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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttatatttgttgtttttattattctatattgatgtgtctcttggttagcttttcacctattatcatatgctaaatctgttacctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG

Basic information

species Vitis vinifera
transcript Vv09s0002g02530.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G01510.2 (Glycine max), 3'ss of exon 13
ttttttatatttgttgtttttattattctatattgatgtgtctcttggttagcttttcacctattat-catatgctaaatctgttac-ctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG
  | || | ||     | |  |  |||| || |  |     |    | | | | |  ||  |  |     |||  | |||||  |   |   ||| ||||||||||  ||||||||||||||||| || ||||| || | ||||||||||||||| || |||||||||||||||||||| |||
gatcttctcttcaacttatggaagattcaatttcaacac--caaacgttaaacatgacatttggtggatctatctttaatcttctgttcccattgcttgcagGTTGTGGCTGGAGAACTTGAACTGAATCATGAATGCAGTTTGATGCACTGGTCACCGGAGGACTTTGAATCTAAATTGCAG

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G20930.2 (Glycine max), 3'ss of exon 13
----ttttttatatttgttgtttttattattctatattgatgtgtctcttggttagcttttcacctattatcatatgctaaatctgttacctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG
    || | |  |  | | |   ||   |||  |     |    |        |  | |||   |    | | |    |||   |     |   ||| ||||||||||  ||||||||||||||||| || ||||| || | ||||||||||||||| || |||||||||||||||||||| |||
gatcttctcttcaactatggaagtttcaatttcaacaccaaacattagaca--tgacatttggacgg--acctttctttaatcttccgttccccttgcttgcagGTTGTGGCTGGAGAACTTGAACTGAATCATGAATGCAGTTTGATGCACTGGTCACCAGAGGACTTTGAATCTAAATTGCAG

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G28010.1 (Glycine max), 3'ss of exon 4
ttttttatatttgttgtttttattattctatattgatgtgtctcttggttagcttttcacct--attatcatatgctaaatctgttac-ctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG
    || | ||     |       |||| || |  |       | |  |   | |  ||  |  ||   | | |  | |||||      ||  ||| ||||||||||  ||||||||||||||||| || || || || | ||||||||||||||| || |||||||||||||||||||| || 
-gacttctgttcaacttagggcagattcaatttcaacaccaaacat--tagacatgacatttggatggacctttctttaatcttccgttctccttgcttgcagGTTGTGGCTGGAGAACTTGAACTGAATCACGAATGCAGTTTGATGCACTGGTCACCAGAGGACTTTGAATCTAAATTGCAA

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G32870.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------ttttttatatttgttgtttttattattctatattga--tgtgtctcttg--gttag-cttttcacct--attatcatatgctaaatctgttac-ctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG
                                                        ||  |  || |  ||||    ||||   | ||| |  |    | |      |||| | |  ||  |  ||   | | |  | |||||  | | ||  ||| ||||||||||  ||||||||||||||||| || || || || | |||||| |||||||| || |||||||||||||           
gtacaaccactttcatttctgatactgccatgatgaaaatgcagattttatccaccttaattgatcttctgttcaacttatggcagattcaatttcaacaccaaacattagacgtgacatttggatggacctttctttaatcttctgctctccttgcttgcagGTTGTGGCTGGAGAACTTGAACTGAATCACGAATGCAGTTTGATACACTGGTCACCAGAGGACTTTGAAT-----------

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|352776720|gb|FQ472607.1|FQ472607
EST:     GAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG                         GTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
genomic: GAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGGgtatgcacac ... ttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
EST: gi|352768323|gb|FQ469498.1|FQ469498
EST:     GAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG                         GTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
genomic: GAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGGgtatgcacac ... ttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
EST: gi|352776730|gb|FQ472617.1|FQ472617
EST:     GCTGGTGCTGGAGGG                         GTTGTTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
genomic: GCTGGTGCTGGAGGGgtatgcacac ... ttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
EST: gi|110374522|gb|EC939340.1|EC939340
EST:     GAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG                         GTTGCTGCTGGGAGA-CTTGAACTAAACCATGAGTGTAATTTGATGCACTG
genomic: GAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGGgtatgcacac ... ttgtttgcagGTTGCTGCTGG-AGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTG
EST: gi|352774062|gb|FQ474585.1|FQ474585
EST:     GGTGCGGGAGGG                         GTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG
genomic: GGTGCTGGAGGGgtatgcacac ... ttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttagcttttcacctattatcatatgctaaatctgttacctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG
                          tgctaaa  putative branch site (score: 2)
                                        cctattt  putative PPT
                tattatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttatatttgttgtttttattattctatattgatgtgtctcttggttagcttttcacctattatcatatgctaaatctgttacctatttgtttgcagGTTGCTGCTGGAGAACTTGAACTAAACCATGAGTGTAATTTGATGCACTGGTCCCCTGAGGACTTTGAATCTAAATTACAG

- - - - - - - - - - - - - - - - -tgatgtg
- - - - - - - - - - - - - - - - - - - - - - -tggttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttacc