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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttccattgtatactaaaccatccgatatcattcttccgattgtctgctatctgtaaggctttgcatttagtttgccctttattatcttgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG

Basic information

species Vitis vinifera
transcript Vv13s0019g01070.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g74190.1 (Oryza sativa), 3'ss of exon 7
cttttccattgtatactaaaccatc--cgatatcattcttccgattgtctgctatctgtaaggctttgcatttagtttgccctttattatcttgtgt----atcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG
    |  | | |  |   || ||||   || |    | ||   |  ||  |     |    |  |||| | |  ||||||    |  | |  | |||    |||||| | || || ||||| ||||||||| ||||||||||||| |||||||||||||| || ||  |||| ||| | ||| | || |||| | | |||||||| 
---ctaaactctgaagctaatcatcgttgacactgatattttaaccgtgggtagcatt---gtttttgtaatctgtttgctgactggtctgctatgttggaatcagCCTGCACGCCCCAAATCAGAAACTACGGGAAACAATTGTTCCAAGTGCAAAGTCATATCCCTTGGAGGCACTAATGGATGACTGCAAGAATTACTTCCTC

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 7
cttttccattgtatactaaaccatccgatatcattcttccgattgtctgctatctgtaaggct-ttgcatttagtttgccctttattatcttgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG
 ||      ||| ||  |   ||       |  |  |      | || | |   | || |  | ||  | |  ||  |   | | || |  | || ||||||||||||||||| ||||||||||| ||||| |||||||| ||||||||||| ||||||||  |||||||| ||||||  || ||||| || ||||| | |
-ttggttcctgtgtataatttcagatagctttttaatggattctttcagatgcatatatgcatattatagtatgtgagttttcttttgtactttgcatcagCTTACATGCTCCTAACCAGAAACTTAGGGAGACAATTGTTCCAAGTGCAAAATCCTACCCATTGGATGCACTTATGAGTGACTGCAGAGAATACTTTCAG

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G07450.1 (Glycine max), 3'ss of exon 7
-----cttttccattgtatactaaaccatccgatatcattcttccgattgtctgctatctgtaaggctttgcatttagtttgccctttattatcttgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG
       ||| | |  | |  | ||   || || | | ||     |  | |||   |  || |     | | || |   ||  | ||| |  | |   | |||||| |||||||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| || ||||||||| ||||||  |||||||| || ||||| | |
agcattattttcttcctgtgtttaatt-tcagagagcttttaaatggat-tctttcagatgcatattctagtatgtgaattttcttttgtacttt---gcatcagCCTACATGCTCCTAACCAGAAACTTAGGGAGACAATTGTTCCAAGTGCAAAATCCTATCCACTGGATGCACTTATGAGTGATTGCAGAGAATACTTTCAG

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 7
cttttccattgtatactaaaccatccg-atatcattcttccgattgtctgctatctgta-aggctttgcatttagtttgccctttattatcttgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG
  ||   ||  | ||  | |   || | |||    || ||  ||||  |   || | |  | | | |  | |   | |     |  |  | | ||| |||||||||||||| ||||| ||||  || ||||| | ||||||||||||||| ||| | || || ||||| |||||||||||||||||  | || |||||||  
--ttctaatcctgtaacatatgctctggatagggctcgtctcattgattttcatgtttctatgttatttactcgttcttgagctgttcttttggtgaatcagCTTACATGCGCCAAATCAGAGCCTCAGGGAGAAAATTGTACCAAGTGCCAAGGCTTATCCGCTGGAAGCAATTATGAAGGATTGTCGTGATTACTTCCAA

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|351046512|gb|FQ453128.1|FQ453128
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|352794375|gb|FQ481606.1|FQ481606
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|351048097|gb|FQ442067.1|FQ442067
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|352786528|gb|FQ479735.1|FQ479735
EST:     ACAATTAGGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|351038424|gb|FQ461116.1|FQ461116
EST:     ACAATTAAGAAGTTGGCTTCTTGCAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|351054685|gb|FQ462715.1|FQ462715
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|351035218|gb|FQ458575.1|FQ458575
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|71874359|gb|DT023414.1|DT023414
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|351032693|gb|FQ462407.1|FQ462407
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|351044866|gb|FQ449120.1|FQ449120
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|352795590|gb|FQ480178.1|FQ480178
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|352793767|gb|FQ481122.1|FQ481122
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
EST: gi|77585559|gb|DV221873.1|DV221873
EST:     ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAG                         CTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA
genomic: ACAATTAAGAAGTTGGCTTCTTACAAACTTCAATCCACATTGGCTATCAGgtgcgtaatt ... tgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgctatctgtaaggctttgcatttagtttgccctttattatcttgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG
                                ccctttattatctt  CT-rich tract
                                   tttattatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttccattgtatactaaaccatccgatatcattcttccgattgtctgctatctgtaaggctttgcatttagtttgccctttattatcttgtgtatcagCTTACATGCTCCAAACCAGAAACTAAGGGAAACAATTGTACCAAGTGCAAAGTCCTACCCTCTGGATGCAATTATGAAGGATTGCAGGGACTACTTCCTG

- -ttccatt
- - - - - - - - - -accatcc
- - - - - - - - - - - - - - - - -ttcttcc
- - - - - - - - - - - - - - - - - - - - - -tgtctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttgca