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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatgtctgtaatgttttttgttctttctcttcttttccctgtagtaattcttcttattacatcatgtgaattttttgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGTGATGAGTTTCGAGGCTTTTTTCCAAGAAATACTAAAGTGAAGTGCCTGA

Basic information

species Vitis vinifera
transcript Vv14s0060g00230.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G22210.1 (Glycine max), 3'ss of exon 5
gtttgatgtctgtaatgttttttgttctttctcttcttttccctgtagtaattcttcttattacatcatgtga-attttttgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGTGATGAGTTTCGAGGCTTTTTTCCAAGAAATACTAAAGTGAAGTGCCTGA
          ||||      | ||        | | |  | | | ||  |  | || || | |  | |  ||  | | ||| || ||||||||||||||||||| ||||| ||||| ||||||||  ||||| | ||||||||||| ||  |||| ||||| |||   | ||| ||||||||||| || |
--------gttgtacacacatatgcatgcatacat-tgctacttatataatcttttgttctcatgttagatgctactatttttgcttcagGCTCTTCTTTCTGGATGCTCGGCTGGTGGTCTGGCTACTATTATACACTGTGATGAATTCAGAGGTTTTTTCCCAGAGACTACCAAAGTGAAGTGTCTTA

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G28230.1 (Glycine max), 3'ss of exon 5
gtttgatgtctgtaatgttttttgttctttctcttcttttccctgtagtaattcttcttattacatcatgtga-attttttgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGTGATGAGTTTCGAGGCTTTTTTCCAAGAAATACTAAAGTGAAGTGCCTGA
          ||||      | ||  |     | | |  | | | || ||||  || || | || | |  |   | | ||| || ||||||||||||||||||| ||||| ||||| ||| ||||  ||||| | ||||||||||| ||  |||| ||||| |||   | ||| ||||||||||| || |
--------gttgtacacacatatgcacacatacat-tgctacttata-taatctttgttctcacgttagatactactatttttgcttcagGCTCTTCTTTCTGGATGCTCGGCTGGTGGTTTGGCTACTATTATACACTGTGATGAATTCAGAGGTTTTTTCCCACAGACTACGAAAGTGAAGTGTCTTA
















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|32271244|gb|CD720403.1|CD720403
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|30324545|gb|CD007807.1|CD007807
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|71864790|gb|DT013845.1|DT013845
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|110373337|gb|EC937563.1|EC937563
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|18458238|gb|BM436516.1|BM436516
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|30327012|gb|CD010274.1|CD010274
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|30327090|gb|CD010352.1|CD010352
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|30321442|gb|CD004704.1|CD004704
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|32268077|gb|CD717236.1|CD717236
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|110696063|gb|EE074792.1|EE074792
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT
EST: gi|30326319|gb|CD009581.1|CD009581
EST:     CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG                         GCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTACACTGT
genomic: CAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAGgtttgatgtc ... tgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttccctgtagtaattcttcttattacatcatgtgaattttttgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGTGATGAGTTTCGAGGCTTTTTTCCAAGAAATACTAAAGTGAAGTGCCTGA
                                        ttttttgt  CT-rich tract
              taattcttcttatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatgtctgtaatgttttttgttctttctcttcttttccctgtagtaattcttcttattacatcatgtgaattttttgtgtttcagGCTCTTCTTTCTGGGTGCTCTGCTGGAGGTCTGGCAGCTATTTTGCACTGTGATGAGTTTCGAGGCTTTTTTCCAAGAAATACTAAAGTGAAGTGCCTGA

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