACACCTTCATACCTCACCGGAGAGTTCCCCGGTGACTATG

Basic information

species Vitis vinifera
transcript Vv00s0181g00180.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0181g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G057281_T02 (Zea mays), 3'ss of exon 2
gtatttcaatt-tcatacatttatattacttatgatgctatgtttgtttttccagtttggtttgtctgggtgctgattgaggtttgtgttggctt--tttggttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTCTCCGCTCAGACACCTTCATACCTCACCGGAGAGTTCCCCGGTGACTATG
|||  |  |   ||   | | |||    |     |||    ||   |  || || |      |           || | | |   ||| | ||||   ||   |  ||||| |||||  | ||||| || |||||||| || |||||| |||| ||||||||||| ||||| || || ||||| ||||| ||||||||||| ||||| |
gtacgtggagcatccatcgtctatcggtccatccatggcccgtcgatggtttcaatcaataatcaggtaaaatcgactaacgagagtgctcgcttcgcttccattgcagGGCAACGACCTGTGGTACGGCCCGGACCGCGTCAAGTACCTGGGCCCCTTCTCCGCCCAGACGCCCTCGTACCTGACCGGCGAGTTCCCCGGCGACTACG

upper sequence: Vv00s0181g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G34770.1 (Glycine max), 3'ss of exon 1
--gtatttcaatttcatacatt-tatattact--tatgatgctatgtttgtttttccagtttggtttgtctgggtgctgattgaggtttgtgttggctttttggttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTCTCCGCTCAGACACCTTCATACCTCACCGGAGAGTTCCCCGGTGACTATG
      |||   |||||   || | | |||||   |  |   | |  | || ||       | || ||  ||     | |||  ||||||||||   | |     |  ||||| || || || ||||||||||| ||| | ||||| ||||||||||||||||| |||||||| ||||||||| | |  ||||| ||||| || || ||||
gtactcttcttcttcatgttttatgttttactatcacaaaagttttatggtgttgattacgtagtgtggttgatatgttatttgggtttgtgtt--ttgtgaacatttcagGGCAATGATTTGTGGTATGGACCAGACAGAGTGAAATACTTGGGACCCTTCTCAGCTCAGACCCCTTCATACTTGAAAGGAGAATTCCCTGGGGATTATG

upper sequence: Vv00s0181g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G35800.1 (Glycine max), 3'ss of exon 1
gtatt-tcaatttcatacat----ttatattacttatgatgct--atgtttgtttttccagtttggtttgt----ctgggtgctgattgaggtttgtg-----ttggctttttgg--ttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTCTCCGCTCAGACACCTTCATACCTCACCGGAGAGTTCCCCGGTGACTATG
||| | || |||  ||| ||    || | ||  | ||  |  |  ||||||   | ||      ||||| |     ||| ||     || |||| ||      |||| ||| ||    |  ||||| || || || ||||||||||| ||| | ||||| |||||||||||||| || |||||||| ||||||||| | |  ||||| ||||| || || ||||
gtactctccattctatagatacccttttcttcttcattttttttaatgtttaactatcacaaaaggtttatggtgttggttgtgtggtgtggttggtaagttattgggtttgtgaacatttcagGGCAATGATTTGTGGTATGGACCAGACAGAGTGAAATACTTGGGACCCTTTTCAGCTCAGACCCCTTCATACTTGAAAGGAGAATTCCCAGGGGATTATG

upper sequence: Vv00s0181g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G54270.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatttcaatttcatacatttatattacttatgatgctatgtttgtttttccagtttggtttgtctgggtgctgattgaggtttgtgttggctttttggttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTCTCCGCTCAGACACCTTCATACCTCACCGGAGAGTTCCCCGGTGACTATG
   | |   ||   |    |  || | ||  | ||  ||    |||||      | |   || |   | |  ||  |||  ||   ||    | | |  |    |||| || ||  | ||||||||||| ||| | ||||||||||| |||||||| |||| ||| || || || |||||||||||||| ||||| || || ||||
--gtctgttttctttttggtcttaat-ctcgtcatattaaaggtgtttc----atctttcttcttgagtttgtgtctgactttcacgtaaaatgtcta-tgtgaagGGAAATGATCTTTGGTATGGACCTGACAGAGTGAAGTACTTAGGACCCTTTTCCGTTCAAACTCCGTCTTACCTCACCGGAGAATTCCCTGGCGATTATG

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|349808444|gb|FQ405588.1|FQ405588
EST:     CTAACCAGCTTAGAGAAGTTGTTCCTATGGGAACTGGAAAATTCACTATG                         GGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTC
genomic: CTAACCAGCTTAGAGAAGTTGTTCCTATGGGAACTGGAAAATTCACTATGgtatttcaat ... tggttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttggtttgtctgggtgctgattgaggtttgtgttggctttttggttcccagGGGAACGAATTATGGTATGGACCGGACCGGGTGAAGTACTTGGGACCCTTCTCCGCTCAGACACCTTCATACCTCACCGGAGAGTTCCCCGGTGACTATG
                  tgctgat  putative branch site (score: 3)
                                        cttttt  putative PPT
                                         ttttt  TA-rich tract