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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTCTCAAGCAGATTGGAATGTTTACTTTCACAGGATTGAACACCGCTCAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacatcaatccttcacttgattatatacaagaaggttcaattttcttttgaaaaggaaaaacaaaattacctctaatctctctaacaatcaaatg...

Basic information

species Vitis vinifera
transcript Vv04s0008g03770.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 11
ACATTCTCAAGCAGATTGGAATGTTTACTTTCACAGGATTGAACACCGCTCAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacatcaatccttcacttgattata--tacaagaaggttc----aattttcttttg-aaaaggaaaaacaaaattacctctaatctctctaacaatcaaatg-------------------------------------------------------------------------------------
||||  | |||||||| |||||||| |||||||| ||  | ||||  | ||||||||| |||||||   | || |||||| | |||||||||||||||||||||     | | |     | |     | |    |||  | |||      || |   | || |     | |||| | || |  | || | ||| ||||| | | |||                                                                                     
ACATCATTAAGCAGATCGGAATGTTCACTTTCACTGGGCTCAACAGTGATCAAGTGGCTTTCATGAGGCAGGAATACCACATTTACATGACATCTGATGGgtaattgtctaatttagctattgtgcaacactcgcaattatgtttgtatgatctaagtctgcagttatacaaactatataatttttagt-tctataacagt-agatgatctatcttactgtttctatggtagtttcctttgctaaatgttcctttttagctcatctttacaagccaaatatttctcttgcag

upper sequence: Vv04s0008g03770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S132_95V6.1 (Physcomitrella patens), 5'ss of exon 12
ACATTCTCAAGCAGATTGGAATGTTTACTTTCACAGGATTGAACACCGCTCAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacatcaatccttcacttgattatatacaagaaggttcaattttcttttgaaaaggaaaaacaaaattacctctaatctctctaacaatcaaatg------
|| |||| ||||||||||||||||| |||||||| ||||||||||   ||||||| |  |||||||||    | || ||| |||||||||| || |||||||    |||| || | |    || || |    |  |||   | | ||| |  |   |   |  |  |||| ||  || | | || |  ||        ||      
ACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgt----acataaaacatcacatttatcactatcctgaaa--ttattttccactacgatctgcgatccaaatttggctttcacctgtacaagtgatttttgtactag
















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|110399226|gb|EC965723.1|EC965723
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|30306097|gb|CB982891.1|CB982891
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|30131422|gb|CB916761.1|CB916761
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|45770794|gb|CN006646.1|CN006646
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|352776804|gb|FQ472691.1|FQ472691
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATTTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|110388301|gb|EC953036.1|EC953036
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|110372200|gb|EC936351.1|EC936351
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|33402663|gb|CF208290.1|CF208290
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|30306178|gb|CB982972.1|CB982972
EST:     CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
EST: gi|29783123|gb|CB349091.2|CB349091
EST:     CTAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGG                         GAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA
genomic: CAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacat ... tatcacgcagGAGGATCAGCATGGCAGGTCTGAGCTCCAAGACAGTCCCTCATCTTGCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTCTCAAGCAGATTGGAATGTTTACTTTCACAGGATTGAACACCGCTCAAGTGGCCTTCATGACCAAAGAGTACCACGTCTACATGACATCTGATGGgtaagaacatcaatccttcacttgattatatacaagaaggttcaattttcttttgaaaaggaaaaacaaaattacctctaatctctctaacaatcaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa