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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAGGACGAGTACATCCGCAGACACCACAGGCATGAGATCAGAGACAACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcatttttcctttttgtctttattttttatttagttttttttttcaagtggcttgtctctctatttttttaacaattcagatccggatgttgtttg...

Basic information

species Vitis vinifera
transcript Vv02s0025g01340.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01340.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os05g12260.1 (Oryza sativa), 5'ss of exon 1
GATGGAGGACGAGTACATCCGCAGACACCACAGGCATGAGATCAGAGACAACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcatttttcctttttgtctttattttttatttagttttttttttcaagtggcttgtctctctatttttttaacaattcagatccggat--gttgtttg----
|  |||||  ||| |||| || || | |||||| || |    | | ||  |||||||||||||| | ||||||||||||||||| ||||||||||| || || ||    || |     |  |      ||  ||    |||||||||||   |  |||   |   | ||| ||  |    |    |  || |  | |  |||    
GGCGGAGGCGGAGCACATGCGGAGGCTCCACAGCCACGCCCCCGGCGAGCACCAGTGCAGCTCCGCGCTCGTCAAGCACATCAAGGCTCCTGTTCACCTCgtgag----ttccacgactcacgacgccttccatcctcttttttttttctgtt--cttcgtttggtgtttgttcgattggttgcgtttggtttggctacttggctc
















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|110384123|gb|EC948539.1|EC948539
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110377836|gb|EC942930.1|EC942930
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|161706649|gb|FC055053.1|FC055053
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110685260|gb|EE063479.1|EE063479
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|30326889|gb|CD010151.1|CD010151
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110392500|gb|EC957964.1|EC957964
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110404624|gb|EC969973.1|EC969973
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|32268747|gb|CD717906.1|CD717906
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110400413|gb|EC966975.1|EC966975
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110398507|gb|EC964919.1|EC964919
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110698782|gb|EE076672.1|EE076672
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|30326243|gb|CD009505.1|CD009505
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAGAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110387130|gb|EC951775.1|EC951775
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
EST: gi|110414350|gb|EC980177.1|EC980177
EST:     ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTG                         GTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT
genomic: ACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcattt ... caatcatcagGTTTGGTCTTTGGTGAGGAGTTTTGATCAGCCACAGAAATACAAACCTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGAGGACGAGTACATCCGCAGACACCACAGGCATGAGATCAGAGACAACCAGTGCAGCTCCTCTCTCGTCAAGCACATCAAAGCTCCTGTTCATCTGgtaagcatttttcctttttgtctttattttttatttagttttttttttcaagtggcttgtctctctatttttttaacaattcagatccggatgttgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC