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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgagtcttttgaccactaattgagtgctttatattgattttaagtacttaccagcccacaatgatgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC

Basic information

species Vitis vinifera
transcript Vv04s0044g01480.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 4
tttgagtcttttgaccactaattgagtgctttatattgattttaagtacttaccagc--ccacaatga-tgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC
  | |   |||| |  | ||  |    |      | ||||||      ||| | |         ||   | |  |   || |  || |  |   | |||  |||||  | || || ||||| ||||| || ||||| || ||||| |||||||| ||||| || ||||||||  | ||||||||||||||||| ||| |||| 
--tcaagattttaattaatagatagccgtacaccactgatttgccagccttgctaataattgtcataccttatctgaatttttattttatgacctgaat-cagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA

upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 4
tttgagtcttttgaccactaattgagtgctttatattgattttaagtacttaccagcccacaatgatgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC
||  ||||| | |   | |  |||  |   ||  || |       |   | |           | ||  | |||||  || |||||||     | | ||| ||| |||||||||| || ||||| |||||||||||  || || ||||||| ||| | || ||||||||| | |||||||||||||||||  ||||||||
ttacagtctatagtatagtttttgtttcacttgcatggtcaccgtgctatcattttgtatgtgtcattgagtagctcatggttgtgagaggacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCATTAGCTTTGTTACATGAAGGCAAAATTGTATTGGGTGTCTTGGCTTGTCCAAATCTTCCACTGGCATCC

upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 4
tttgagtcttttgaccactaattgagtgctttatattgattttaagtacttaccagcccacaatgatgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC
||  ||||| |     |||  |||  |   ||  || | |  |  |   | |           | ||  | |||||  || ||||||| |   | | ||| ||| |||||||||| || ||||| ||||| |||||  | ||||||||||| ||||| || ||||||||| | ||||||||||| |||||  ||||||||
ttacagtctatattatactttttgtttcacttgcatggttactgtgctatcattgtgtatgtgtcattgagtagctcatggttgtgagatgacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGGCAAAGTTGTATTGGGTGTCTTGGCTTGTCCAAACCTTCCACTGGCATCC

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|351054641|gb|FQ456838.1|FQ456838
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351038015|gb|FQ460757.1|FQ460757
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351042217|gb|FQ442684.1|FQ442684
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351057082|gb|FQ450789.1|FQ450789
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351056977|gb|FQ443604.1|FQ443604
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351039598|gb|FQ461465.1|FQ461465
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGTTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|352794444|gb|FQ481676.1|FQ481676
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|122688865|gb|EC927133.1|EC927133
EST:     ATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: ATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351038675|gb|FQ464541.1|FQ464541
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|352793784|gb|FQ481938.1|FQ481938
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|352786467|gb|FQ479076.1|FQ479076
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
EST: gi|351042941|gb|FQ451235.1|FQ451235
EST:     GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGG                         TTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG
genomic: GGTTCTAATGGCCAACACTGGGTTTTGGATCCTATTGATGGCACCAAAGGgtgagcttgg ... tttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttaccagcccacaatgatgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC
                                           ttttt  CT-rich tract
                                           tttttaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgagtcttttgaccactaattgagtgctttatattgattttaagtacttaccagcccacaatgatgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC

- - - - - - - ccactaa
- - - - - - - - - - - tgagtgc
- - - - - - - - - - - - - - - - - - - - - - - - cttacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cccacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtg