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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatcaactaaatgaaccttaatccccttacctggcccatcagccacatagatctatatccgccgttctcctgtatttaagtcatctcccatctc...

Basic information

species Vitis vinifera
transcript Vv08s0056g00620.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S68_127V6.1 (Physcomitrella patens), 5'ss of exon 5
CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatg---aaatcaactaaatgaaccttaatccccttacctggcccatcagccacatagatctatatccgccgttctcctgtatttaagtcatctcccatctc
  ||||||||||||| |||||| |  |||| |||   || || |  ||||||||||| |||||||| ||||| |||||||||   ||| | |||||||||||| |   |  |  ||   ||||   | ||     || |     |  | | | | ||  ||  | ||     ||      ||| | |  | |  |        
TACAGGAGGAGTGGTGTTGGCTACCAAGGATGGGCGCATTGTATTGGAGAACACTCTAGATGCACGCTTGGAAGTTGTATTCAAGCAGCAGCTGCCTGAGgtaggcccacttttacgctatgattttcaactttttttctgcaactctaaccaagatcaattgacatat-tagtgactgggtactgatattaggttttgag--
















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|349832600|gb|FQ421958.1|FQ421958
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGGTCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110698903|gb|EE076929.1|EE076929
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|30133266|gb|CB918605.1|CB918605
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110423860|gb|EC990211.1|EC990211
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|351023437|gb|FQ432820.1|FQ432820
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACA-GTTGTTGCT
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCT
EST: gi|110378220|gb|EC943340.1|EC943340
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTG---CTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110419865|gb|EC986119.1|EC986119
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110376043|gb|EC941082.1|EC941082
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110411460|gb|EC977174.1|EC977174
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110702891|gb|EE079258.1|EE079258
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACA-GTTGTTGCTTGAT
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGAT
EST: gi|110702889|gb|EE079256.1|EE079256
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTAGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110687935|gb|EE065911.1|EE065911
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACA-GTTGTTG
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTG
EST: gi|110411538|gb|EC977258.1|EC977258
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|32456707|gb|CD797881.1|CD797881
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|27586418|gb|CB009113.1|CB009113
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110702890|gb|EE079257.1|EE079257
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACNAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|34361775|gb|CF403360.1|CF403360
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
EST: gi|110362618|gb|EC926164.1|EC926164
EST:     ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG                         ATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC
genomic: ACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatc ... atctatgcagATCAGAAAGCTTCTTTTTGGACAAGTTGTTGCTTGATCATCTTGGATCCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAGgtatgaaatcaactaaatgaaccttaatccccttacctggcccatcagccacatagatctatatccgccgttctcctgtatttaagtcatctcccatctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctccc