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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttgaagtgttggggatttgaattgtttcaattgatgattatactctaatactctttgccattggggtaattggctttttataatcttcttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGTATCGGTAAGAACTCTCACATCAAAAGAGCGATCATCGACAAGAATGCTC

Basic information

species Vitis vinifera
transcript Vv12s0057g01480.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 7
atgttgaagtgttgg-ggatttgaattgtttcaattga--tgattatactctaatactctttgccattggggtaattggctttttataatcttcttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGTATCGGTAAGAACTCTCACATCAAAAGAGCGATCATCGACAAGAATGCTC
 | |     ||     | || |||||    | ||| |   ||| | || |   |    |  | | |   |    ||||| ||| |   ||| |  ||||||||||||| ||||| | | |||||||    || ||||| ||||||||||||||||| || | ||||||||| |||||||| || || ||||||||||||||||
-tataagtttgcaattgcatgtgaataaggttaataggattgactttagttagactagcagtcctaactgcaacattggttttctg--atcgttgtgttccagACGGAGGCTGATAAGAGGTTTCTGGCTGCTAAAGGCAGTGTTCCAATTGGTATAGGCAGGAACTCTCATATCAAAAGGGCAATTATCGACAAGAATGCTC

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 7
atgttgaagtgttgg-ggatttgaattgtttcaattga--tgattatactctaatactctttgccattggggtaattggctttttataatcttcttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGTATCGGTAAGAACTCTCACATCAAAAGAGCGATCATCGACAAGAATGCTC
 |||     ||     | || || ||    | ||| |   ||  | || | | |    |  | | |   |    ||||| ||| |   ||  |  ||||||||||||| ||||| | | |||||||    || ||||| ||||||||||||||||| || | ||||||||| |||||||| || || || |||||||||||||
-tgtgagtttgcaattgcatgtggataagattaataggattggctttagtttgactagcagttctaactgcaacattggttttctg--attgttgtgttccagACGGAGGCTGATAAGAGGTTTCTGGCTGCCAAAGGCAGTGTTCCAATTGGTATAGGCAGGAACTCTCATATCAAAAGGGCAATTATTGACAAGAATGCTC
















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|33409675|gb|CF215302.1|CF215302
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|30125071|gb|CB910410.1|CB910410
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|110688952|gb|EE068088.1|EE068088
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|110423492|gb|EC989838.1|EC989838
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|110378789|gb|EC943937.1|EC943937
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|352777901|gb|FQ466954.1|FQ466954
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTTTGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|71889085|gb|DT038140.1|DT038140
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|352776770|gb|FQ472657.1|FQ472657
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|32245488|gb|CD711307.1|CD711307
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|83275545|gb|DV939553.1|DV939553
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|32245967|gb|CD711786.1|CD711786
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|33403137|gb|CF208764.1|CF208764
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT
EST: gi|30253354|gb|CB970905.1|CB970905
EST:     AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG                         ACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGCGTTCCAATTGGT
genomic: AGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAGgtagtactaa ... cttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaatactctttgccattggggtaattggctttttataatcttcttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGTATCGGTAAGAACTCTCACATCAAAAGAGCGATCATCGACAAGAATGCTC
 ctctaat  putative branch site (score: 3)
                                         tcttcttgttcc  putative PPT
                                tttttataatcttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttgaagtgttggggatttgaattgtttcaattgatgattatactctaatactctttgccattggggtaattggctttttataatcttcttgttccagACGGATGCTGACAGGCGGTTTCTAATGGCAAAAGGTAGTGTTCCAATTGGTATCGGTAAGAACTCTCACATCAAAAGAGCGATCATCGACAAGAATGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - gttgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcttt