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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACATTTCAATTATTCCATTTGCCGCCACATTTCCTTTTGAGATATGGATTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatcaattctgggtccagaatattaaatgcaaattgattttcttgttcttgctgtttattgaagaatatgagctcttatttgattaagtttgtta...

Basic information

species Vitis vinifera
transcript Vv08s0007g07430.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G26930.1 (Glycine max), 5'ss of exon 2
TTACATTTCAATTATTCCATTTGCCGCCACATTTCCTTTTGAGATATGGATTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaa----tcatcaatt-ctgggtccag--aata-ttaaatgcaaattgattttcttgttcttgctgtttattgaagaatatgagctcttatttgattaagtttgtta
 | | ||||| |  |||| ||||| || || |||||||||||||||||||||||||| ||| | ||| || |||| ||||||||| | ||   ||| ||||||     || | | || |   |||  |   ||  |||| ||| ||    ||   ||| |||   | |          ||||||| | | | || |  | |       
CTTCTTTTCACTGGTTCCTTTTGCTGCTACTTTTCCTTTTGAGATATGGATTGTTCCTCGGTACCACACTGCTCACTTCCATGAATTGGATGCTGAAAAGgtaccacttctttatttgcaaagtcttgttgatgcttaagtgccaaacatttagtttgatctcaatataatgcatcttatatgaggtgtgaattaa--aggc------
















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|110384352|gb|EC948782.1|EC948782
EST:     TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAG                         GCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
genomic: TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatca ... atttgtgcagGCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
EST: gi|110718380|gb|EE095149.1|EE095149
EST:     TGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAAGAAG                         -CAGTTGATCTTGGT
genomic: TGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGA-GAAGgtaatcatca ... atttgtgcagGCAGTTGATCTTGGT
EST: gi|161715883|gb|FC065502.1|FC065502
EST:     TTGTTCCACGGGATCACTCTCCTCATTTC-ATGAAATAGACAGTGAGAAG                         -CAGTTGATCTTGGTGGTT-ACTG
genomic: TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatca ... atttgtgcagGCAGTTGATCTTGGTGGTTTACTG
EST: gi|110386337|gb|EC950925.1|EC950925
EST:     TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAG                         GCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
genomic: TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatca ... atttgtgcagGCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
EST: gi|110726746|gb|EE102795.1|EE102795
EST:     TTGTTCCACGGGATCACTCTCCTCATTTCC-TGAAATAAACAGTGAGAAG                         GCAGTTGATTCTTGGTGGGTTACTGAAA
genomic: TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatca ... atttgtgcagGCAGTTGAT-CTTGGTGGTTTACTGAAA
EST: gi|30127804|gb|CB913143.1|CB913143
EST:     TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAG                         GCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
genomic: TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatca ... atttgtgcagGCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
EST: gi|32457438|gb|CD798612.1|CD798612
EST:     TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAG                         GCAGTCGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG
genomic: TTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatca ... atttgtgcagGCAGTTGATCTTGGTGGTTTACTGAAATTGATGCTTCAGAAGATGTCTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACATTTCAATTATTCCATTTGCCGCCACATTTCCTTTTGAGATATGGATTGTTCCACGGGATCACTCTCCTCATTTCCATGAAATAGACAGTGAGAAGgtaatcatcaattctgggtccagaatattaaatgcaaattgattttcttgttcttgctgtttattgaagaatatgagctcttatttgattaagtttgtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaata