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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattatctaattcatggcatgtgtcataaatttggtggttgctgagaattgagaacccttgaattgccatataaataaatgacttgatcctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT

Basic information

species Vitis vinifera
transcript Vv05s0029g00240.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 6
--ccattatctaattcatggcatgtg--tcataaatttggtggttgctgagaattgagaacccttgaattgccatataaataaatgacttgatcctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT
    |  | | |  | ||   || ||   |||  ||||  |  ||  ||| | |  ||      |   | | ||  |   | | ||     || |  |||||||||||| | |||| ||||||| ||||| ||||| || || |||||||||||||||||||| |||| |||||||||||| || ||||| |||||  | || |
ttggaacaccaatattattatatctgatgcatggatttattcttt--tgacattcaagggtatctatctcgtca-gtggctga-tgttaacattcctttttcagGGAAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAGCGGCTCTATGCTACCAACTCACTATTTAGTACTTGGGACAAACAAT

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 6
-ccattatctaattcatggcatgtgtcataaatttggtggttgctgagaattgagaacccttgaattgccatataaataaatgacttgatcctg-ttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT
    |||||| ||     || |         |  |  | |   || | ||||  || ||||| | | |    |     | |   |   ||  |  |||||||||||| | |||| |||  || ||||| ||||| ||||| ||||| ||||| |||||||| |||||||| ||||||||||||||| |||||||| | || |
tattttatcttatgtgatgcttaaacgtggtacataattgc-actcataattttga-ccctttagtggtttaaggtgaagagatcaaaattttaattttcagGGAAATAAGTTGAGAGCTGGCCCTCAGATGATTCAGTTGAGTTTGGATGGTAAGCGGCTATATGTTACAAACTCACTCTTCAGTGCATGGGATAAACAAT

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G36670.1 (Glycine max), 3'ss of exon 6
---ccattatctaattcatggcatgtgtcataaatttggtggttgctgagaattgagaacccttgaattgccatataaataaatgacttgatcctg--ttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT
   |||||     || || |||   |||  || ||    |  ||| |    ||| |      |     |  | | | | |   |||  | | | |   ||||||||| || | |||| ||||||| ||||| ||||| || || |||||||||||||| ||||| |||| |||||||||||| || |||||||||||  | ||||
ttgccatttatgcatgca-ggctcttgttttacatggatttattgttcgacattaaagggtatc----tatcttgtcagtggctgatgttaacattccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAACGGCTCTATGCTACCAACTCACTATTTAGTACATGGGACAAACAGT

upper sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 6
ccattatctaattcatggcatgtgtcataaatttggtggttgctgagaattgaga-----acccttgaattgccatataaataaatgacttgatcct-gttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT
   |  | ||  |  ||  |||   | ||||  ||||   |  |   | || | |     |||||| | | |    |     | |   |   ||  |   ||||||||||| | |||| |||  || ||||| ||||| ||||| ||| | ||||| |||||| | |||||||| ||||||||||||||| |||||||| | || |
---tattttatcttgtgttatg---cttaaacgtggtaaataattgcactttaaattttgaccctttagtggttgaaggtgaagagatcaaaatttttaatttcagGGAAATAAGTTGAGAGCTGGCCCTCAGATGATTCAGTTGAGTCTGGATGGTAAGCGGGTATATGTTACAAACTCACTCTTCAGTGCATGGGATAAACAAT

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|26257072|gb|CA808135.1|CA808135
EST:     CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGCGGTCCAG                         GGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
genomic: CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAGgtgagttcta ... ctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
EST: gi|110378930|gb|EC944090.1|EC944090
EST:     CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAG                         GGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
genomic: CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAGgtgagttcta ... ctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
EST: gi|110407600|gb|EC973206.1|EC973206
EST:     AGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAG                         GGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
genomic: AGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAGgtgagttcta ... ctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
EST: gi|33401496|gb|CF207123.1|CF207123
EST:     CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAG                         GGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
genomic: CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAGgtgagttcta ... ctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
EST: gi|26257690|gb|CA808753.1|CA808753
EST:     CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAG                         GGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
genomic: CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAGgtgagttcta ... ctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
EST: gi|110425331|gb|EC991715.1|EC991715
EST:     CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAG                         GGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG
genomic: CGTTGGCAGAAGATGGTACAACATGGCAGTCTGAGGTTCCAGAGGTCCAGgtgagttcta ... ctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaattgagaacccttgaattgccatataaataaatgacttgatcctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT
                                     acttgat  putative branch site (score: 5)
                                           tcctgttttc  CT-rich tract
                        atataaataaatgact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattatctaattcatggcatgtgtcataaatttggtggttgctgagaattgagaacccttgaattgccatataaataaatgacttgatcctgttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT

- - - - - - tcatggc
- - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacttg