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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtattaatgttttttgaggaaattccaaagaattaattttactctctctctctctctctctctctggcatgcgcgcatgcgcacacatacacgcacacatatatttctgtctcattttatgagacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGATGGAGACATGGACTTCTGGAGGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g02550.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g49110.1 (Oryza sativa), 3'ss of exon 3
gttggtattaatgttttttgaggaaattccaaagaattaattttactctctctctctctctctctctctggcatgcgcgcatgcgcacacatacacgcacacatatatttctgtctcattttatga-gacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGATGGAGACATGGACTTCTGGAGGAG
                                                  | | |   |   || | ||| ||||   |  ||  |||||| |     |     |||  |    ||| |||| ||| ||  |||||| ||||| ||  | ||||||||||| |||||||| || |||||||| || ||||| ||||| ||||| || |||
-------------------------------------------------gtgtgtgattaaatc-cactgacatgaatg-gtgaacacacacaattagattttgatagattgagctcgttttgtgatgatctgcagGGGAAGATGATGCTCCTATTGGAGCTATGCCTGGGTGCTATAGGCTTGGTTGGAGGCATGGGCTTCTTGATGAG

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 2
gttggtattaatgttttttgaggaaattccaaagaattaattttactctctctctctctctctctct-ctggcatgcgcgcatgcgcacacatacacgcacacatatatttctgtctcatttta--tgagacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGATGGAGACATGGACTTCTGGAGGAG
                                         | ||||   | ||  |   |  | || || |  ||     ||  || |      |        |  ||        ||||| |  |   |||||||||||||||||| || || ||||| || ||||||||||| || ||||| || ||||| ||||||||| | || |||
-------------------------------------ggggtatactaattttcatttgttggcactactaggttgtata-atatgctcttgattatttgattttggatcatgagaacatttgagtttgaacttgcagGTGAAGAGGATACTCCAATTGGGGCTATGCCTGGATGCTACAGGCTTGGGTGGAGGCATGGACTTGTAGAAGAG

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G12110.1 (Glycine max), 3'ss of exon 2
gttggtattaatgttttttgaggaaattccaaagaattaattttactctctctctctctctctctctctggcatgcgcgcatgcgcacacatacacgcacacatatatttctgtctcattttatgagacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGATGGAGACATGGACTTCTGGAGGAG
                                       ||  || | |   | | |   |    ||  |   |    | |||| |     ||   |       ||  |     |   |    |   |||| ||||||||||||| || || || || || ||||||||||| || ||||| || ||||| ||||||||| | || |||
----------------------------------ggggcatactaattttcatttgtaggtactactaggttgtata-gtatgctcttgattatttgattttggattatgagaacatttgagtttgaacttacagGTGAAGAGGATACTCCAATCGGGGCTATGCCTGGATGCTACAGGCTTGGGTGGAGGCATGGACTTGTAGAAGAG

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|352789677|gb|FQ476275.1|FQ476275
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351023176|gb|FQ432559.1|FQ432559
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351039238|gb|FQ457913.1|FQ457913
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|349830570|gb|FQ416868.1|FQ416868
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351044281|gb|FQ447635.1|FQ447635
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351036615|gb|FQ457328.1|FQ457328
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|349828957|gb|FQ419290.1|FQ419290
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351052784|gb|FQ456511.1|FQ456511
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|110386828|gb|EC951456.1|EC951456
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351044566|gb|FQ443097.1|FQ443097
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|110373793|gb|EC938150.1|EC938150
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|110732090|gb|EE107070.1|EE107070
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTTTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351055179|gb|FQ440518.1|FQ440518
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351012975|gb|FQ433702.1|FQ433702
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351020103|gb|FQ445710.1|FQ445710
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|161718611|gb|FC068206.1|FC068206
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351054528|gb|FQ452004.1|FQ452004
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|161714115|gb|FC064398.1|FC064398
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|349830492|gb|FQ416790.1|FQ416790
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTAGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|351015476|gb|FQ447305.1|FQ447305
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
EST: gi|349826066|gb|FQ415871.1|FQ415871
EST:     AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAG                         GTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT
genomic: AACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCTTTATTCATGAAGgttggtatta ... agacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgcacacatacacgcacacatatatttctgtctcattttatgagacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGATGGAGACATGGACTTCTGGAGGAG
                    acatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtattaatgttttttgaggaaattccaaagaattaattttactctctctctctctctctctctctggcatgcgcgcatgcgcacacatacacgcacacatatatttctgtctcattttatgagacttgcagGTGAAGAGGACACCCCTATTGGAGCCATGCCTGGATGTTATAGGCTAGGATGGAGACATGGACTTCTGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG