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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggttcag

Basic information

species Vitis vinifera
transcript Vv03s0038g03270.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 5'ss of exon 7
TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggttcag
|||||| || |||||||| ||||||||  |  ||||| | |||||||||||||||||  | |||   ||||| ||||||||||||||||| || |||||||||| |      |||  | |  ||  ||| || ||| |      || |   || ||  |  |    | | |       |     || | |||
TCTATCCCCCATGGGTGAAGCCTGTTCTAGGATGGACATGACAGCAATCCATCAGATTCTAGTTGCCACACATTACAGAGATGATGAAGGGACTAATGAGgtaaata-----ttggagcactttgatttctgtcatatggcagatcgt-tgtctaa--gaaatctatctcttcatcaatctccctgttgcag

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os10g39670.1 (Oryza sativa), 5'ss of exon 7
TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggt--------ttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggttcag---------------
 || || || ||||| |||||||||||  |  ||||||| || || |||||||||||| | |||   ||||| ||||||||||||||||| || ||||||||||      | | ||  |  ||        | |||| | ||   |    |  ||     |    |     |   ||    ||| |  || |       |               
ACTTTCTCCCATGGGAGAGGCCTGTTCCAGGATGGACCTTACTGCCATCCATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctgcag

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G48030.1 (Glycine max), 5'ss of exon 5
TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggttcag
||| ||| ||||||||||||| |||||| || ||||||| || ||||| |||||||||||||||  ||||||||||||||| ||||||||||| |||||||||| |||   ||  ||   |||||   |||   || | |           |   ||| |  |   |     |||   ||| ||||||||||
TCTTTCAGCAATGGGTGAGGCTTGTTCAAGAATGGACCTAACTGCAATACATCAGATCTTGGTTGCGACACACTACAGAGACGATGAAGGAACTAATGAGgtaactgatgggtgcattg-ggtttaaatttactatttttg---------gttggatgatatgccataaggtttgaatttggattggttcag

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA14G00540.1 (Glycine max), 5'ss of exon 5
TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggttcag
||| ||| ||||||||||||| |||||| || ||||||| || ||||| |||||||||||||||  ||||||||||||||| ||||||||||| |||||||||| |||        ||   |  ||  |||   || |   || | ||| ||   ||| || |   |     |||   ||| ||||||||||
TCTTTCAGCAATGGGTGAGGCTTGTTCAAGAATGGACCTAACTGCAATACATCAGATCTTGGTTGCGACACACTACAGAGACGATGAAGGAACTAATGAGgtaactga--------tgggtgcattggttttaaatttac-tattttta-attggatgatgtgccataaggtttgaatttggattggttcag

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 7
TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggtt-cag
 || || ||| | ||||||||||| ||| || |||| |||||||| || |||||||| ||||| |||||||| |||||||| || || || || || ||||||||  | | ||      || |||  |||      ||  |     ||| |   | |  ||| |   || |   | |  | ||| | || |||
ACTTTCGCCATTAGGTGAGGCCTGCTCAAGAATGGATCTCACAGCTATTCATCAGATTTTGGTCATGACACATTACAGAGACGACGAGGGCACAAACGAGgtaatcaaatggt------agttttggtttcaattgctaaaatgctttaaaaagagtcttgactaacttttggggtttatctatggatttcag

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|33405170|gb|CF210797.1|CF210797
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|110396180|gb|EC961861.1|EC961861
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|110358197|gb|EC922241.1|EC922241
EST:     GAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: GAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|110386358|gb|EC950948.1|EC950948
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|110368581|gb|EC932568.1|EC932568
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|30325969|gb|CD009231.1|CD009231
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|22014191|gb|BQ799225.1|BQ799225
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|33405090|gb|CF210717.1|CF210717
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|30328105|gb|CD011367.1|CD011367
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
EST: gi|30136281|gb|CB921619.1|CB921619
EST:     ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAG                         TTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG
genomic: ATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagt ... attggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATCACCAATGGGTGAGGCCTGTTCACGACTGGACCTCACAGCAATCCATCAGATCTTGGTTATGACACACTACAGAGATGATGAAGGAACCAATGAGgtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA