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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttcttctaataattttctacaatattttatttcttttgttcag

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 7
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttcttctaataattttctacaatattttatttcttttgttcag
|||||| ||||| |||||||||||||| ||||| || || ||||| ||||| |||||||||||| | ||||| |||||  | |  |  | |||   || ||||||| |||      |  | || |||  |    |  |  |  |  || |||  | |   |||  |||
AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAGgtagtgtcat--tgtgacagtttaatttttatttatttgtacttttt-tttggtgcggtgctgattgatcatctttgttattcattga-cag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM5G835213_T01 (Zea mays), 5'ss of exon 8
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttcttctaataattttctacaatattttatttcttttgttcag
|||||| |||||||||||||| ||||| || || || || ||||||||||| |||||||||||| | || || |||||  | |   | ||   |    |  || |   ||   | ||   | | ||    ||  |  ||     |  ||| | |||  |  |   |||
AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgccattatttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 7
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttcttctaataattttctacaatattttatttct-tttgttcag
|||||| ||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| ||||||||||| |   |||     | ||||  ||| ||  |||   |   || |  | |  || | ||  ||||     | |||||  ||   ||| |  ||
AGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAGgtccaaattt-----ggttttataatcttaatttttggtgtgacaaggctctttattatggttttgacttagatttttcttgaatttttgtag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 7
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttcttctaataatttt--ctacaatattttatttcttttgttcag
|||||| ||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| || ||||||||             | ||||  ||| ||  ||| | |    | |  | |  || | ||  ||||  ||  ||  |||| ||   ||| |  ||
AGATGCAAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAACCAACAGgt-------------ggttttagaatcttaattttctgtgtaacagggctctttatgatgtttttgacttaaaatttttcttgaatttttgtag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttct----tctaataattttctacaatattttatttcttttgttcag
 ||||| || ||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| |||   | | |  |  | ||| |  || | |  |||  |   ||   | |     || ||   || || ||| || ||||||| ||  | |||
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgactgtct--aactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaa-atcttatttcctt-atgcag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 7
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgt--tcttttttcttttgatttttcaat---ttttttttccaga-cagatattgtttcttctaataattttctacaatattttatttcttttgttcag
 |||||||| ||||||||||| || || |||||||| || ||||| ||||| |||||||| |||||||||||||||||  | |   ||||||  ||  | || |   ||||| ||  ||  ||   ||||||  |  |    |||      ||   || ||||| ||||  |||
GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatttg--cag

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|71890328|gb|DT039383.1|DT039383
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GACGCCCAAAGTGCTATCAATGACATAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG
EST: gi|33409957|gb|CF215584.1|CF215584
EST:     TGGATTTGTTTCTTTCCGCAATCAACAG                         GATGCCCAAAGTGCTATCAATGACATAACCG
genomic: TGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG
EST: gi|161716028|gb|FC065534.1|FC065534
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCA-TCAACAG                         GATGCCCAA-GTGCTATCA-TGACATAACCGGAA
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCGGAA
EST: gi|161705670|gb|FC055790.1|FC055790
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GATGCCCAAAGTGCTATCAATGACATAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG
EST: gi|110694202|gb|EE071104.1|EE071104
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GATGCCCAAAGTGCTATCAATGACATAAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAA-CCG
EST: gi|110696392|gb|EE072470.1|EE072470
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GATGCCCAAAGTGCTATCAATGACATAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG
EST: gi|351031018|gb|FQ439054.1|FQ439054
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GACGCCCAAAGTGCTATCAATGACATAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG
EST: gi|161707025|gb|FC055133.1|FC055133
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GATGCCCAAAGTGCTATCAATGACATAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG
EST: gi|77582239|gb|DV220083.1|DV220083
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GATGCCCAAAGTGCTATCAATGAC
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGAC
EST: gi|110357183|gb|EC920553.1|EC920553
EST:     AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG                         GACGCCCAAAGTGCTATCAATGACATAACCG
genomic: AGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttctttttt ... ttttgttcagGACGCCCAAAGTGCTATCAATGACATAACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttcttctaataattttctacaatattttatttcttttgttcag

- - - - - - - - - - - - - - - - - - -  AAGAGG