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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGGATGCGGAGGTGGCTCTGTTGTACTTGTCACGTGGAAGAGCCTTACCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttccttgattcctgttgcttcctgacatatgctttgaaagttttgaacattagtctggaattacatattggtgaaatttaatggttttagagga...

Basic information

species Vitis vinifera
transcript Vv05s0124g00360.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 2
GGCAGGATGCGGAGGTGGCTCTGTTGTACTTGTCACGTGGAAGAGCCTTACCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttccttgattcctgttgcttcctgacatatgctttgaaagttttgaacattagtctggaattacatattggtgaaatttaatggttttagagga-----
   ||||||||  ||||||| |||||||||||||| ||||||||| ||||||  ||||||||||  || | | |||||||||| |||||  |   |||||||   |||| || |||  |  | | | |||   | |       |  | |||   | || |   |||  |  ||   || || |  || || |  | |  |     
ACAAGGATGCGTCGGTGGCTTTGTTGTACTTGTCAGGTGGAAGAGTCTTACCCATCAAATGAAAATGAACACCTGAAAAGCCCAAGGAATTATGGAGATGgtgagtttc-ttaatt--taatccattctgttgttttgcccaga--tattgtttactacttgagaaagaagtaaaagtaaattacaaaggatacaaaaaaaaaac
















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|161709819|gb|FC058898.1|FC058898
EST:     CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
EST: gi|110385254|gb|EC949761.1|EC949761
EST:     CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
EST: gi|110730792|gb|EE108276.1|EE108276
EST:     CGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
EST: gi|110686851|gb|EE063746.1|EE063746
EST:     CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
EST: gi|110698518|gb|EE076104.1|EE076104
EST:     CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
EST: gi|110699258|gb|EE076097.1|EE076097
EST:     CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
EST: gi|110698344|gb|EE075749.1|EE075749
EST:     CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATG                         GAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA
genomic: CCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttcc ... ggcaattcagGAAACCCAAAAGGCTCAAAGGTGTCAGCTCCTGTTAGAAGTGAAGTGCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAGGATGCGGAGGTGGCTCTGTTGTACTTGTCACGTGGAAGAGCCTTACCAGTCAAATGAAAGCGAGCTCTTGAAAAGCCCCAGGAACCACACAGATGgtatatttccttgattcctgttgcttcctgacatatgctttgaaagttttgaacattagtctggaattacatattggtgaaatttaatggttttagagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgaaa