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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacaacttaccattgactcgtttatggatacttaaaggaatgtttttgataatttgggataagaaggtttaacatttacttcaatttgtgtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG

Basic information

species Vitis vinifera
transcript Vv10s0003g03120.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------taacaacttaccattgac---------tcgtttatggatacttaaaggaatgtttttgataa-tttgggataagaaggtttaacatttacttcaatttgtgtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
                                                                            |  || | | | |  |||         |  | | |  ||  |  |||| ||  || || ||| |     || |   | |  || |  ||||   | |||||      ||||||| || |||||||| |||||||||||| |||| ||||| || || || || || ||||| |||||||| |||||||| ||  | ||||| ||||| ||
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtg------cagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G08970.1 (Glycine max), 3'ss of exon 3
taacaacttaccattgactcgtttatggatacttaaaggaatgtttttga---taatttgggataagaaggttt--aacatttacttcaatttgtgtca-ctgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
        |   ||  |     ||     ||| ||    | ||||||| |   ||| || |      || | ||   | ||| |||| | ||| | ||  ||||||||||  | |||||||||||||||||||||||||| |||||||||||||| |||||||| || ||||| ||||| ||||||||||||||||| || || ||
------tatgatatcaatcttattgcacttacatatgtcattgttttttaaattaagttagatcccaaaagctttggatattcacttgagtttctttcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G34470.2 (Arabidopsis thaliana), 3'ss of exon 4
-taacaacttaccattgactcgtttatggatacttaa----------aggaatgtttttgataatttggga--taagaaggtttaacatttacttcaatttgtgtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
 | |    | |    |  || |||  || ||| ||||          |   |  ||| || |  |   |||   ||  || | | | ||   |||    ||||||   |||||||||||||||||| |||||||| || ||| | || |||||||| || || || || |||||||| | |||||| ||||| || || ||||| ||||| ||
gtgaggtttcatttctagctagttcttg-atagttaatctgcacgatatatagatttctgtttctcaaggaaccaatgagatatga-ataggcttagtgttgtgt-gttgcagATAATTTAGCTGCTAATTTCAGTAGAGAACTAGCTGACTATATCATCTACATCATCGATGTATCGGCTGGTGATAAAATACCCCGTAAAGGCGGCCCTGG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------taacaacttaccattgactcgtttatggatacttaaaggaatgtttttgataatttgggat----aagaaggtttaacattta--cttcaatttgtg------tcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
                                                         || |    |   | ||| |  | ||  | | | |     | ||  ||||    || |   |     |  | |  |    || |  ||  | |||||       |  ||||||| ||| |||| || || |||||||||||  |||| ||||| |||||||| || || |||||||| |||||||| ||||||||||| || || || |||||
gtaatactcctcagtatcttattacggtattgttaattggactggaattacacgtattacctgtgtttaaatga-taatgtaaagtttcattcgaaattggatttggagtttcgaatttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ21803 (Selaginella moellendorffii), 3'ss of exon 4
taacaacttaccattgactcgtttatggatacttaaaggaatgtttttgataatttgggataagaaggtttaacatttacttcaatttgtgtcac---tgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
                                                         | |||| |  ||||   |        || | || ||     |||||||||  | || || || |||||||||||| | |||||||| || || ||||| || ||||| ||||| || |||||||||||||| ||||| || || ||
---------------------------------------------------------gtataacactgttttctaccgcaactaactcgtttcttgtttgcagATAACCTCGCGGCAAACTTCAGCAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ34189 (Selaginella moellendorffii), 3'ss of exon 4
taacaacttaccattgactcgtttatggatacttaaaggaatgtttttgataatttgggataagaaggtttaacatttacttcaatttgtgtcac---tgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
                                                         | | || |  ||||   |        || | || ||     |||||||||  | || || || |||||||||||| | |||||||| || || ||||| || ||||| ||||| || |||||||||||||| ||||| || || ||
---------------------------------------------------------gtacaacactgttttctaccgcaactaactcgtttcttgtttgcagATAACCTCGCCGCAAACTTCAGCAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGG

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|110396928|gb|EC962635.1|EC962635
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|30297699|gb|CB974493.1|CB974493
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|110377199|gb|EC942256.1|EC942256
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|110370143|gb|EC934323.1|EC934323
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|30297767|gb|CB974561.1|CB974561
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|110389282|gb|EC954107.1|EC954107
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|110695590|gb|EE073783.1|EE073783
EST:     CTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: CTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|30297878|gb|CB974672.1|CB974672
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|34320115|gb|CF372869.1|CF372869
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGNCAATTTCAGCAGGGAATTGNCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|34363050|gb|CF404635.1|CF404635
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|22014004|gb|BQ799038.1|BQ799038
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|22012463|gb|BQ797497.1|BQ797497
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|110703836|gb|EE081029.1|EE081029
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
EST: gi|22015218|gb|BQ800252.1|BQ800252
EST:     GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAG                         ATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA
genomic: GCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgtt ... gtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgataatttgggataagaaggtttaacatttacttcaatttgtgtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG
                      gtttaac  putative branch site (score: 3)
                       tttaacatttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacaacttaccattgactcgtttatggatacttaaaggaatgtttttgataatttgggataagaaggtttaacatttacttcaatttgtgtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - cttacca
- - - - - - - - - - - - - - - - - aaaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataagaa