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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacgttttaggggaatgattttcatcttcttaggcattcaattgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG

Basic information

species Vitis vinifera
transcript Vv04s0044g01840.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G36040.1 (Glycine max), 3'ss of exon 4
---tacgttttaggggaatgattttcatcttcttaggcattcaat-tgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
   |    |   | |   || ||   |     | |  |||      | || |||| |  | | |  | ||||||     | | |  |||  |     | |||||||||||||| ||||| |||||||| ||||| || ||||||||||||
tgttggaatactgtgagctgtttgaaaggaattgatacataagtcataatataatataatataatat-attaatacagttctctgtcttcaacc---tatgcagGACATGTACCACTGTCTCATGGACTTTTCGGGGATTTTATGAGAAG

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G09370.2 (Glycine max), 3'ss of exon 4
tacgttttaggggaatgattttcatcttcttaggcattcaat-tgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtg-tgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
|  |  |   | ||    |||  ||    || |  |   ||| | || |||| | |  | |  | ||  |||   |   ||  || || |     | ||||||||||| || ||||| |||||||| ||||| || ||||||||||||
ttggaatactgtgagctgtttgaatggaatt-gatacataatataatataatatataat-atataatatattaatacagttctctgttttcaaccgatgcagGACATGCACCACTGTCTCATGGACTTTTCGGGGATTTTATGAGAAG

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G21840.1 (Glycine max), 3'ss of exon 5
tacgttttaggggaatgattttcatcttcttaggcattcaattgatttaattt--gttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
      | |      ||     | | ||  | ||   || |||    ||||||  ||| |    |  || |  |||   | |   || |    | | ||||||||||| || || ||||||||||| ||||| | |||||||||||||
-gaaaatcataatgttggggcactttttaatgggtgatctatttggataatttaggttatttatttgttgaagtgatgctctctgttctcaaattt-tgcagGACATGCACAACAGTTTCATGGACTTTTCGGGTTTTTTATGAGAAG

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G32820.1 (Glycine max), 3'ss of exon 3
----tacgttttaggggaatgattttcatcttcttaggc-attcaattgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
    || |||||   ||   ||  | ||| |   |   | |||    | | |||  || ||  |   |  ||||  | |||  | ||  ||       | | ||||||||| || || ||||||||||| ||||| | |||||||||||||
ttattatgtttttttgggg-gacatgcatatgggtgatctatttggataacttaggttatttac---ttgttaaagt-aatgctctctgttctcaaattttacagGACATGCACAACAGTTTCATGGACTTTTCGGGTTTTTTATGAGAAG

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S131_109V6.1 (Physcomitrella patens), 3'ss of exon 4
-tacgttttaggggaatgattttcatcttct---taggcattcaattgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
  |  | || | | | || ||||    || |   |  ||   |     ||    | | ||   |||  | |    |||    ||    | |    | |   |||||||||||| ||| |||||||| ||||||||||||| |||||||||
acaaatgtttgtgcattgcttttttcgttgtgtgtgtgcgcgcgcgcaatactctctatttgtaggatactgtgctga----ttgaaatatgaactcttcacagGACATGTACGACTATTTCATGGTCATTTCGAGGTTTCTATGAGAAG

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S66_226V6.1 (Physcomitrella patens), 3'ss of exon 3
-----tacgttttag-gggaatgattttcatcttcttaggcattcaattgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
     | | ||| |  | |   | ||    |   |||   | | || |  |  |  | |||||  |||    |    |||   ||      | | | | |   |||||| ||||||||  |||||||| | |||||||| ||||||||||||
gttgttgcatttcaatgagggcggttcatgttcactttt-cctgcagt--accttctgtgttcgtaggatgctgtgctga---ttgaaagatgaatttcttcacagGACCTGTACTACAATTTCATGGTCGTTTCGAGGCTTTTATGAGAAG

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|110703600|gb|EE080590.1|EE080590
EST:     ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA                         GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
genomic: ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAAgtatgataat ... gtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
EST: gi|32248497|gb|CD714316.1|CD714316
EST:     ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA                         GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
genomic: ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAAgtatgataat ... gtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
EST: gi|32249759|gb|CD715578.1|CD715578
EST:     ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA                         GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
genomic: ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAAgtatgataat ... gtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
EST: gi|32247711|gb|CD713530.1|CD713530
EST:     ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA                         GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
genomic: ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAAgtatgataat ... gtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
EST: gi|110688872|gb|EE067920.1|EE067920
EST:     ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA                         GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
genomic: ACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAAgtatgataat ... gtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG
                  gattaat  putative branch site (score: 3)
                              ttttttccttttattg  putative PPT
                 tgattaatttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacgttttaggggaatgattttcatcttcttaggcattcaattgatttaatttgttctcaggtgattaatttgaattttttccttttattgtgtgtgcagGACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - -ggaatga
- - - - - - - - - - - catcttc
- - - - - - - - - - - - - - - - -gcattca