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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggactggttttggtttgtattgttgtagttataccagctttcttgaaatatgaccttacatgtggctatttgtttcttaaatcctaatttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA

Basic information

species Vitis vinifera
transcript Vv05s0020g00460.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G14490.1 (Glycine max), 3'ss of exon 7
agggactggttttggtttgtattgttgtagttataccagctttcttgaaatatgaccttacatgtggctat----ttgtttcttaaat---cctaatttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA
      | ||||||  ||  ||   ||||||| | | | | || |     |||    || | |     | |    ||| || || |||   |||   || | |||||||||  | |  | ||||  |||||||| ||||||||||||||||||| |||  |||||||||||| ||||||||||||||||| ||||||||||| || |
------ttgttttgaattcaataaatgtagtt-tgctatccttttatgtctattttattgcttaaacttgttacattgattatttaatgtcccttgcttatttgcagATAATGTATTTGAAAGGTTTGGAAATGCTGAAAATATTCAAAAATCATACATTGAAGACATCTTTGCTTGATGACTTTATGTACTATGAAAACCGTCAAA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 3
agggactggttttggtttgtattgttgtagttataccagctttcttgaaatatgacc-ttacatgtggctattt-gtttcttaaatcctaat--ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA
      | |||    ||||||   ||  |         || || || |    | ||  |||  ||  |  |||| |    | ||| || | |  | || |||||||||  | ||   ||||  |||||||| |||||||||||||||| || |    |||||||||||| |||||||||||||||||||||||||| || ||||
----ttttgttaccttttgtagattttcaaggggggttgcattttttatccctaactattatttgaagtaattttgaccatcaaaccccattcctcttgtgcagATAATGTATAGTAAAGGTTTGGAAATGCTGAAAATATTCAAAAACCATAATTTGAAGACATCTTTGCTTGATGACTTTATGTATTATGAAAATCGTCAGA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 6
agggactggttttggtttgtattgttgtagttataccagctttcttgaa-atatgac--cttacatgtggctatttgtttcttaaat---cctaatttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA
      | | ||||  ||  ||   ||||| | ||  | | || |||   || | |   |||| |  ||     ||| || || |||   |||   || | |||||||||  | |  | ||||  |||||||| ||||||||||||||||| | |||  |||||||||||| ||||||||||||||                    
-----tttgctttgacttcaataaatgtagct-tattatcctttttgtctattttattgcttaaacttgttacattgattatttaatatcccttgcttatttgcagATAATGTATTGGAAAGGTTTGGAAATGCTGAAAATATTCAAAAATAATACACTGAAGACATCTTTGCTTGATGACTTTAT--------------------

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G36110.1 (Glycine max), 3'ss of exon 7
agggactggttttggtttgtattgttgtagttataccagctttcttgaaatatgacc-ttacatgtggctat-ttgtttcttaaatcctaat--ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA
      | |||    ||||||   ||  |         || || || |  | | ||  |||  ||  |  || |||  | | ||| || | |  | || |||||||||  | ||   ||||  |||||||| | |||||||||||||| ||      |||||||||||| |||||||||||||| ||||||||||| || ||||
----ttttgttaccttttgtagattttcaagggggtgtgcattttttatctgttactattatttgaagtaatcttgactatcaaaccccattcctcttgtgcagATAATGTATAGTAAAGGTTTGGAAATGCTTAAAATATTCAAAAACCATCATTTGAAGACATCTTTGCTTGATGACTTTATATATTATGAAAATCGTCAGA

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|161717120|gb|FC069558.1|FC069558
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAAATCACAC
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAA-TCACAC
EST: gi|30321411|gb|CD004673.1|CD004673
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
EST: gi|30129749|gb|CB915088.1|CB915088
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
EST: gi|30127739|gb|CB913078.1|CB913078
EST:     GAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: GAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
EST: gi|30134355|gb|CB919693.1|CB919693
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
EST: gi|71862152|gb|DT011207.1|DT011207
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
EST: gi|30321832|gb|CD005094.1|CD005094
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
EST: gi|27581269|gb|CB003964.1|CB003964
EST:     TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAG                         ATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA
genomic: TAGAGAACAATGAGAATAAGCCAGTGACTAATAGTAGAGACACTCAAGAGgtacatttag ... ttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatatgaccttacatgtggctatttgtttcttaaatcctaatttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA
                                      tcctaat  putative branch site (score: 2)
                                            tttttctgc  CT-rich tract
                       tatttgtttcttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggactggttttggtttgtattgttgtagttataccagctttcttgaaatatgaccttacatgtggctatttgtttcttaaatcctaatttttctgcagATAAGATTTAAGCAAGGCCTGGAAATGTTGAAAATATTCAAAAATCACACAACGAAGACATCTTTACTTGATGACTTTATGTATTATGAAAACCGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- ggactgg
- - - - - - tggtttg
- - - - - - - - - - - - - - - - - -ccagctt
- - - - - - - - - - - - - - - - - - - - - - -tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg