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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaaatgtttagtcaacatttactagtacgtttttaaagtgctcgataggatcatgaggttgactgattggaattaccactttttgaactcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGAAGGAACAGTTGTGATTCGAGATTCCCCTGAAGTTATAGACAAAATAGGT

Basic information

species Vitis vinifera
transcript Vv15s0048g01990.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G45990.1 (Glycine max), 3'ss of exon 6
-tagaaatgtttagtcaacatttactagtacgtttttaaagtgctcgataggatcatgaggttgactgattggaattacc-----actttttgaactcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGAAGGAACAGTTGTGATTCGAGATTCCCCTGAAGTTATAGACAAAATAGGT-
 | | ||  |  ||  ||||   || | | | | ||||   || |  | |   | ||| |  | |   || |   | |||     |  ||   | ||   |||||| ||||  ||||| ||||||||||||||||| |||||||| |||||||| || ||||| || ||| |  | ||| |||||||||| || |||| | ||| | 
ttggtaacataaag--aacaa--acaaatgcctctttac--tgatacaaaatgttatgtgcataaacaat-gagctcaccctgatagcttcacaccttcattgcagaTGTACTCTTGTTGATTTGATGGTGGAAATTGATCGAATGTTGCGTCCTGAGGGAACTGTGGTGGTAAGGGATGCCCCTGAAGTAATTGACAGAGTAGCTC

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G08360.1 (Glycine max), 3'ss of exon 6
tagaaatgtttagtcaacatttactagtacgt---ttttaaagtgctcgata--ggatcatgaggttgactgattggaattaccactttttgaactcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGAAGGAACAGTTGTGATTCGAGATTCCCCTGAAGTTATAGACAAAATAGGT
    ||||   | | |  || || ||  |  |   |   |     | | | |  |  ||| |    | |     | |  | | | ||| |||| ||   |||||| |||| |||| | ||||||||||||||| | |||||||| || || |||||||| || |||||| |  | ||| |||||||||| || || ||| ||| |
----aatgcaaaatgattatctattataatttgtatcccagcagacacaacaatgtttcacgtaaataatgagctcgcctgatcgcttcttga-cttgattgcagATGTAGCCTTCTTGATTTGATGGTGGAACTCGATCGAATTTTACGCCCAGAAGGCACTGTTGTGGTGAGGGATACCCCTGAAGTAATTGAGAAAGTAGCT
















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|71868271|gb|DT017326.1|DT017326
EST:     GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
EST: gi|30300158|gb|CB976952.1|CB976952
EST:     GTAACTAGTATCGAATCATTGATAAAAATTTTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
EST: gi|29783073|gb|CB348973.2|CB348973
EST:     GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGAAAATGGATCGAATATTGCGTCCAG
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAG
EST: gi|110425458|gb|EC991843.1|EC991843
EST:     GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
EST: gi|34544982|gb|CF513214.1|CF513214
EST:     GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
EST: gi|30300088|gb|CB976882.1|CB976882
EST:     GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
EST: gi|34545974|gb|CF514206.1|CF514206
EST:     GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAG                         GTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA
genomic: GTAACTAGTATCGAATCATTGATAAAAATTCTAGGTTCTGGCAAGAACAGgtactcttta ... tcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataggatcatgaggttgactgattggaattaccactttttgaactcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGAAGGAACAGTTGTGATTCGAGATTCCCCTGAAGTTATAGACAAAATAGGT
                                          aactcac  putative branch site (score: 2)
                                            ctcactt  CT-rich tract
                                    tttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaaatgtttagtcaacatttactagtacgtttttaaagtgctcgataggatcatgaggttgactgattggaattaccactttttgaactcacttgcagGTGTAACCTTGTGGATTTGATGGTGGAAATGGATCGAATATTGCGTCCAGAAGGAACAGTTGTGATTCGAGATTCCCCTGAAGTTATAGACAAAATAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - -catttac
- - - - - - - - - - - - - - - - - - - - - - - - - - tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg