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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaagtctattaaatagagatgtagtcattgttttatatctcttacaaaaaggaagatttttttttttttttttaatgtagtttaagtttcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCAAGATCAACCTCATTGGCAAGGACCTTATCACCTCGAGTTTTGGAAAGTC

Basic information

species Vitis vinifera
transcript Vv11s0016g00350.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA17G04990.1 (Glycine max), 3'ss of exon 20
--tctaagtctattaaatagagatgtagtcattgttttatatctcttacaaaaaggaagatttttttttttttttttaatgtagtttaagtttcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCAAGATCAACCTCATTGGCAAGGACCTTATCACCTCGAGTTTTGGAAAGTC
  |    ||    | | |||   |  | |  || |||| |   | |  |   |       |  |  ||| | | | ||      ||  | | |  ||  |||||||||||| || |  | || || ||||||||||| ||||| || |||||||||||||| |||||||| |||||  | || ||  ||||||| |||| ||
tattgtcgtaccatgattaggatttaattttttattttgtcgatttagctttagtatcactaatactttatgtctctatcaatattggaatatggtt--cagGAGCATCTACGAAGACTTCTAAGAGGTCAAGCCTCTCTATTTGAATGGTCAAGATCAACTTCATTGGCGAGGACACTGTCTCCAAGAGTTTTAGAAAATC

upper sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: AT1G73430.1 (Arabidopsis thaliana), 3'ss of exon 20
--------------------------------------------------------------------------tctaagtctattaaatagagatgtagtcattgttttatatctcttacaaaaaggaagatttttttttttttttttaatg--tagtttaagtttcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCAAGATCAACCTCATTGGCAAGGACCTTATCACCTCGAGTTTTGGAAAGTC
                                                                          | |   | ||   | |  ||||||  |   |  || |  | |||| |      || || |||  |   ||| |  |||      | | |      |    |||| ||  | ||  | |||||||| |||||||| ||||| || |||||||| || ||||||||  | ||||||||| | ||||||||||||||||| ||||
gttagttcctcaacattcaagtctacttcgtatgatagatctaattttttctttatcgccttttgagaggttcttatctttatacagatttcagatgtttttcctccttca-gtttctttctttgttgatgactttgctaactttctccaataatccatgtcaaaaatgtggttagGAACACTTGAGGAGGATACTTAGAGGTCAAGCGTCACTTTTTGACTGGTCTAGGTCAACCTCTCTAGCAAGGACCCTGTCACCTCGAGTTTTGGAGAGTC
















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|110701225|gb|EE078568.1|EE078568
EST:     ATATAGAATTTTCAGTCACACACAAAGAACTTGATTTCTCTCATTTACTG                         GAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCA
genomic: ATATAGAATTTTCAGTCACACACAAAGAACTTGATTTCTCTCATTTACTGgtttgtacct ... tcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCA
EST: gi|349827691|gb|FQ422559.1|FQ422559
EST:     CACACACAAAGAACTTGATTTCTCTCATTTACTG                         GAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCA
genomic: CACACACAAAGAACTTGATTTCTCTCATTTACTGgtttgtacct ... tcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaaaggaagatttttttttttttttttaatgtagtttaagtttcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCAAGATCAACCTCATTGGCAAGGACCTTATCACCTCGAGTTTTGGAAAGTC
                          ttttaat  putative branch site (score: 3)
                                           tttcattt  putative PPT
            attttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaagtctattaaatagagatgtagtcattgttttatatctcttacaaaaaggaagatttttttttttttttttaatgtagtttaagtttcatttacagGAGCATCTAAGACGCATACTTAGGGGTCAAGCCTCACTATTCGACTGGTCAAGATCAACCTCATTGGCAAGGACCTTATCACCTCGAGTTTTGGAAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - aaataga
- - - - - - - - - - - - - - - - - - - - - - -acaaaaa