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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgctctttgttattttatcttattttatttttaaattttttaacctttttctttgttgcatgattatagaactgtgattgtgtttttaggtta...

Basic information

species Vitis vinifera
transcript Vv05s0020g00570.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00570.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G07200.1 (Glycine max), 5'ss of exon 2
ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggat-gctctttgttattttatcttattttatttttaaattttttaacctttttctttgttgcatgattatagaactgt-gattgtgtttttaggtta---
|| || ||||| || || ||||||||||||||  ||||| | ||||| ||||||||||| ||||| ||||||||| | | |||| |  |||| || ||| |||||  |   ||||| |    || |  | |||| ||||| ||| | | ||  |   |||     | || | |||    || | |  | |  ||||   | |   
ATAGACAAGGCGTACCCTCGTGATTTCATGCAGAGAGGGCGCGTGAGGGTGTTGCTGAAGAAGGAGGATGGAACTCTCTTTAATTCAACCATCTCATCCAgtaagatttaatctttctaccctttttatgtttttttttttaatatatgaatatgaatct-----gaatcaatatgttgcttttggctattattttcattcatcc
















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|71890504|gb|DT039559.1|DT039559
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|77580101|gb|DV218940.1|DV218940
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|110364564|gb|EC927913.1|EC927913
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|71868537|gb|DT017592.1|DT017592
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|71867217|gb|DT016272.1|DT016272
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|22008948|gb|BQ793982.1|BQ793982
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|110375143|gb|EC940104.1|EC940104
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|110416251|gb|EC982219.1|EC982219
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|30128384|gb|CB913723.1|CB913723
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|110407038|gb|EC972629.1|EC972629
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|71866966|gb|DT016021.1|DT016021
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|83275344|gb|DV939352.1|DV939352
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|83275320|gb|DV938471.1|DV938471
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|110378561|gb|EC943698.1|EC943698
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
EST: gi|110385463|gb|EC949995.1|EC949995
EST:     GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC                         GAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA
genomic: GTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgc ... tataatccagGAAAAGAGCTGATGCGTCATGTTGCTGAGTTGGTACCCAGACATCCTGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCCgtaaggatgctctttgttattttatcttattttatttttaaattttttaacctttttctttgttgcatgattatagaactgtgattgtgtttttaggtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA