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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagtgaaattcaggggctttccactcagatgaataaagaacataagagaaatatgaatggatcagtttccctttttattaaaacatgatctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG

Basic information

species Vitis vinifera
transcript Vv01s0010g02760.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: 13114.m00152 (Oryza sativa), 3'ss of exon 5
tgaagtgaaattcaggggctttccactcaga---tgaataaagaac-ataagagaaatatgaatggatcagtttccctttttattaaaacatgatc-tgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG
    | | |  |       ||  | ||       || |||||   |  || | ||||     || | |||   |   |  || | |     || || |||||||||| |||||| |||| |||||||| ||||||||   ||||||||||||||||||||| || ||||| ||||||
--ccgcgtagcttctctatttgtcccttgctttttgcataaactcctgtaggtgaaaatcttatagttcataattattacttttca---tctgttcatgatgcagGTTATGATGCGACCTATGTTTGGTGCATTTGGAGGGGCTGGAAGTGCCAACTCTATAGCATTTGTGAGCAAG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AC196072.3_FGT001 (Zea mays), 3'ss of exon 1
tgaagtgaaattcaggggctttccactcagatgaataaaga--acataagagaaatatgaatggatcagtttccctttttattaaaac---atgatctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG
     | |  |  ||   |||     | |  |   | || |     |      ||||||  |      ||| |    | |||          || ||||||||||||  ||||| |||| |||||||| |||||||| |||||||||||| |||| || ||||| ||||| ||||||
-----ttatttatagcaccttattgttaaagtatttgaacatggtgtgcatataatatgtttactcaggttgcaacatctatgggttttttttgttctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAATTCAATTGCATTTGTGAGCAAG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 17
------------------------------------tgaagtgaaattcaggggctttccactcagatgaataaagaacataagagaaatatgaatggatcagtttccctttttatta-aaacatgatctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG
                                      || ||     ||     |||  | ||| |     ||  |   | |   |  | | ||| ||   | |||   |    |   ||||   ||||  || ||||||| ||||| || ||||| |||||||||||||||||||| ||| |  |||| ||||||||||| ||||||
gtaatgttttcatatgcattgggatatgatccagtgccaactggtgc-caaacttttttaaatcacactttcaataacttttatcca--tctaaatagaaatgcttcaactaaactaggaaactcaatct--tgtagGTGATTATGAGGCCTATGTTCGGAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 16
tgaagtgaaattcaggggctttccactcagatgaataaagaacataagagaaatatgaatggatcagtttccctttttattaaaacatgatctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG
      | |||       ||  | |||    |  | |       |      || | |  |  |        ||||| | |||    |||||     | |||||||    ||||| ||||||||||||||||| ||||| |||||||  |||||| |||| ||||||||||||
------gtaatc--attactgactactagattctagactcgttttcttgacaacacgtctctaaagacggtcctttcttttattttatgatg----gtagGTGATATCAAGACCTATGTTTGGAGCATTTGGAAAGGCCGGAAGTGAAAACTCTGTTGCATTTGTCAGCAAG

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|122688779|gb|EC925600.1|EC925600
EST:     CATGGGCTAACATGGGTGATCCAAATGCTAGCATCCCTACACCTGAACCG                         GTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAAC
genomic: CATGGGCTAACATGGGTGATCCAAATGCTAGCATCCCTACACCTGAACCGgtaaattatt ... tctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagaaatatgaatggatcagtttccctttttattaaaacatgatctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG
                                            atctgat  putative branch site (score: 4)
                            tttttattaaaacatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagtgaaattcaggggctttccactcagatgaataaagaacataagagaaatatgaatggatcagtttccctttttattaaaacatgatctgatgcagGTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- aagtgaaa
- - - - - - - - - - - ccactca
- - - - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - - - - -aagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacat