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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatcatgcaaacattagatatagattttcgaggcttcttcaagtttcattagatgaatatttgattaatttagatcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA

Basic information

species Vitis vinifera
transcript Vv19s0014g04740.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 7
-----tgaatcatgcaaacattagatatagattttcgaggcttcttcaag---tttcattagatgaatatttgattaatttagatcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA
       ||  |   ||    || | ||   ||   || |      ||||   ||  ||| ||| | ||  || | |||||  |  ||| |    | |    || ||||||||| | || || |||||||| ||||| ||||| ||  |||  || ||||| ||||| || |||||||||||||| |||||||| || || || || |
agttactaactagtaaagttgtaaaaatct-ttcctgatgtcagaacaaggaattctatttgatca-tacgtgctcaattttca--atctctctgtca----tttcagTTTGCTTTACACTATTCATGGTCAACTGAAGCACGCGCTAGACAAGCCTTGGCAAATGTGTCTGCATTACTTCGTCCTGGAGGCATTTTTATTGGGACAA

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 6
-----tgaatcatgcaaacattagatatagattttcgaggcttcttcaagtttcattagatgaatatttgattaa----tttagatcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA
     |  |  || |    |||  ||| | ||| |    | |  ||| |  || |  |  || ||||| | |||     | |||      |     || |||  ||||||||||  ||||||||||||||||||| ||||| || || || |  || ||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| |
gcagttagactattc---tattcaatacaaattat----gttcattccatcttga--aagtgtatattggtttatactttctagtctgataaactttttaatgctgcagTTTGCATTGCATTACTCATGGTCTACGGAGGCCCGTGCCCGGCAAGCATTGGCTAATGTGTCAGCTTTACTTCGCCCAGGAGGCATTTTCATTGGAACAA

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 8
tgaatcatgcaa--acattagatatag--attttcgaggcttcttcaagtttcat-tagatgaatatttgattaatttagatcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA
  | | |  | |   ||||  ||| |   || |||    | |||| || ||  || | | |   || ||   || | |     || | ||  ||||||  ||||||||||  ||||||||||||||||||  ||||| || || || |  || ||||| ||||| ||||| |||||||  ||||||||||| ||||| ||||| |
gcagttagactattgcattgaatacaattatgttctttccatcttgaaattgtatgttggtttgtacttt-ctagtctg----ataaacttcttaaatgctgcagTTTGCATTGCATTACTCATGGTCTATAGAGGCCCGTGCCCGGCAAGCATTGGCTAATGTGTCAGCTTTACTTCACCCAGGAGGCATTTTCATTGGAACTA

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 6
tgaatcatgcaaacattagatatagattttcgaggcttcttcaagtttcattag--atgaatatttga-ttaatttaga---tcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA
    | |  |    |||   | | || | || |    |  | || ||   |      ||||  | | | ||  |||  |   |  | | ||  ||||||  ||||||||||  ||||||||||||||||||| ||||  || || || |  || ||||||||||| ||||| || || || ||||||||||| ||||| ||||| |
----ttacactcttattg--tctcgactctctacaaattatgaacttctttccatcttgaaagtgtaagttggtttctagtctgctgaactttttaaatgctgcagTTTGCATTGCATTACTCATGGTCTACAGAGGTCCGCGCCCGGCAAGCATTGGCCAATGTGTCAGCTTTGCTACGCCCAGGAGGCATTTTCATTGGAACTA

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G20650.1 (Arabidopsis thaliana), 3'ss of exon 6
tgaatcatgcaaacattagatatagattttcgaggcttcttcaagtttcattagatgaatatttgattaatttaga-tcatcacctgatta---aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA
    |  | |  || |   |||| ||  ||  ||  |  || || | |  |||| ||  || ||    | | || | | | ||  | |||    || | || ||||||||||||||||||||||| ||||||||||||| |||||||| |||||||| ||||| ||||| |||||||||||||||||  |||| |||||||| |
---gtttttcccac-tggcatattgaagttgtagcgtggttgaaatatagttagttgtgtagttatggattctaaagttaccaagtcattgtttaactgtgtagTTTGCTATGCATTACTCATGGACTACTGAGGCACGTGCACGACGAGCTTTGGCAAATGTTTCAGCTTTACTTCGTCCAGGAGGTGTCTTTATCGGAACAA

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|71882642|gb|DT031697.1|DT031697
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGC
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGC
EST: gi|351017257|gb|FQ435609.1|FQ435609
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|351029176|gb|FQ435376.1|FQ435376
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|352786282|gb|FQ478893.1|FQ478893
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|71889110|gb|DT038165.1|DT038165
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|349809402|gb|FQ411900.1|FQ411900
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|349829213|gb|FQ419745.1|FQ419745
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|349814559|gb|FQ399199.1|FQ399199
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|351041305|gb|FQ447432.1|FQ447432
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|349823220|gb|FQ400199.1|FQ400199
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|71888703|gb|DT037758.1|DT037758
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|71884044|gb|DT033099.1|DT033099
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|351046268|gb|FQ442646.1|FQ442646
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACAACATGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|349809129|gb|FQ398926.1|FQ398926
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|349824512|gb|FQ413179.1|FQ413179
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|351056793|gb|FQ443420.1|FQ443420
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
EST: gi|351038453|gb|FQ464319.1|FQ464319
EST:     TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAG                         TTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG
genomic: TGGACAGAGTTTTGGAAGATGATGCACCTTTCGATATTTGCAGTTGCCAGgtgagtgatt ... aattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcattagatgaatatttgattaatttagatcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA
     ttagatgaatatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatcatgcaaacattagatatagattttcgaggcttcttcaagtttcattagatgaatatttgattaatttagatcatcacctgattaaattttgcagTTTGCTATGCATTACTCATGGTCTACTGAGGCACGGGCACGACGTGCTTTGGCCAATGTATCAGCATTACTTCGTCCAGGAGGCATCTTCATCGGAACGA

- - tcatgca
- - - - - - - - - - - - - - - - - -cttcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcacc