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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG

Basic information

species Vitis vinifera
transcript Vv18s0166g00300.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
|||||  | || |   | |  ||| |  | ||  |||| |||       || || || ||   |||  |||||| ||||| |||||||||| |||||||| ||||| ||||| |||||||| || |||||||||||||| ||||||
gtatttatctatt--tttgtttgaaaattatag-tcatgatg-------ttgttcttgtt--ctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G13910.2 (Glycine max), 3'ss of exon 6
gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
|||||  | || |   | | |||| |  | ||  |||| |||       || || || ||   |||  |||| | ||||| |||||||||| |||||||| || || ||||| |||||||| || |||||||||||||| ||||||
gtatttatctatt---ttgtatgaaaattatag-tcatgatg-------ttgttcttgtt--ctgaccaatgctttcctgcagGAGGTACTGTATTGTGCAAAAAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ21362 (Selaginella moellendorffii), 3'ss of exon 5
gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
                         || | | | |   |  ||||  | || | |   ||| | ||  ||         | |||| ||  | |||||||| ||||||||||| |  ||||| ||||| ||||||||||| ||||||
-----------------------gtacgtttgttttcct-cgaaa--agttgtcaagcttagTGGAGCAA---------GCAGGAAGTTTTATATTGTGCTAAGAAAGCTGGAGCTACTCACATCCTAAAAGCTGGAGGAGCACAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ21512 (Selaginella moellendorffii), 3'ss of exon 4
gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
                     |  |   | ||| |   |  ||||  | || | |   ||| | ||  |          | |||| ||  | |||||||| ||||||||||| |  ||||| ||||| ||||||||||| ||||||
--------------------gtacgtgttttattttcct-cgaaa--agttgtcaagcttagtggagca---------cgcagGAAGTTTTATATTGTGCTAAGAAAGCTGGAGCTACTCACATCCTAAAAGCTGGAGGAGCACAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ27113 (Selaginella moellendorffii), 3'ss of exon 6
gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
                         || | | |    ||     |  | || | |   ||| | ||  ||         | |||| ||  | |||||||| ||||||||||| |  ||||| ||||| ||||||||||| ||||||
-----------------------gtacgtgttttgttttcctcgaaaagttgtcaagcttagtggagcaa---------gcagGAAGTTTTATATTGTGCTAAGAAAGCTGGAGCTACTCACATCCTAAAAGCTGGAGGAGCACAG

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|351043930|gb|FQ431361.1|FQ431361
EST:     AGACTGTTGTCCTTGCAACTCCCCCTAGTCAAGATGGCGGCATCTGCAAG                         GAGGTACTCTATTGT
genomic: AGACTGTTGTCCTTGCAACTCCCCCTAGTCAAGATGGCGGCATCTGCAAGgtattctttt ... tctcctgtagGAGGTACTCTATTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
                                    gattaat  putative branch site (score: 3)
                                          tgttctcct  CT-rich tract
        attatgaaatcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG