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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctgcttaaaactgcaaatgctgtacagatattttttgccctttgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG

Basic information

species Vitis vinifera
transcript Vv03s0038g01780.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 2
ttttctgcttaaaactgcaaatgctgtacagatattttttgccc-tttgcatgtcgttttagtttgt-tataattgacatttttcatttttg---tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG
        || ||| |   | ||   |      ||   || |   ||    || |  |  | | | | | || |||   ||| | |  ||||   ||   | ||||| || ||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||| |
-----catttgaaattttgattgtcatggcataatcaattactagttcagttgactctgcaatatatctctatttggtttttattacctttgctgttatctctagAACGGAACAAAAGACTCCATCAGTAAGCTTGTTGCTGACTTGAACAGTGCAAAATTGGAGCCTGATGTTG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 2
--ttttctgcttaaaactgcaaatgctgtacagatattttttgccctt-tgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG
        || ||   |   | ||    ||    |||||| | |     | ||   | | ||  | |  | |  || | |       | ||| ||   |  |||||||||| |||||||||||||| |||||||| ||||||||||||||||||| ||||||| ||||||| |
aaccactagcctattgcattacatagaatat---tattttctccttcaatacactgcctctttctctactttttttaaaaaaaaaattatttcttatctccagAATGGGACCAAAGACTCCATCAGCAAGCTTGTCTCTGACTTGAACAGTGCAACATTGGAGCCTGATGTTG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 2
-ttttctgcttaaaactgcaaatgctgtacaga-tattttttgccctttgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG
   |||| |    | |         |  | |||  ||| ||| | | ||   |    |     |||  | | |   | |    | |||| |  |   |  |||||||||| |||||||||||||| |||||||| ||||||||||||||||||| ||||||| ||||||| |
ccattctaccactagcctattgcattacatagaacattattttctccttcagtacactgcctctttacttttaaaaaaaaaaattatttcttatc--tccagAATGGGACCAAAGACTCCATCAGAAAGCTTGTCTCTGACTTGAACAGTGCAACATTGGAGTCTGATGTTG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 2
---ttttctgcttaaaactgca-aatgctgtacagatattttttgccctttgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG
     || || |    || ||  |||    |||   |    ||  | || || || ||  | || ||  || | |||  |  ||  | || |||||   | ||||| || ||||||||||| ||||| ||||||||| |||||||||||| ||||||||||||| ||||||| |
tgaaattttgatcgtcacggcttaatcaattactagttcggttgactctatgtatatc--tctatttgattcttattacc--ttacctttgttgttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCAAAATTGGAGCCTGATGTTG

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|110730538|gb|EE107734.1|EE107734
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|34545318|gb|CF513550.1|CF513550
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|30321676|gb|CD004938.1|CD004938
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110713056|gb|EE088645.1|EE088645
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110692798|gb|EE068468.1|EE068468
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|27580841|gb|CB003536.1|CB003536
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|352798567|gb|FQ480592.1|FQ480592
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|161721774|gb|FC070490.1|FC070490
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|27580521|gb|CB003216.1|CB003216
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110713655|gb|EE089776.1|EE089776
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|351015203|gb|FQ445487.1|FQ445487
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|351055931|gb|FQ453392.1|FQ453392
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|161719285|gb|FC068261.1|FC068261
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|351042327|gb|FQ442794.1|FQ442794
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|71855995|gb|DT005050.1|DT005050
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110687322|gb|EE064629.1|EE064629
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|33406430|gb|CF212057.1|CF212057
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|161715107|gb|FC064265.1|FC064265
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|71860392|gb|DT009447.1|DT009447
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|351038588|gb|FQ464454.1|FQ464454
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|294963826|gb|GW836701.1|GW836701
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|30321727|gb|CD004989.1|CD004989
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110684631|gb|EE062130.1|EE062130
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|351044839|gb|FQ449093.1|FQ449093
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|27578848|gb|CB001543.1|CB001543
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110705429|gb|EE082267.1|EE082267
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|294966365|gb|GW837616.1|GW837616
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110720871|gb|EE097170.1|EE097170
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|352790810|gb|FQ478533.1|FQ478533
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|56408461|gb|CX016713.1|CX016713
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|351036824|gb|FQ459346.1|FQ459346
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|71862083|gb|DT011138.1|DT011138
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
EST: gi|110721976|gb|EE097800.1|EE097800
EST:     TTCTTTGTCGGAGGAAATTGGAAGTGT                         AATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA
genomic: TTCTTTGTCGGAGGAAATTGGAAGTGTgtaagtactt ... tttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG
                        aattgac  putative branch site (score: 3)
                                tttttcatttttgttt  CT-rich tract
          ttttagtttgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctgcttaaaactgcaaatgctgtacagatattttttgccctttgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - -cttaaaa
- - - - - - - - -caaatgc
- - - - - - - - - - - - - - - - - - - -tgccctt
- - - - - - - - - - - - - - - - - - - - - - - -gcatgtc