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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgtcttttgtttaattagacttggatttcattttgtttttcaatgtttattctttatttttaacaccatgttttcatatgaattgtgcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAACACCAGGGCTGATGTTGTGAATGAAAAGGATGACAAAATGGTCTCCAGTA

Basic information

species Vitis vinifera
transcript Vv01s0150g00590.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G24350.2 (Glycine max), 3'ss of exon 7
gtgctgtcttttgtttaattagacttggatttcattttgtt--tttcaatgtttattctttatttttaacaccatgttttcatatgaattgtgcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTT-------GAAGAGTTTGGTTGAGAACACCAGGGCTGATGTTGTGAATGAAAAGGATGACAAAATGGTCTCCAGTA
   |   |  | || |||   ||  |     ||||||  ||   || | | |  |        |  |||  |  |   |  |   |   |        | |||||||||||||||| |||||||| ||||||||       ||  |  ||| |  | ||||  ||| |     |  |||    | |||   |    ||||         
-atccaacgatggtgtaaactgatctct-cctcatttaattaccttaactatgaaaaggactgtaataatgcagtacatctaatcggtgtacatgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGATGAAAAACATGAGGACATGATTCATGACGATAGAGGTCAAGCTGATGGAG-------
















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|110382187|gb|EC938718.1|EC938718
EST:     CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG                         GCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
genomic: CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
EST: gi|110712685|gb|EE087945.1|EE087945
EST:     CGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTNGAAAAG                         -CATTGAAGTCAGGGCAGCTTTCAACAAATTTGAAGAGTTTGGTTGAGAA
genomic: CGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAA
EST: gi|110710820|gb|EE087309.1|EE087309
EST:     CCGCAATTGTGAATTCACAGACTCTTGAAGAGGGTGCAAGGCTTGAAAAA                         GCATTGAAGTCAAGGCAGCTTCCAACAAATTTGAAGAGTTTGGTTGA-AAC
genomic: CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
EST: gi|110707870|gb|EE084759.1|EE084759
EST:     CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG                         GCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
genomic: CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
EST: gi|32269037|gb|CD718196.1|CD718196
EST:     CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG                         GCATTGAAGTCA
genomic: CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCA
EST: gi|110701540|gb|EE079224.1|EE079224
EST:     CGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTTGAAA-G                         GCATTGAAGTCAAGGCAGCTTCCAGCAGATTTGAAGAGTT-GGTTGAGAA
genomic: CGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAA
EST: gi|110388633|gb|EC953405.1|EC953405
EST:     CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG                         GCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
genomic: CCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAAC
EST: gi|110702872|gb|EE079225.1|EE079225
EST:     CGCAATTGTGAATTCACAGACTCTTGAAGAAGTTGCAAGGCTTCGAAA-G                         GCATTGAAGTCACGGCAGCTTCCAGCAGATTTGAAGAAGTTGGGT-GAGA
genomic: CGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAAGgtgctgtctt ... gcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGA-GTTTGGTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtttattctttatttttaacaccatgttttcatatgaattgtgcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAACACCAGGGCTGATGTTGTGAATGAAAAGGATGACAAAATGGTCTCCAGTA
                ttttaac  putative branch site (score: 2)
     ttattctttattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgtcttttgtttaattagacttggatttcattttgtttttcaatgtttattctttatttttaacaccatgttttcatatgaattgtgcttgggtagGCATTGAAGTCAGGGCAGCTTCCAGCAGATTTGAAGAGTTTGGTTGAGAACACCAGGGCTGATGTTGTGAATGAAAAGGATGACAAAATGGTCTCCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG