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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctacaatcacaatgaaccttgtgagctgtttccatgtcagtttcccagttccaggactctttctgagtcattaatctcacaatgctgtgtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGCGATGTATACAGCTATGGAGTAGTTATGCTTGAACTGGTATCTGCTAGGC

Basic information

species Vitis vinifera
transcript Vv08s0056g00100.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00100.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA08G34790.1 (Glycine max), 3'ss of exon 18
gtctacaatcacaatgaaccttgtg-agctgtttccatgtcagtttcccagttccaggactctttctgagtc-attaatc-tcacaatgctgtgtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGCGATGTATACAGCTATGGAGTAGTTATGCTTGAACTGGTATCTGCTAGGC
  |  |   |    | ||  ||||  ||||      ||   ||| |   ||      |  | ||     | | ||| ||  |   ||||||       ||||||||||||| ||||| || ||||| ||||| |||||||| ||||||||||| ||||| ||||| | ||||||||| |||||||||||  || || | ||||
-ccatcccccctcctaaattttgtttagctaaaa--ataaaagtatttaagcctttcgttttttaaactgccgattgatagttgaaatgcttaacatctgcagGGTTATCTGGATCCAGAGTATTATATGACCCAACAACTCACTGAGAAGAGTGATGTGTACAGTTTTGGAGTAGTCATGCTTGAACTAATAACTTCAAGGC

upper sequence: Vv08s0056g00100.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA16G18090.1 (Glycine max), 3'ss of exon 18
gtctacaatcacaatgaaccttgtgagctgt---ttccatgtcagtttcccagttccaggactctttctgagtcattaatc-tcacaatgctgtgtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGCGATGTATACAGCTATGGAGTAGTTATGCTTGAACTGGTATCTGCTAGGC
 ||   |||   ||  || ||     | |||   || ||| |   |||| |  ||  |    |       | |  || ||  |   ||||||       ||||||||||||| ||||| || ||||||||||| |||||||| || |||||||| ||||| ||||| | ||| ||||| |||||||||||  || || | || |
atcactaattgtaa--aatctccatggttgtgtctttcattttgatttcac--ttttatttttggcaacaactgtttgataattgaaatgcttaacatctgcagGGTTATCTGGATCCCGAGTATTACATGACGCAACAACTCACAGAGAAGAGTGATGTGTACAGTTTTGGGGTAGTCATGCTTGAACTAATAACTTCAAGAC
















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|33406477|gb|CF212104.1|CF212104
EST:     TATCAGACAGTGCAAAAGGGCATGTTTCAACTCAAGTCAAAGGCACATTG                         GGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGC
genomic: TATCAGACAGTGCAAAAGGGCATGTTTCAACTCAAGTCAAAGGCACATTGgtaagtgttt ... gtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGC
EST: gi|27585360|gb|CB008055.1|CB008055
EST:     TATCAGACAGTGCAAAAGGGCATGTTTCAACTCAAGTCAAAGGCACATTG                         GGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGC
genomic: TATCAGACAGTGCAAAAGGGCATGTTTCAACTCAAGTCAAAGGCACATTGgtaagtgttt ... gtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGC
EST: gi|33407530|gb|CF213157.1|CF213157
EST:     TATCAGACAGTGCAAAAGGGCATGTTCCAACTCAAGTCAAAGGCACATTG                         GGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGC
genomic: TATCAGACAGTGCAAAAGGGCATGTTTCAACTCAAGTCAAAGGCACATTGgtaagtgttt ... gtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccagttccaggactctttctgagtcattaatctcacaatgctgtgtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGCGATGTATACAGCTATGGAGTAGTTATGCTTGAACTGGTATCTGCTAGGC
                              atctcac  putative branch site (score: 3)
                        tcattaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctacaatcacaatgaaccttgtgagctgtttccatgtcagtttcccagttccaggactctttctgagtcattaatctcacaatgctgtgtggttgcagGGTTATCTTGATCCTGAATATTACATGACTCAACAACTAACTGAGAAGAGCGATGTATACAGCTATGGAGTAGTTATGCTTGAACTGGTATCTGCTAGGC

- - -caatcac
- - - - - - aatgaac
- - - - - - - - - - - - - - - - -ccatgtc
- - - - - - - - - - - - - - - - - - - - - tttccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgct