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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
gcaacttccagtaacagcaggttaattccat-ttgttgcacctaaaaattcattt-----accaattttgttaaaaatgaatggttgt-----aacaaatttatattt---cagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
               || |   |||||   | || ||||| || || ||||||||     ||   || | || ||||  |    || |     ||||  | ||  |     ||||||||| | |||||||| |||||||||||||| |||||||| |||||||| || ||||| ||||| |||||||| |||| ||| |||||||||||||||
--------------tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaattta----tatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
   |  |  || |  |  |  ||   || || ||||| |       |||    | | ||||   ||   | |   |   |||||| | | |      |||  ||||||| ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||| ||||| |||||||| || |||||||||||||||||||||
--catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttctt--ctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
----gcaact--tccagtaa---cagcaggttaattccatttgttgcacctaaaaattcatttac-caattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
    | ||||  |||||| |   ||    | |   |   ||| || |    | | |   ||  |  || || | ||   ||| |   | ||          |||||  |||||||  | |||||||||||||| || ||||| ||||||||||||||||||||||| || ||||| |||||||| || |||||||||||||||||||||
agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctg----------atattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 6
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgt-------aacaaatttat----atttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
           |      | | | ||    ||         |  ||| |  | | |     |||||   ||    ||| | |       || | |||||      | |||||||||| | |||||||| |||||||| || ||||||| ||| |||||||| || ||||| |||||||| ||||| || | ||| ||||||||||| |||
-----------tggtcaaatgcttatctgtttgaacaagtttctaaacttttcttcagtccttgtttccaacagttggatctccatctgaaaatatttactcccgtatcagGTTGGCCTACCAGCTCGTGGTAAAACCTTCACTGCAGTTAAGCTTACAAGGTACCTTCGTTGGTTGGGCCATGAAACTAGACATTTCAATGTTGGGAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaat---ggttgtaacaaatttatattt--cagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
      |   | || |      || |||||| ||| |  | | ||| || | | |  |||||| | |||||| |||     || |||| ||||| | ||    |||| ||  ||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
----ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagtt-agtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 7
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaa---------caaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
       |  | || |    || | |||||||||| |  | | ||| ||  |  |     ||| |||||| | |||  || | |          || ||| |  |  |||| ||  |||||||  ||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
-------ctggcaaaaat--gtcatttccatttgtagttcatcaaagttagtaaatttggttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
gcaacttccagtaacagcaggtta-attccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttg-taacaaatttatatttc--agGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
       |  | || |  | |  | ||||| ||   | |  |     ||| | | |   |   | ||  ||||||||  ||  |||| | ||| | ||||  ||||  | |||||||||||||| || ||||  ||||||||||||||||||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
----tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaataatttctaactagtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaa---------caaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
       |  | || |    || | |||||||||| |  | | ||| ||  |  |    |||| |||||| | |||  || | |          || ||| |  |  |||| ||  |||||||  ||||||||||||| ||||||||||||||||||||||||||||  ||||| |||||| | |||||||||||||||||||| |||
-------ctggcaaaaat--gtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatt-tatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
  | ||   |  || |       | | |||| ||| |  | |  || ||  |  |  ||  |  || |||||||||  ||  |  |  || | |   | ||||  | |||||||||||||| || ||||  |||||||||||||| |||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
-tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------------------------------------gcaacttccagtaac-agcaggttaattccatttgt---------tgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
                                                                                | |  ||   ||  |  ||   || |||  | || |         || |   |||||   |   ||    | |  | |     |    |     |||| || ||||  ||||||||||||| |||||||| || |||||||||||||| ||  | ||||||||||| ||||||||||| ||||| || ||||| || ||||||||||||
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtatt--agGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
       ||||||    |  |  || |||| | |   || |  |    |  ||   ||   |||   ||||| | |   |   |||| |      |  ||| ||||||||| | || |||||||| || |||||||| |||||||| || || ||||||||  | ||| | || ||||| ||||||||||||||||||||||||
tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactga-acttgtcatgg---tggatt-cagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
gcaacttcc-agtaacagcaggttaattccat----ttgttgcacctaaaaattcatttaccaattttgttaaaaat-gaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
     |||| ||||       ||| |    ||    |  |||   | |||    |  |    |  |  | |   | | |||||   ||  |  ||     ||||||||||| || || ||||| || || || || |||||||||||||| || |||||| | || ||||| |||||||| ||||| |||||||||||||| |||
-tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttgaatga--gtctctgat---ggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S414_24V6.1 (Physcomitrella patens), 3'ss of exon 6
----gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaat--ttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
    || | ||  |  ||  | ||   ||       | || ||  | |||||  |||     | ||| ||  |||| | |  |  ||     |  ||    |||||||||| || || || ||||| || || ||||| ||||| ||| | || ||||||||| | ||| | || ||||| || |||||||||||||||||||| 
cagcgcga-ttaaacgaattgaagcagaagcgtcgatttttcatgtgaaaat--att---ggaatttctttcaaataactcatcctactggttgctttgggttcagGTTGGGTTACCTGCACGAGGCAAGACGTTTACGGCAGCAAAATTGACGAGATATCTTAGGTGGCTAGGCCATGATACTAAACACTTCAATGTTGGAAAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
                                                |   ||  |    || ||||   | | |  ||| | |   ||     | ||||| ||||| |||||  | || |||||||| ||||| |  || || |||||||||||||| ||| | |||||||| || ||||||||||| |||||||| 
-----------------------------------------------gtagattgtcgtcattcttaactctta-tctttgaatcgggttc----tacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ07831 (Selaginella moellendorffii), 3'ss of exon 2
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
                                                |   ||  |    || ||||   | | |  ||| | |   ||     | ||||| ||||| |||||  | || |||||||| ||||| |  || || || ||||||||||| ||| | |||||||| || ||||||||||| |||||||| 
-----------------------------------------------gtagattgtcgtcattcttaactctta-tctttgaatcgggttc----tacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACCAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA

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|122689918|gb|EC946355.1|EC946355
EST:     CTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG                         GTTGGCTTGCCAG
genomic: CTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTGgtattttctg ... tatatttcagGTTGGCTTGCCAG
EST: gi|122690284|gb|EC950420.1|EC950420
EST:     CTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG                         GTTGGCTTGCCAG
genomic: CTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTGgtattttctg ... tatatttcagGTTGGCTTGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
                                 ttgtaac  putative branch site (score: 2)
     atttaccaattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

-caacttc
- - - - -agtaaca
- - - - - - - - - - - - - -ccatttg
- - - - - - - - - - - - - - - - - - -cacctaa
- - - - - - - - - - - - - - - - - - - - -taaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaacaa