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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgaatcactgttgtcttatgtttttaccttttttagcagtcctcttttagcacttccccagtaatttcatttaattcattttttttttgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATA

Basic information

species Vitis vinifera
transcript Vv16s0050g01510.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G37440.1 (Glycine max), 3'ss of exon 3
ctctgaatcactgttgtcttatgtttttaccttttt---tagcagtc-ctcttttagcacttccccagtaatttcatttaattcattttttttttgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATA
   |  ||  ||  ||| || |||  ||      ||   | |||||  ||  | ||  | || |  ||     | || ||| |   |||  | || | |   || || ||||| || ||||||||||||||||| ||||||||||||||  | || |  || ||||| ||||| || |||||||| | ||| ||| ||||||| 
--ttacattcct--tgtgttgtgtccttggtcaattggattgcagttactactatactatttactaagcttcgtgatgtaactttatttggtattttgttgtagTACCGCATGCATCAAGCTTGAGGAATATCAGACTGCTAAGGCAGCTCTAGAGATGGGTGCTTCATTGGCTCCTGGAGATTCTAAATTTACTGATTTGATC

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 2
ctctgaatcactgttgtcttatgtttttacctt---ttttagcagtcctcttttagcacttccccagtaatttcatttaattcattttttttttgtttca-------cagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATA
        ||    | | |||| ||||||| ||   | ||  || | || | |      |||  | ||  | |  || | || ||||||  |||||| ||       ||| ||||| || |||||||||||||||||| | ||||||||||| ||  | ||    || || || ||| | || |   | ||||| ||  ||| |||||| 
--------catc-ctattttatatttttacattggatgttctcaattctttatccttg-ttcaactgtgctatacttgatttaatttttgctttgttgcatcaattgcagTACTGCGTGCATGAAGCTTGAGGAATATGAGACTGCTAAGGCTGCTCTAGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 2
ctctgaatcactgttgtcttatgtttttaccttttttagcagtcctcttttagcacttccccagtaatttcat--ttaattca-ttttttttttgtt-------tcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATA
        || |  | | |||| |||| || ||   | | | ||   | ||    |||   ||    |   ||  || ||| | |||||  |||| |       |  ||| ||||| || |||||||||||||||||| ||||||| ||||| ||  | ||    || || || ||| | || |   | ||||| ||  ||| |||||| 
--------ca-tactattttatattttgacattagat-gtactcaattctttatccttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC

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|110712988|gb|EE088514.1|EE088514
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|71859342|gb|DT008397.1|DT008397
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|161710647|gb|FC059030.1|FC059030
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATAT
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATAT
EST: gi|110733197|gb|EE109180.1|EE109180
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|29782866|gb|CB348559.2|CB348559
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         TACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|29783203|gb|CB349232.2|CB349232
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110694395|gb|EE071465.1|EE071465
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|161712354|gb|FC061928.1|FC061928
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110686508|gb|EE064228.1|EE064228
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|32271506|gb|CD720665.1|CD720665
EST:     GCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: GCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|37187277|gb|CF606630.1|CF606630
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|46917631|gb|CN546960.1|CN546960
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|294964470|gb|GW838273.1|GW838273
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110729024|gb|EE105164.1|EE105164
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCTA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|28969441|gb|CB348474.1|CB348474
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         TACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|71863962|gb|DT013017.1|DT013017
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|71859797|gb|DT008852.1|DT008852
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|161707617|gb|FC057397.1|FC057397
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTAT
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTAT
EST: gi|110687406|gb|EE064790.1|EE064790
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110693950|gb|EE070628.1|EE070628
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110711614|gb|EE088295.1|EE088295
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|161711760|gb|FC058309.1|FC058309
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|32249238|gb|CD715057.1|CD715057
EST:     GCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: GCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110732977|gb|EE108734.1|EE108734
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|110723197|gb|EE100235.1|EE100235
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|161718657|gb|FC067946.1|FC067946
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|71857115|gb|DT006170.1|DT006170
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
EST: gi|71873209|gb|DT022264.1|DT022264
EST:     AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG                         CACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA
genomic: AGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGgtaagagcct ... tgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttagcacttccccagtaatttcatttaattcattttttttttgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATA
                          atttaat  putative branch site (score: 4)
                                ttcattttttttttgt  CT-rich tract
                 agtaatttcatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgaatcactgttgtcttatgtttttaccttttttagcagtcctcttttagcacttccccagtaatttcatttaattcattttttttttgtttcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
ctctgaa
- - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - - agtcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcccca