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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgggcacattagcatagtcctggggttgcatgaactaaaatctgcacattattgacaattgaaagtaaatgcttatatgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g09320.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 6
-ttgttgg---gcacattagcatagtcctggggttgcatgaactaaaatctgcacattattgacaattgaaagtaaatgcttatatgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG
  |    |   | |  ||||   | |     | ||  |   |||    | | || ||  | ||   || |  ||   | ||| | | |  | |||||    ||||| |||||||||||||| || ||||||||| |||| || |||| | | ||||||||||| ||||||||||| || ||||||||
gctaaaagattgaattttagatcacttgcctgtttctagatactcttctttccagatc-tggaggtttcattgtctcttcttttttaatgt-taatccg--cagGTGCTTGGGACAGATGAACTGAATGCATATCTGAATAAGTATCATCTGGAGCTTGATCCTCAACTTGATGCACTGGTTGGAAG

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 6
ttgttgggcacattagcatagtcctggggttgcatgaactaaaatctgcacattattgacaattgaaagtaaatgct--tatatgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG
  ||        ||  || | |       |||     | ||   |  | || |  ||     ||  |||| | || |  ||  |   |||| || | |  |||| |||||||| ||||| || ||||||||| | || || |||| | | ||||||||||| ||||||||||| |||||||||||
gagtaacttttctttccagatttaatttattgttattattattgttagtacttggttattgtttttaagttattgttattaattattatgtgatatgt--agGTGCTTGGGACTGATGAACTGAATGCATATCTTAATAAGTATCATCTGGAGCTTGATCCTCAACTTGATGCACTTGTTGGAAG

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 6
ttgttgggcacattagcatagtcctggggttgcatgaactaaaatctgcacattattgacaattgaaagtaaatgcttata--tgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG
  |     |   |      ||   |  | |    | |  ||   |  |  | |  ||     || |||||  ||  |  ||  |   || |    | |  |||| |||||||| |||||  | ||||||||| | || || |||| | | ||||||||||| ||||||||||| |||||||||||
-agagatacttttctttccagatttaagttattgtta-ttattgttagtgcttggttatttttttaaagtttatattattaattattatttgtgatatgtagGTGCTTGGGACTGATGAATTGAATGCATATCTTAATAAGTATCATCTGGAGCTTGATCCTCAACTTGATGCACTTGTTGGAAG

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G22250.1 (Glycine max), 3'ss of exon 6
----ttgttgggcacattagcatagtcctggggttgcatgaactaaaatctgcacattattgacaattgaaagtaaatgcttatatgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG
       |||    |   | ||    ||      |  ||  |||    | | || ||  | |  | || |  ||   |  || | |   |||| |  ||  ||||| |||||||| ||||| || || |||||| |||| || |||| | | ||||||||||| ||||||||||| || ||||| ||
taaaagattgaattctagaccacttgccccttcctagat--acttttctttccagatc-tggggatttcattgtcttttttttttttttatgttaa-tccgcagGTGCTTGGGACTGATGAACTGAACGCATATCTGAATAAGTATCATCTGGAGCTTGATCCTCAACTTGATGCACTGGTTGGGAG

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------ttgttgg-gcacattagca-tagtcctggg--gttgcatgaactaaaatctgca----cattattgacaattgaaagtaaatgcttatatgacatgtaatctct--tcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG
                                     ||    || |||| | | |  | |||    ||| |     ||    |   ||    |||  || |   ||     ||||| || || |    ||| | ||    |||||| || || ||||||||| ||||| |||||||||||||||| ||  | || || ||||| || || || ||  | ||||| ||
gtgctcggaaatctcatttactatcagccttcaatcagtcactgctcattcgtaatttttctgaatcgtttctcctcctgtgtttctcaaggccatgtttaaatcttcgttctaaat-ctaatctttgttgttacctgaaatcagGTGCTGGGTACAGATGAGTTAAATTCATATTTGAACAAATACCGACTGGAACTAGATCCCCATCTCGAAGCGTTGGTTGGCAG

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|26265141|gb|CA816204.1|CA816204
EST:     CATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAG                         GTTCTTGGGACAGATGAGCTGAATGCATATTTGAACAAATATCGTTTAGAG
genomic: CATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAGgtaatgacaa ... atctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAG
EST: gi|26267081|gb|CA818144.1|CA818144
EST:     CATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAG                         GTTCTTGGGACAGATGAGCTGAATGCATATTTGAACAAATATCGTTTAGAG
genomic: CATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAGgtaatgacaa ... atctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAG
EST: gi|34549230|gb|CF517462.1|CF517462
EST:     CATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAG                         GTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAG
genomic: CATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAGgtaatgacaa ... atctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcacattattgacaattgaaagtaaatgcttatatgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG
        tattgac  putative branch site (score: 2)
                                              tctcttc  putative PPT
               aattgaaagtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttgggcacattagcatagtcctggggttgcatgaactaaaatctgcacattattgacaattgaaagtaaatgcttatatgacatgtaatctcttcagGTTCTTGGGACAGATGAGCTAAATGCATATTTGAACAAATATCGTTTAGAGCTTGATCCACAACTTGATGCTCTTGTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
-tgttggg
- - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - -ctgcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgta