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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgctagacgacaaatgatagttaatc...

Basic information

species Vitis vinifera
transcript Vv04s0008g01970.t01
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 26
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaa--atcaatc--gcttttg-gtttctacttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgctagacgacaaatgatagttaatc
|||||  |||||||||||||||||||||||||| |||||||| |||||||||||||| ||||  ||  |||| ||||| || | ||||||||||||  ||||||  || | ||  ||| ||| | |||| ||   |   |    | |  |  |    ||||  | |  ||   || |  |      | | || || |   | |  
TCTCAATGAAAAGTCTGATGTCTACAGCTATGGCATTGTTCTGCTTGAGCTGCTGACCGGAAAAAAGCCAGTGGACAACGAGTGCAATCTCCATCACTTGgtaactatgattcatgctcttgtgattcttctgttaatctgtcattttcttcagcttattttactttgga---ttctggtagccctcaataattgctgaatga--

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GRMZM5G809695_T03 (Zea mays), 5'ss of exon 25
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaat------caatcgcttttggtt-tctacttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgctagacgacaaatgatagttaatc
 ||||  || |||||||||||||||||||| || || ||||| || ||||||||||| || | |||  |||| ||||| || | ||||||||||||  |||||| |      || || | |    || || | ||  |     |       |   |||  |||| |||       |||  || | || |        ||| ||  | 
CCTCAACGAGAAGTCTGATGTCTACAGCTACGGCATCGTTCTGCTGGAGCTGCTGACCGGCAAGAAGCCAGTGGACAACGAGTGCAATCTCCATCACTTGgtaactattcttcagtctcctgcatttgtcgagttagaagccggaagtcgcttccttctcttta-catcg----ctttggattccag-cagtgctcaataattgct-

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA17G34380.2 (Glycine max), 5'ss of exon 25
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgctagacgacaaatgatagttaatc------
|||||| || ||||||||||| ||||| || || |||||| |||||||| |||| |||||||||||||| || |||||||||||||| ||||| |||||||| | |  |   |      |||| |  |  || | || |   |  ||   |              | ||||||||| |   |         |  | |         
TCTCACTGAGAAGTCTGATGTGTACAGTTACGGTATTGTTTTACTTGAGTTGCTAACTGGAAGGAAAGCTGTTGACAATGAATCCAACCTCCACCATCTGgtgagttcacaacac---atttcaatatacacgtgcgcg---agcgagcacacacacatgcagacagttttttatgtttagccttggtcttttatgagctttaggt

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA14G11220.2 (Glycine max), 5'ss of exon 26
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtgtctattgaattccatttagcatgaga--aattttttatgctagacgacaaatgatagttaatc-
|||||| || ||||||||||| ||||| ||||| |||||| |||| ||| |||| |||||||||||||| || |||||||||||||| ||||| ||||| |||| |   |  ||     |||  |    | | | ||||| ||   |  | |     |  |        | |||||||      |  | ||  |  ||  || 
TCTCACTGAGAAGTCTGATGTGTACAGTTATGGTATTGTTTTACTCGAGTTGCTAACTGGAAGGAAAGCTGTTGACAATGAATCCAACCTCCACCATCTTgtaagt---ttactacaaatttgaatacaagcgtgcgtgtatacacacatgctgacggattagccttggtcttttatgaacttaggtatatatttattgctct

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA04G05910.1 (Glycine max), 5'ss of exon 18
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaat---caatcgcttttggtttcta--cttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgc-tagacgacaaatgatagttaatc
 ||||| || ||||||||||| || |||||||| |||||  | |||||||| ||||||||||||||||| || ||||||||||| || ||||| |||||||| | |   | |  |  | ||| || ||    | |    ||    || |  ||   | |    ||    || |||||||||   | |||     | |  | |||  
CCTCACTGAGAAGTCTGATGTGTATAGCTATGGTATTGTATTGCTTGAGCTCCTGACTGGAAGGAAAGCTGTTGACAATGAATCAAACCTCCACCATCTGgtgagtcttctagtgtgtctggcttgtaggtctcacaactcacaactttcaaagcacct----caatgaaatttttttatgtacaaacgtacttttaggggtaa--

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 27
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtg---tctattgaattccattt--agcatgagaaattttttatgctagacgacaaatgatagttaatc
 ||||| || ||||| ||||| || |||||||| || ||  | |||||||| || ||||| |||||||| || ||||| ||||| || |||||||||||||| | ||      | |  || |    |  |    ||      |  || | |  |||||   |   |  |  | || ||    | |    |||| ||  |||    
CCTCACTGAGAAGTCCGATGTGTATAGCTATGGTATCGTATTGCTTGAGCTTCTAACTGGGAGGAAAGCTGTTGACAACGAATCAAACCTCCATCATCTGgtgagtcttctagtgtgtgtctggtttgtaggtgtcacaaatttcatagcaccccattggaaaagtatgtgacttgttggattggct--caaacgaatgttt---

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 26
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgctagacgacaaatgatagttaatc
 ||||| || || || ||||||||||| |||||||| || || |||||| || | ||  |||||||||| || ||  | |||||||||||||| ||||||||   |   ||  | |||  |    ||   | || |   ||| || |  || | |  | |    |  || |||    |     ||  |    ||      
GCTCACTGAGAAATCCGATGTCTACAGTTATGGAATAGTCCTTCTTGAGTTGTTAACCCGAAGGAAAGCCGTTGATGACGAATCCAATCTCCACCATCTGgt---ttgttctttcttgcctatctctctcagctgc---tctgtttaggtcaagtccgta----atcttgttttcattgattcacttacatcag------

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|351032632|gb|FQ462346.1|FQ462346
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|352786698|gb|FQ479905.1|FQ479905
EST:     CGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCTATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351043857|gb|FQ452651.1|FQ452651
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTAATCCAAA-CAACCA-CAATGCTGTGATGGAGACTGTTGATCCTGA
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTA-TCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGA
EST: gi|351054408|gb|FQ450491.1|FQ450491
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351047766|gb|FQ458986.1|FQ458986
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351039249|gb|FQ457924.1|FQ457924
EST:     CGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCCAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351048041|gb|FQ441213.1|FQ441213
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351048270|gb|FQ442240.1|FQ442240
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351045309|gb|FQ451757.1|FQ451757
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|352790304|gb|FQ481503.1|FQ481503
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|352798821|gb|FQ478456.1|FQ478456
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351035908|gb|FQ463753.1|FQ463753
EST:     CGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|351048645|gb|FQ448919.1|FQ448919
EST:     TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGATGGAGACTGTTGATCCTGAT
EST: gi|352786929|gb|FQ481304.1|FQ481304
EST:     CGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTG                         ATCCTATCCAAA-CAGCCAACAATGCTGTGAT
genomic: TGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaat ... cttgccttagATCTTATCCAAAACAACCAACAATGCTGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtgtctattgaattccatttagcatgagaaattttttatgctagacgacaaatgatagttaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacgacaa