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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaaagcagttacaaatagctcttataggacatatatttgttgtttatgctttaagttgtggttttctaatttgctatttcgctgtacatgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGGACTCGGATCAACACAGCATGCTTTGTGGAGTCAATTCCATTAGACATGG

Basic information

species Vitis vinifera
transcript Vv18s0072g00720.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA10G36120.1 (Glycine max), 3'ss of exon 20
gcaaaagcagttacaaatagctcttataggacatatatttgttgtttatgctttaagttgtggttttctaatttgctattt--cgctgtacat---gtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGGACTCGGATCAACACAGCATGCTTTGTGGAGTCAATTCCATTAGACATGG
      |   ||  |  | | |   || ||   |        |  || |   || | |  || || |  ||||| |||| |   ||||||  |   || |   || ||||||||||||| | ||| || ||| | |||||  |||||||||| ||||| || || |||||||||||||||| ||| ||  |||| || |||   |
---gtgggttttctatgttg-tgaaatgggttctgataccaatcattgtctgttgaatcctg-ttgttaaatttactatctaaagctgtattttgggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGGACACGCATTAACACAGCATGCTTTGCGGAATCTTTTCCTTTGGACTCTG

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA20G31490.2 (Glycine max), 3'ss of exon 20
gcaaaagcagttacaaatagctcttataggacatatatttgttgtttatgctttaagttgtggttttctaatttgctattt--cgctgtacat---gtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGGACTCGGATCAACACAGCATGCTTTGTGGAGTCAATTCCATTAGACATGG
   |     |||    || | | | |       | |  |  | ||   ||  || | || || ||    ||||| |||| |   ||| ||  |   || |   || ||||||||||||| | ||| || ||| | |||||  |||||||||| ||||| || || ||||||||||||||||  || || ||||| || |||    
---atgctggttttctat-gttgtgaagtcggttctgatactagtcagtgtgttgaattctg-ttgctaaatttactatctaaagctatattttgggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGGACACGCATTAACACAGCATGCTTTGCAGAATCTATTCCTTTGGACTCTT
















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|30303353|gb|CB980147.1|CB980147
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|110362617|gb|EC926163.1|EC926163
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|110405113|gb|EC970647.1|EC970647
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|33407691|gb|CF213318.1|CF213318
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|33405401|gb|CF211028.1|CF211028
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|110410742|gb|EC976434.1|EC976434
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|30303425|gb|CB980219.1|CB980219
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|33407610|gb|CF213237.1|CF213237
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
EST: gi|33405464|gb|CF211091.1|CF211091
EST:     TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATT                         GCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG
genomic: TTGCTGATGATAGACAGCAAGTAATGTCTGTGTCGCCAGATGACCTGATTgtaagaacct ... tgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgctttaagttgtggttttctaatttgctatttcgctgtacatgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGGACTCGGATCAACACAGCATGCTTTGTGGAGTCAATTCCATTAGACATGG
                    ttctaat  putative branch site (score: 2)
                  ttttctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaagcagttacaaatagctcttataggacatatatttgttgtttatgctttaagttgtggttttctaatttgctatttcgctgtacatgtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGGACTCGGATCAACACAGCATGCTTTGTGGAGTCAATTCCATTAGACATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- aaaagca
- - - - - - acaaata