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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 3
--tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
      |  ||  | ||      | || |  |||   |   | | |   |||| || | || |     |   |||    ||| |||||| |||||||  |||||||| |||||||| ||||| ||||||||||||||||||||||| || || || || ||||   |||||||||||||||| ||||||
caattgaatattgcttttgcagaagca-actattttgcataagcctc-tttttcttgtattgatgccttgtttaccagtatttctttcattcttgataacagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
--tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
  |   |   |  | ||      | || |  |||   |  || | |   |||| || |||| |     |   |||    |||| ||||| |||||||   ||||||| |||||||| ||||| ||||||||||||||||||||||| || || || || ||||   |||||||||||||||| ||||||
tttgtgaatgtggcttttgcagaagca-actattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattc-tttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
tccaatcatcacattcatgccaacacatcat--tgcactagatcattacttttattatctttaactaattcc----tacagta-attcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
       |  |   || || ||  |  || |  |  ||  | |||||  ||   ||  |||     |||||     |  | ||  |||||||||    |||   |||||||||||||||||  |||| ||||||||||||||||| ||||| || ||  | || |||||  |||||||||||||||| ||||||
-------acaatgctcttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 2
tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcct-------acagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
      ||   |  |  |    |    | | |  ||  |||||||  |||   | || |||  | | | ||       ||| |  |||||||||    |||    ||||||||||||||||  |||| ||||||||||||||||| ||||| || ||  | || |||||  |||||||||||||||| ||||||
------caatgctcttgtcaggatgtcttactttacatgatcatttttttccctttccttacgtgaattcttggttttacaatg-ttcctttcatctctgacaaaagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
-tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatcttta-actaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
 |  || ||     ||  |   ||   |||  |      |  ||| ||||   || |||| |  |    |   ||    ||| |||||| ||||||    |||| || |||||||| ||| | || ||||||||||||||||||||||| ||  | || || |   |||||||||||||||| ||||||
ttataaacagggattttgtctgaaagaatcccttagtctg--cataacttaatttttcttgatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
tccaatcatcacattcatgccaacacatcat-tgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
|  || ||     ||  |   ||   |||   |   ||  || |      || || |   |  ||  ||    ||  | || |||||| ||||||    |||| || |||||||| ||| | || ||||||||||||||||||||||| ||  | || || |   |||||||||||||||| ||||||
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctggatgccttgtttaaccaaca-tttctttcattcttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcc-tacagtaattcctttcactcttgatg---gcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
    |  |||| ||   ||       || | |    |   |  | |||   |  ||  |||  |||||   |    | | |  ||||    ||| |    | || |||||||||| || ||| || ||||||||||||| ||||||||||| || ||||| || ||||| ||||||||||| |||||||||
--acagaatcagatct-tggggttttattagtttgatctgttgtgactca-aggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
tccaatcatcacattcatgccaacacatcattgcac-tagatcattacttttattatctttaactaattcctacagtaattcctttcactcttg----atggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
     ||  ||  |   || | |    | | |     |||   | |  |  |||  |||| |    ||   || ||| | | ||||   | ||      | |||||| |||||||| || ||| || | ||||||||||||||||||||||| ||  | || || |||||||||||||| ||||||||||||
-----tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
tccaatcatcacattcatgccaacacatca-ttgcactagatcattacttttattatctttaactaattcct-acagtaattcctttcac--tcttgatg--gcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG-------------
  || |||| ||   | ||   |  || ||  |  ||||   ||  |    ||| |||  |   || |     | | | |||  ||  |   | ||||     ||||| |||||||| || ||||| || ||||||||||||||||||||||||||| | || || ||  ||||| |||| |||||||||||              
-acattcattac--ccgtggtgatgcaacaactatactaacacaa-atcactatgatccatg--tagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG

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|33409748|gb|CF215375.1|CF215375
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|33408202|gb|CF213829.1|CF213829
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|71879035|gb|DT028090.1|DT028090
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|71879209|gb|DT028264.1|DT028264
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAGTTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|37190531|gb|CF609880.1|CF609880
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|71881039|gb|DT030094.1|DT030094
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     CTTTGAGGAATTCCAAATTTTTTCAG                         TCCGATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|33406260|gb|CF211887.1|CF211887
EST:     CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAG                         TCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCCCCTCCCACGCCTTCGCCTTTGAGGAATTCCAAATTTTTTCAGgtaaagttgt ... ttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
                                 ttcctttcactctt  CT-rich tract
     tattatctttaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
-ccaatca
- - - - - - -ttcatgc
- - - - - - - - - - caacaca
- - - - - - - - - - - - - - cattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttca