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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatattctggtgtccatagttttttattttttaattagttaattttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01090.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
gtgatattc--tggtgtccatagttttttattttttaattagttaatt-ttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG
|||| |||   || | |   ||  |   ||  | | |  || |||  | |   |  | ||| | || |   |    |  |||  | |||||    |  ||||||||||| |||||||| ||||||| ||||| ||| || | ||| ||||| || ||||| ||||| || || || || |||||||| ||||
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcata-tgatgaatcttgcctgtgattctgtttct----tttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 12
-gtgatattctggtgtccatagttttttattttttaattagttaatt-ttaataataataataataataataatt-taggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG-
 |  ||  | || | |  |||  |   || || | |  || |||  | |   |  | |||  |  |||  |     |  |||  | |||||    |  ||||||||||| |||||||| ||||| | ||||| ||| || | ||| ||||| || ||||| ||||| || || ||||| |||||||| |||| 
tgaaattatatgatttatataaatcagtacttgtcatataattagctatctgttttcatatgatgaatcttgcccatgtgattctgtttct----tttcaggAATGGATCATGGAACAGTGGGAAAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTTGTGGTGATGTCAAAAGG

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgatattctggtgtccatagttttttattttttaattagttaattttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG
          | ||||    |||| |   ||  | |||  |  || |   |  |   ||  || ||  ||  | ||  | | || | |     | ||||||||||||||||| || ||||||| |||||  || || ||||| ||||||||||| | ||||||||| ||| | ||||| ||||| ||||
----------gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaa-gatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG

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|110704026|gb|EE081433.1|EE081433
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACCAG                         GAATGGATTAGGGAAC
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAAC
EST: gi|352786685|gb|FQ479892.1|FQ479892
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|351049335|gb|FQ429078.1|FQ429078
EST:     CACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|351057055|gb|FQ448572.1|FQ448572
EST:     CACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|161718474|gb|FC065043.1|FC065043
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|110363867|gb|EC927492.1|EC927492
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|110698357|gb|EE075776.1|EE075776
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTACGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|351049006|gb|FQ431550.1|FQ431550
EST:     CACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|34543792|gb|CF512024.1|CF512024
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|110382715|gb|EC947034.1|EC947034
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|110388914|gb|EC953715.1|EC953715
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|110698358|gb|EE075777.1|EE075777
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
EST: gi|110698359|gb|EE075778.1|EE075778
EST:     CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAG                         GAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT
genomic: CTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattct ... gacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG
                                         ttctgac  putative branch site (score: 2)
                                      tttttctg  CT-rich tract
     aataataataataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatattctggtgtccatagttttttattttttaattagttaattttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG