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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttggtatgaaattattttcattgcatcaaactgagcattagcttttcgttacaccattttcttagtttctaattcattaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA

Basic information

species Vitis vinifera
transcript Vv16s0039g01410.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 5
ttttttggt---atgaaattattttcattgcatcaaactgagcattagcttttcgttacaccattttcttagtttctaattcattaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA
||     ||    ||||||   |||  | | || |   |  || |   ||      | |    |   | |  ||  |  || |||   |  ||| |    |||||   ||| ||||||  ||||| ||||  ||||||||||||||   ||| ||||||| |   |||||||||||||| |||||||||||||||||||| ||
ttgcagagtttcttgaaatgtgttttgtagtattatttttggcctggactaggaacttc-ttgtcgacctgattgtt--ttaatttgatactttttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGATACAAGAAGAATCTGATTAAGTTTGCCATCATTACATGTCGAAAGCCTGA

upper sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G35680.1 (Glycine max), 3'ss of exon 5
ttttttggtatgaaattattttcattgcatcaaactgagc-attagcttttcgttacaccattt----tcttagtttctaattcattaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA
    |   | ||   | ||| | |||   |    |||| | |  | ||| | |||  ||   ||    | ||| |||   | |  |||| | |||| ||   |||||   ||||||||||  ||||| ||||  ||||||||||||||   ||| ||||||| ||  ||||||||||||   |||||||||||||| ||||| ||
----tgaatgtgttttcattattatttt-ttggcctgacctaggaacttcttgttgaactgattagtattttaatttgatactttttaattttttttttgtccagGACTTAAAACCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGATACAAGAAGGATCTGATTAAGTTTAGCATCATTACATGTCGGAAGCCTGA

upper sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G01690.1 (Glycine max), 3'ss of exon 5
--ttttttggta-tgaaattattttcattgcatcaaactgagcattagcttttcgttacaccattttcttagttt-ctaattc--attaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA
  ||| ||| || || |    || | |||   |    |||  |   |        ||| || | ||  | |  ||  | |||    ||  ||   || ||  ||||||   ||||| |||| |||||| ||||  ||||||||||||||    || |||||||  |  || ||||||||||| ||||||||||||||||| || ||
aatttcttgttagtgcatgctttgttattattttggcctggactagaa------attaaacgacttgttgaacttgttgattttggttttgttactttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGATACAAGAAAGATCTAATTAAGTTTGCCATCATTACATGTCGAAAACCTGA

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|32249778|gb|CD715597.1|CD715597
EST:     GATACGCTCTGCTT-GACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|22010470|gb|BQ795504.1|BQ795504
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|22012614|gb|BQ797648.1|BQ797648
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|110360881|gb|EC924323.1|EC924323
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|110423065|gb|EC989400.1|EC989400
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|34547143|gb|CF515375.1|CF515375
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|30327692|gb|CD010954.1|CD010954
EST:     GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32249517|gb|CD715336.1|CD715336
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32271736|gb|CD720895.1|CD720895
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32269217|gb|CD718376.1|CD718376
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32247466|gb|CD713285.1|CD713285
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32270284|gb|CD719443.1|CD719443
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|83275165|gb|DV939261.1|DV939261
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAANCCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32268132|gb|CD717291.1|CD717291
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|110425522|gb|EC991909.1|EC991909
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32248194|gb|CD714013.1|CD714013
EST:     GATACGCTCTGCTT-GACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|32247586|gb|CD713405.1|CD713405
EST:     GATACGCTCTGCTT-GACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|34547232|gb|CF515464.1|CF515464
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|110421515|gb|EC987813.1|EC987813
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|110416731|gb|EC982731.1|EC982731
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
EST: gi|110376167|gb|EC941211.1|EC941211
EST:     GATACGCTCTGCTTTGACTTTCAAGGGCTTCATATCACTGTTACGCAGTG                         GATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT
genomic: GATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCAGTGgtaagtttag ... tctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcgttacaccattttcttagtttctaattcattaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA
                         ttctaat  putative branch site (score: 2)
                                          ttttctttatc  putative PPT
                        tttctaattcattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttggtatgaaattattttcattgcatcaaactgagcattagcttttcgttacaccattttcttagtttctaattcattaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - -gaaatta
- - - - - - - - - - - - - gcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tacacca