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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttttgattgcttcagtattgcataattgttctaagttaatggctctcctttggaacatatcacttgcctgtgatgaaatgcttcatgttgatg...

Basic information

species Vitis vinifera
transcript Vv18s0001g13370.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 5'ss of exon 5
AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttttgattgcttcagtattgcataattgttctaagttaatggctc-tcctttggaacatatcacttg-------cctgtgatgaa-atgcttcatgttgatg----------------------------------------------
 ||||||||  ||||||||||| ||||||| ||||||||||||||||| || || || |||||  |||||  ||| || ||||| || || || || | ||||| | | ||||||  ||  |  |  |    |  || ||||| ||     | |   ||   | |  | | |||       ||| |||  || |    |  | || ||                                               
TAGGGATCGCAGGGAACTGGAAAATATTATATTCAAGCTTTTTGAAAGACAGCCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatat-tcttgatttatttggcgtctc----tatttttaagtgaaaaaaacattggttaagatactttatttgtggtgttcctatgaacaacaaatattttattcattactctcaatggttgctttgtgattgtttgtgcttcgttttatgcag

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G049091_T01 (Zea mays), 5'ss of exon 5
AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtat------gtcttttgattgcttcagtattgcataattgttctaagttaatggctctcctttggaacatatcacttgc-ctgtgatgaaatgcttcatgttgatg------------------
 |||||||||  |||  ||||| | ||||| ||||||||||||||||||||||| || |||||  |||||  ||| || ||||| || || || || | |||||       ||| ||   || |     | ||   |||   |||| | |||      | |      | ||||  |||    |||  |   |   ||||||| | |                   
TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgcatctctttcctgatatgtcagtgggaaatgcatctatgataagcaggttgcaactacatatatttcttctattgttctctgactgttcatgtggttattatttatgtctatacag

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G03030.1 (Glycine max), 5'ss of exon 5
AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttttgattgcttcagtattgcataattgttctaagttaa-tggctctcctttggaacatatcacttgcctgtgatgaaatgcttcatgttgatg-
||| ||||| || || ||||| ||||| ||||||||||| |||||||| || ||||| |||||||| || ||||| ||||||||||| ||||||||||| |||||  |||    | || |  | ||   |   ||||||   | |  ||  |||         |     ||   |   | |  | |  || |   ||| |  
AAGAGATCGGGGAGAGCTGGAGGATATAATGTTCAAGCTATTTGAAAGACAGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgcttttctgct-ctgccttttttttttggtgttctttttcacctgagtctagagaaatgctagcaacacactctttagaacactctac-cattgcttg

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G03070.1 (Glycine max), 5'ss of exon 5
AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttttgatt--gcttcagtattgcataattgttctaagttaatggctctcctttggaacatatcacttgc---ctgtgatgaa-atgcttcatgttgatg
||| ||| | || || ||||| ||||| ||||||||||| |||||||| || ||||| |||||||| || ||||| || |||||||||||||||||||| |||||  |||    |  | ||   | ||   |   || |||   | | | |     ||   ||| ||   |   ||   || |  |||| |    | ||| |    
AAGAGATAGGGGAGAGCTGGAGGATATAATGTTCAAGCTATTTGAAAGACAGCCTAATTGGGCCTTGAAACAGCTCGTTCAAGAGACAGATCAACCTGCAgtatgcttttctgctctgttttttttttttgttggtggtctttttaactagagt--ctagagaaaatgctagcagcacactcttttgaacacaaattatgat----

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|34543665|gb|CF511897.1|CF511897
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|110712491|gb|EE090172.1|EE090172
EST:     AACCTAATTGGGCCTTAAAGCACCTAGTCCAAGAAACGGATCACCCTGCG                         CAATTTT-GAAAGAGATCCTGA-CGAGCTCTGCGTGTACAATAAA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAA
EST: gi|30303404|gb|CB980198.1|CB980198
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTTTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|33410257|gb|CF215884.1|CF215884
EST:     AACCTAATTGGGCCTTAAGGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|110701992|gb|EE080196.1|EE080196
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|33408011|gb|CF213638.1|CF213638
EST:     AACCTAATTGGCCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|33407925|gb|CF213552.1|CF213552
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|45368167|gb|CK906526.1|CK906526
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|110414213|gb|EC980040.1|EC980040
EST:     AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|33410334|gb|CF215961.1|CF215961
EST:     AACCTAATTGGGCCTTAAGGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTCCAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|45770574|gb|CN006426.1|CN006426
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTTTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|34543741|gb|CF511973.1|CF511973
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|110713762|gb|EE089967.1|EE089967
EST:     AACCTAATTGGGCCTTNAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         N
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcag-
EST: gi|110713762|gb|EE089967.1|EE089967
EST:     AACCTAATTGGGCCTTNAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         N
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcag-
EST: gi|110702596|gb|EE081122.1|EE081122
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|34362773|gb|CF404358.1|CF404358
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
EST: gi|110363914|gb|EC927546.1|EC927546
EST:     AACCTAATTGGGCCTTAAAGCAGCTAGTCCAAGAGACGGATCAACCTGCG                         CAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA
genomic: AACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttt ... ttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtatgtcttttgattgcttcagtattgcataattgttctaagttaatggctctcctttggaacatatcacttgcctgtgatgaaatgcttcatgttgatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa