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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattggattttgaatttcttgtattttgtatcaatttgtggcgttttctttggtaatgcag

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 1
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattggattttgaatttcttgtattttgtatcaatttgtggcgttttctttggtaatgcag
||| || ||  | |  |        |  |||||    || |||||| ||||||||||| |||| || |||||||| || |||||||||||||| ||||||||       |||||| | |||   || |||  |  ||||  |  |  ||  ||||   || ||   |    | || |     |   | ||
CGACCCCGCCCCTCCCCACCTCCATGGCCGCATCTCCTTCCACCGCCTCAACATCAAGAACGACTCCAGGCTCGAGGGCCTCATCAAGATGGCCGATCTGgtct----ctccctc-tctctccctcctgctctcaatttcaatctcatttcatttctgat-aacacgccttgattccggatctg-cgtag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G167872_T01 (Zea mays), 5'ss of exon 1
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattggattttga---atttcttgtattt-tgta--tcaatttgtggcgttttctttggtaatgcag--------------------------------------------------------------
||| || ||  | |  |      | |  |||||    || |||||| ||||||||||| | || || |||||||| || |||||||||||||| ||||||||  | |  | |  |     ||||||  |     |||||      ||   || || |  | ||  ||||| ||       | |      | | | |                                                              
CGACCCCGCGCCGCCGCACCTCGCGGGGCGCATCTCCTTCCACCGCCTCAACATCAAGAATGACTCCAGGCTCGAGGGCCTCATCAAGATGGCCGATCTGgtgagagcctgctgccaccatatttcgggacccagatttcatctcatcagttatactagtataattcaatatgcacttggtacccaaaaagttctgctcccactcaagaattccttcccttcccatctcctgctgctgcttgggtggtggatctgaag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA12G30490.2 (Glycine max), 5'ss of exon 1
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgt----tcgtgattccctcgtttctatttcttgca---ttggattttgaat---ttcttgtattttgtatca---atttgtggcgttttctttggtaatgcag
 || ||     | |  |||||| ||  |||||| ||||| || ||| |||||||||||||||||||  | |||||||| |||||||| ||| ||||||||||    | || || | ||  ||| |||| |   ||   |   |  || ||    | |   ||||    ||||   | || |   | ||  |||  |  | || 
GGAACCCCACACGCTCCCTTGGGCCTCTCGCATCCAGTTCCATCGCCTCAACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagttatccactt-tttttattccagacaccctccaacgttaaaaatatgcggatattgctcatcatagagttataa-gattgatttaatggttca-

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 1
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattggattttgaatttcttgtattttgtatcaatttgtggcgttttctttggtaatgcag
||| ||  | |     || ||| |||  |||||    || |||||| |||||||||| ||||| ||  | |||||||| |||||||||||||||||||| ||   | || || || ||||| ||||||    |   | ||  ||||  | ||  | |||||  ||  |    |    ||  |        
CGAACCCTCCGATTCCCCCTGGGCCGGCCGCATCACCTTCCACCGCCTCAACATCAAACACGACTCTCGCCTCGAAGGCCTCATCAAGATGGCAGATCTCgta-ataataccttcttttctctttcttttcctctttgttttattttctttacatcgtatcgtttctt--tctccgtttcag--------

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 1
CGAGCCGGCTGCACAT--CCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgt----------tcgtgattccctcgtttctattt------cttgcattggattttgaatttcttgtattttgtatcaatttgtggcgttttctttggtaatgcag--------
   ||||  | | |    |||||| | |  |||||    || |||||| |||||||||| ||||| ||  | |||||||| |||||||||||||||||||| ||          || |   ||  || ||||| |||       || |     || ||  |||| |||| || | |||  ||||        |   |||||    |          
--CGCCGATTCCCCCCTCCCTTGGGCTGGCCGCATCACCTTCCACCGCCTCAACATCAAACACGACTCTCGCCTCGAAGGCCTCATCAAGATGGCAGATCTCgtaataataacatcatttctctttcttttctttttattctctttactccctatctttcattttttgttttat-tattcatttactctacctcacttggtgtctctctctttcag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 1
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattgg-attttgaatttcttgtat-------------tttgtatcaatttgtggcgttttctttggtaatgcag---------------------------------------------
 ||||| | | |   ||  ||| | | ||| || |||||||| || |||||||| ||||| ||||| || || |||||||| ||||||||||||||||||||   ||  | | ||||||||  ||  |  || |  | | ||||  | ||| ||             | ||  ||  | ||||   |    ||| | | ||  |                                             
TGAGCCTGATACCGTTCAATGGGCTGGTCGGATCCAGTTTCATCGTATCAACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttg--ttcttcgtttcttcttagtaaatcgttaatgtgaaaatgttgaatgtgaagactcagatctgattcgttatgtgaaatcgaatttcgaattgtggatgtcttgtttaattaatctgttgttgttgttttggattttgcag

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|110732834|gb|EE108465.1|EE108465
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71857780|gb|DT006835.1|DT006835
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71857207|gb|DT006262.1|DT006262
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|110387369|gb|EC952029.1|EC952029
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71864027|gb|DT013082.1|DT013082
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCACCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71865169|gb|DT014224.1|DT014224
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71855267|gb|DT004322.1|DT004322
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71859790|gb|DT008845.1|DT008845
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|110686702|gb|EE064638.1|EE064638
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|110359156|gb|EC920189.1|EC920189
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|161710980|gb|FC060335.1|FC060335
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|30253074|gb|CB970625.1|CB970625
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|30320980|gb|CD004242.1|CD004242
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|110685502|gb|EE062276.1|EE062276
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71862682|gb|DT011737.1|DT011737
EST:     ACATCAAGCACGATTCAAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|77585098|gb|DV221638.1|DV221638
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71855470|gb|DT004525.1|DT004525
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|161707299|gb|FC055150.1|FC055150
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
EST: gi|71858973|gb|DT008028.1|DT008028
EST:     ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTG                         ACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT
genomic: ACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgatt ... ggtaatgcagACTGTCAATCTGGCTGCGATCTGTACTCCCGCAGACTACAATACTCGTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattggattttgaatttcttgtattttgtatcaatttgtggcgttttctttggtaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT