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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacactttcttaactccaaatggtttctttagtttgatcttcttagttttatggttgacgtgaaaaataaaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA

Basic information

species Vitis vinifera
transcript Vv09s0002g04680.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G361605_T02 (Zea mays), 3'ss of exon 9
--gtaattacactttcttaactcca--aatggtttcttt--agtttgatcttcttagtt--ttatggttgacgtgaaaaa------taaaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA
   |   || |    || || | ||  | || |  |  |  ||  |  |||||||  ||  || ||| | |  ||| |          ||||||||||   || || ||||||||||  ||  |||||||||   | ||  ||||  |    || |||||||| || |||||||||||||||| ||||||||| ||| 
gtattcctatatgcactgaattacagcactgctagccatggagacttctcttcttgcttgcttgtggattagatgacatgagttttctaaaattgcagATTGGCGATCCAATTGAGGCACGGCACAAGGAGTGGACGGAAAGGGGTTCCTCTGTAGATCAACTGGTGTATTGTATCAATAGTTTCAGAGAGGCTGCAT

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G43630.2 (Glycine max), 3'ss of exon 7
-------------gtaattacacttt-cttaactccaaatggtttctttagtttgatcttcttagttttatggttgacgtgaaaaataaaa--attgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA
              |  |  || ||| | |||   |    | |     ||  ||  | || |   ||||    |     || | | | | |  ||||||||||||||| |||||||| ||||| |||||||| |||   ||| |||| |||||  ||||||||||||  |||||||| |||||||| ||||| || ||||
ccttcagttattttttgtagcattttgcataaacgcctgcgataaggatatatttttgttttagtttttgccatcttaatggatatttacatgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACAGTAATTGATCAACTTGCCTATTGTATAAATAGTTATAGAGAAGCTGCAA

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G01750.1 (Glycine max), 3'ss of exon 7
-------gtaattacactt-tcttaactccaaatggtttctttagtttgatcttcttagtt---ttatggttgacgtgaaaaata-----aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA
        || ||    |  | | |     |||||    ||  |     || || ||  ||   || | |    | | |   |||     |  ||||||||||||||| |||||||| ||||| ||||| || |||   ||| |||| |||||  | ||||||||||| |||||||| |||||||| ||||| || ||||
ccttgtattatttttggtagtatcatgcataaatgccagctaaaaggaaatatttttgtttaagtttttgccatcttaatggatatttacatgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAAGAATACATGGAGAGGGGTACAGTAATAGATCAACTTGTCTATTGTATAAATAGTTATAGAGAAGCTGCAA

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|71856570|gb|DT005625.1|DT005625
EST:     AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGGACTTAAGAAG                         CAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
genomic: AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacac ... aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
EST: gi|71857129|gb|DT006184.1|DT006184
EST:     AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAG                         CAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCG
genomic: AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacac ... aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCG
EST: gi|32245466|gb|CD711285.1|CD711285
EST:     AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAG                         CAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
genomic: AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacac ... aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
EST: gi|110721835|gb|EE097540.1|EE097540
EST:     AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAG                         CAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
genomic: AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacac ... aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
EST: gi|110364620|gb|EC928007.1|EC928007
EST:     AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAG                         CAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
genomic: AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacac ... aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
EST: gi|110699605|gb|EE076751.1|EE076751
EST:     AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAG                         CAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA
genomic: AGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacac ... aaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttagtttgatcttcttagttttatggttgacgtgaaaaataaaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA
                            ggttgac  putative branch site (score: 4)
                                    tgaaaaataaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattacactttcttaactccaaatggtttctttagtttgatcttcttagttttatggttgacgtgaaaaataaaaattgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG