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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttaattccttcggcaaagaccaaaaatgtttggttgtctttatttttttggataagtggtgatctctgaaatgatactcatatatctaattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGGACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG

Basic information

species Vitis vinifera
transcript Vv13s0084g00620.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 3'ss of exon 6
-----------ctgttaattccttcggcaaagaccaaaaatgtttggttgtctttatttttttggataagtggtgatctctgaaatgatactcatatatctaattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGGACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG
            || |  ||    |    |  ||  |  |||||    |  |   ||| |  | ||  | |     |||||    | ||  | |   || |       ||||| || || || || ||  |  | | |||| | ||||||||||| || || ||||||||||||||||| || || || |||||||| ||    || ||||
tctcaggctaggtggtgtttttacctattactacgtaccatgttaacctaccaccattctaattga--aataac--tctctattgtcatgttaaatcattt-------cagAGGGTGCTAGGGGATGGTATGCTTGCTGTGCGGAAGATCGAGAATGTTGCAACTGGACCAAACAACCGACCGAAGCTCGCATGTGTCATAAGCGAGTGTG

upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G11960.1 (Glycine max), 3'ss of exon 6
-ctgttaattccttcggcaaagaccaaaaatgtttggttgtctttatttttttggataagtggtgatctctgaaatgatactcatatatctaattc-tgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGGACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG
    ||  |  ||  | |  |    |||  |   | |   ||||| || |     |    || |    | |  | | |  | ||| | ||   ||  |||||||||| |||||||| || ||||||||||| || ||||| |||||||| || || ||||| || |||||||| ||| | || ||||| |||||||||||||
tgcatttttatctctgccttatttgaaatgttactagc-atctttcttctccaaaactgttgatatgtttttcatttac-cacatgtctcccctttatgcagAGAGTGCTTGGAGATGGTCTTTTGGTTGTCAGGAAGATTGAGAACGTGGCAACCGGACCCAATAACCGGCCAAAATTAGCTTGTGTCATTGCTGAATGTG

upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G37190.1 (Glycine max), 3'ss of exon 6
-ctgttaattccttcggcaaagaccaaaaatgtttggttgtctttatttttttggataagtggtgatctctgaaatgatactcatatatctaattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGGACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG
  | |||||   |  | |  |    |||  |   | |   ||||| || |  |  |    |  |    | || | | |    |     ||   || |||||||||| |||||||| || ||||||||||| || ||||| |||||||| || ||  |||| || |||||||| ||| | ||||| || |||||||||||||
cattttaatctatgtgccttatttgaaatgttactagc-atctttcttgtcctaaactgttaatatgttttgcatttaccacctgtcttcccgttatgcagAGAGTGCTTGGAGATGGTCTTTTGGTTGTCAGGAAGATTGAGAACGTGGCAACGAGACCCAATAACCGGCCAAAATTAGCATGCGTCATTGCTGAATGTG

upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G26260.1 (Glycine max), 3'ss of exon 6
-ctgttaattccttcggcaaagaccaaaaatgtttggttgtctttatttttttggataagtggtgatctctgaaatgatactcatatatctaattc-tgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGG-ACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG
    ||  | |||  | |  |    |||  |   | |   ||||| || |  |  |    || |    | |  | | |  | ||| | ||   ||  |||||||||| || ||||| || ||||||||||| || ||||| |||||||| || || || ||| || |||||||| ||| | || ||||| |||||||||||| 
tgcatttttacctctgccttatttgaaatgttactagc-atctttcttctcctaaactgttgatatgtttttcatttac-cacatgtctcccctttatgcagAGAGTGCTGGGAGATGGTCTTTTGGTTGTCAGGAAGATTGAGAACGTGGCAACCGGGACCCAATAACCGGCCAAAATTAGCTTGTGTCATTGCTGAATGT-

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|110689345|gb|EE065486.1|EE065486
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|110369676|gb|EC933841.1|EC933841
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|32459581|gb|CD800755.1|CD800755
EST:     TCACATGCTCGAAACGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|30330499|gb|CD013761.1|CD013761
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|30330447|gb|CD013709.1|CD013709
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|22009195|gb|BQ794229.1|BQ794229
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|71890647|gb|DT039702.1|DT039702
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|27586714|gb|CB009409.1|CB009409
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|110397718|gb|EC963561.1|EC963561
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|110377315|gb|EC942381.1|EC942381
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|71875212|gb|DT024267.1|DT024267
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|71871923|gb|DT020978.1|DT020978
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|110421609|gb|EC987908.1|EC987908
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|110408091|gb|EC973714.1|EC973714
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|32459126|gb|CD800300.1|CD800300
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
EST: gi|71876171|gb|DT025226.1|DT025226
EST:     TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG                         AGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC
genomic: TCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctc ... aattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttggataagtggtgatctctgaaatgatactcatatatctaattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGGACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG
                                         atctaat  putative branch site (score: 3)
                                   tcatatatctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttaattccttcggcaaagaccaaaaatgtttggttgtctttatttttttggataagtggtgatctctgaaatgatactcatatatctaattctgcagAGAGTTCTTGGAGAAGGCCTTTTGGTTGTGAGAAAGATCGAGAACGTAGCCACTGGACCAAACAACCGGCCTAAACTGGCATGTGTGATTGCTGAATGTG

- - - -ttccttc
- - - - - - - - - -agaccaa
- - - - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgaa