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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
----ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgaga-attgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
    || |  ||||  | | |  |||   || ||     |||  | |      |   ||  |||||| | | ||| |    | |  |      | | ||| |||||||||||| ||||| || |||||||||||||| ||||| || |||||||| |||||||| |||||
tatatttat-tctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaa----tatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
---ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgaga-attgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
   || |  ||||  | | |  |||   ||  |     |||  | |      |   ||  |||||| | | ||| |  | ||     ||   | | ||| |||||||||||| ||||| || ||||| |||||||| ||||| || ||||| ||||||||||| |||||
atattaat-tctacttctgtcatgtgttattgcttgaaagttctgtttttcagctgatccttgagacactatctaatatgttaggaaaa---taatttttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
ttgacgtctagattttttgtgttcaatgtcagt--gcagtcatttgaacttgtgaattattgaga-attgtctgact--tttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
     |||||  |  | |   | ||   |   |    |||  | |   ||| |   |  |||| | | | | |  ||  ||| || |  | |      || |||||||||||| ||||| || ||||| |||||||| ||||| || ||||| || ||||| ||||||||
----tgtctacctcctgt-catgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
-ttgacgtctagatttt--ttgtgttcaat--gtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
   |   |  ||||| |  || ||  | |    |  ||  | ||  |  | || |||||||      |||| ||| ||  ||  | | ||     || || |||||||||||| ||||| || ||||| |||||||| ||||| || ||||| || || || ||||||||
ccagtaattcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaa-----acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
-----ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
     | |   |  ||||| | | | |    |     |    | |||    || |||||||      |||| ||| ||  ||  | | ||     || || |||||||||||| ||||| || ||||| |||||||| ||||| || ||||| || || || ||||||||
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaa-----acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
---ttgacgtctag--attttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
    | | ||||||  | |  | || |     |||| |    |||| |  |  ||   |   |  |  | | ||| | ||| | |   |||  | |||||| ||||||||||| ||||| || ||||| |||||||| ||||| || || || || ||||| ||||||||
atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctg---accctgaaagactatctaa-tttataatgaaacaattacttta-cagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG

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|33409748|gb|CF215375.1|CF215375
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|33408202|gb|CF213829.1|CF213829
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|71879035|gb|DT028090.1|DT028090
EST:     CCTTGCATGTCCCGCTTCTCCTANNNNNNNATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: CCTTGCATGTCCCGCTTCTCCTATTTTTT-ATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|71879209|gb|DT028264.1|DT028264
EST:     CCTTGCATGTCCCGCTTCTCCTANNNNNNNATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: CCTTGCATGTCCCGCTTCTCCTATTTTTT-ATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|37190531|gb|CF609880.1|CF609880
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|71881039|gb|DT030094.1|DT030094
EST:     CCTTGCATGTCCCGCTTCTCCTANNNNNNNATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: CCTTGCATGTCCCGCTTCTCCTATTTTTT-ATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
EST: gi|33406260|gb|CF211887.1|CF211887
EST:     ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG                         ACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA
genomic: ACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAGgttagtatat ... actttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
                                  acttaac  putative branch site (score: 3)
                                           tcacttt  putative PPT
       aattattgagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - -caatgtc
- - - - - - - - - - - - - - - - -gcagtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctga