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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacacacgtttcttttttggttggtttagaagagtttgaattggaaattggtgtcttaggtcaacttagtcttgatcattatgatggatttggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATG

Basic information

species Vitis vinifera
transcript Vv08s0007g04310.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 1
gacacacgtttcttttttggttggtttagaagagtttgaattggaaattggtgtcttaggtcaacttagtcttgat-cattatga--tggatttggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATG
   |  | | |  | |||    | | |   |  ||||  | || ||  ||       |    |  |  || || || ||| |  |  || | ||||  ||||||| || || || ||||| ||||| ||||||||||||||||||||  |||| |  |||  ||||||||  |||||||||||||| || || || || ||||
-ggagtcttgttgtgtttaagagatgttatatggttt--actgaaagatgagtgaacaacatacgtgtgtgttaatgcatgagtatttgaaattggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGACGGAATTGTTGGAAAAGGGGGTTATCTGCTCGTCTGCTGGGAACCATG

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G07340.1 (Glycine max), 3'ss of exon 1
gacacacgtttcttttttggttggtttagaagagtt--tgaattggaaattggtgtcttaggtcaacttagtcttgatcattatgatggatttggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATG
 |   |   || | |||  |     |||   |  ||  ||||     | |      | || ||     |   |   || | |||  || | ||||  | ||||| || || || ||||| ||||| ||||||||||||||||||||  |||| |  |||  ||||||||| |||||||| ||||| || || || |||||||
aatggagtcttgtgtttaagagatgttatgtggtttactgaaggatgagtgaacaacatacgtgtgtgttaacg-aatgaatatt-tgaaattggggtttagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGAGGGAATTGTTGGAAAGGGGGGTTATATGCTCGTCTGCTGGCAATCATG

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------gacacacgtttcttttttggttggtttagaagagtttgaattggaaattggtgtcttaggtca-acttagtcttgatcattatgatggatttggt--ttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATG
                        | |||  ||  ||  ||  || | | |     || || | | || | |    ||| ||||   |  |  | |||  |    || ||  |    |  || |||||||| || || ||||| ||||| ||||| ||||||||||  ||| |||||  ||| || |||| || ||| ||||||||||||||||| ||||| ||||
gtaagtaatgaagcttctccctttatacattttggttgattttttaggtgaattatgtatggaattgagacta-catctgaggttttatgtgttgttgtactgagtggtgactggaattgttttagGTATTCTCGTTTAAGCTTCGTGGAGCTTACAATATGATGGTGAAACTTCCAGCAGATCAATTGGCAAAAGGAGTTATCTGCTCTTCAGCTGGAAACCATG

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|352782068|gb|FQ469366.1|FQ469366
EST:     CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCC                         GTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
genomic: CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCCgtaatgtttt ... tggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
EST: gi|351028931|gb|FQ434932.1|FQ434932
EST:     CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCC                         GTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
genomic: CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCCgtaatgtttt ... tggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
EST: gi|352769243|gb|FQ471392.1|FQ471392
EST:     CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCC                         GTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
genomic: CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCCgtaatgtttt ... tggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
EST: gi|351025411|gb|FQ435103.1|FQ435103
EST:     CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCC                         GTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
genomic: CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCCgtaatgtttt ... tggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
EST: gi|34551096|gb|CF519290.1|CF519290
EST:     CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCC                         GTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
genomic: CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCCgtaatgtttt ... tggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
EST: gi|352764055|gb|FQ467625.1|FQ467625
EST:     CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCC                         GTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA
genomic: CCGAAAGGCTTGGCGCTCAAATCTGGCTCAAGAGAGAGGATTTACAACCCgtaatgtttt ... tggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattggtgtcttaggtcaacttagtcttgatcattatgatggatttggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATG
                        tcttgat  putative branch site (score: 4)
                             atcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacacacgtttcttttttggttggtttagaagagtttgaattggaaattggtgtcttaggtcaacttagtcttgatcattatgatggatttggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
gacacac
- - - - - - - - -tggttgg
- - - - - - - - - - - - - -agaagag
- - - - - - - - - - - - - - - - - - - -attggaaa
- - - - - - - - - - - - - - - - - - - - - - - - tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgga