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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaggggaaacttcttctatgatcagagctcctctactaagaagtaatctttcatggatactgttactgattgcatttgaaatccttggtatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g02550.t01
intron # 6
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 6
lower sequence: GLYMA06G12110.1 (Glycine max), 3'ss of exon 6
taaaggggaaacttcttctatgatcagagctcctctactaagaagtaatctttcatggatactgt--------tactgattgcatttgaaatccttggtatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG
  || | | |    ||  | ||  || | ||        ||||||   || ||| |   ||  ||        |||| ||| ||||  | ||||||| ||| |||||||||| || ||||||||||||||||| |||||  |||||||||||||||| || |||
--aaagagtaggagctattctg--caaaactttga----aagaagcggtccttcttaattaaggtcaatagaatactaattacattatatatccttgatattctgtagGAGTTATTATGAATGATGAGACAGTTCATCAGCTATGTAAACAAGCTGTAGCCCAG

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 7
taaaggggaaacttcttctatgatcagagctcctctactaagaagtaatctttcatggatactgt--------tactgattgcatttgaaatccttggtatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG
  || | | |    ||  | ||  || | ||        |||||||  || ||| ||  || |||        |||| ||| ||||  | ||||||  ||| ||| |||||| || ||||||||||||||||| |||||  |||||||||||||||| || |||
--aaagagtaggagctattctg--caaaactttga----aagaagtggtccttcttgattaatgtcaattgagtactaattacattatatatccttcatattctgcagGAGTTATTATGAATGATGAGACAGTTCATCAGCTATGTAAACAAGCTGTAGCCCAG

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ25898 (Selaginella moellendorffii), 3'ss of exon 6
taaaggggaaacttcttctatgatcagagctcctctactaagaagtaatctttcatgg-atactgttactgattgcat-ttgaaatccttggtatcctgt---agGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG
                                            |||| |    |||   | | ||   |  |   ||  | || | |||  | ||  ||   ||| || || ||||| ||||| || || |||||| |||| ||||||||||||||||||
--------------------------------------------gtaagcacggatgctgttccgtcgtttttgtaatgctaaactgctttctttctcgtgtaagGCGTGATCATGAACGATGAAACTGTCCATCAACTATGCAAACAAGCTGTTGCTCAG

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ10919 (Selaginella moellendorffii), 3'ss of exon 6
taaaggggaaacttcttctatgatcagagctcctctactaagaagtaatctttcatggatactgttactgattgcatttgaaatccttggtatcctgtagGA-GTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG
                                      |||| |   ||  |     |    | ||  ||||   |       | |||  | || |||| |  || || ||||| ||||| || || |||||| |||| ||||||||||||||||||
-------------------------------------gtaagcacggatgctgttccgtcgtttttg-tgatgctaaactgctttctt--tctcgtgtaagGCGTGATCATGAACGATGAAACTGTCCATCAACTATGCAAACAAGCTGTTGCTCAG

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:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGCCATAAAGAATGATGACACAGTGCATC
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATC
EST: gi|351023176|gb|FQ432559.1|FQ432559
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGA
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGA
EST: gi|349830570|gb|FQ416868.1|FQ416868
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
EST: gi|351036615|gb|FQ457328.1|FQ457328
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
EST: gi|349828957|gb|FQ419290.1|FQ419290
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAAAGAAAATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTA
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTA
EST: gi|351052784|gb|FQ456511.1|FQ456511
EST:     TTAGATCCGTATTCCTCTGATGGGCATGATGGTATTTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
genomic: TTAGATCCGTATTCCTCTGATGGGCATGATGGTATT-GTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
EST: gi|110386828|gb|EC951456.1|EC951456
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
EST: gi|351044566|gb|FQ443097.1|FQ443097
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
EST: gi|110373793|gb|EC938150.1|EC938150
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTG
EST: gi|351055179|gb|FQ440518.1|FQ440518
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAAACA-GCTGTT
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAA-CAAGCTGTT
EST: gi|351054528|gb|FQ452004.1|FQ452004
EST:     TTTAAATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCAATT
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATT
EST: gi|349830492|gb|FQ416790.1|FQ416790
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAGTCATAATGAATGATGAGACAGTGCATCCATTATGTAA
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAA
EST: gi|351015476|gb|FQ447305.1|FQ447305
EST:     TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG                         GAATCATAATGAATGATGAGACAGTGCA
genomic: TTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATGgtaagacata ... tatcctgtagGAGTCATAATGAATGATGAGACAGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatctttcatggatactgttactgattgcatttgaaatccttggtatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG
                    tactgat  putative branch site (score: 2)
                              atttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaggggaaacttcttctatgatcagagctcctctactaagaagtaatctttcatggatactgttactgattgcatttgaaatccttggtatcctgtagGAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - -gggaaac
- - - - - - - - - - - - - - - -cctctac
- - - - - - - - - - - - - - - - - - - - agaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttgg