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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgctgtataaaaagaataacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG

Basic information

species Vitis vinifera
transcript Vv06s0009g00960.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgctgtataaaaagaataacttgggaattt----ttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
    |    || |   | |||  | | || |  |  |    ||  |||  |    |||||  |  || || ||  |   |||   |||    ||     || ||||| || |||||||||||| | ||||||||||||||| ||||| |||| || ||||||||||| ||||| || ||||||
--gttgctaataatgccctgcctttctatcttcaatttt-ttagcattccattggacagtcatt-tgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 11
-----aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgctgtataaaaagaataacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
      |    |  | |   | | ||| |   || | ||| ||| | |   | | | | | |     |  |  |||||           | ||      ||||||||||||||||||||||||| | || |||||||||||    || |  ||  | || ||||| ||||| ||||||||||||
aaagacactcttttagggacagaggcagtat-atatctaggtaaacaat--tctgaacatgccacaat--ttatgtattcgtttggctgcatgctgtcatttcagGTATAAATTTGATGATGAACGAGTAACAAAAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattt-taccctacagttgtc---atgctgtataaaaagaataacttgggaattt-ttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
     |   |  | | | ||   |   || || |  ||  ||| | |   |   || ||  |      || |||| |   ||   | || |     |    ||||||||||||||||||||||| | || ||||||||||| |  |||| |||| | || || |||||||| ||||| ||||||
-----agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 7
-aatgtatggat-gagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgct-gtataaaaagaataacttgggaatttttca-gGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
 | |  |  ||| || ||  || |  |  ||    || | |  |   |     | ||    || | ||    | || |   |    || | ||||||    | |||| || || || |||||| | ||||| ||||||||| ||||  | || |||||||| |||||||||||||||||||||
gactagactgattgattaattgtatcgtaataaacagatgacttgtga----gcactggtattcttatctaagaattatttgctccacattggaattgaaaaagGTACAAGTTCGAGGATGAACGAGTGACGAAAGAAGACATGAAACGAGCATTGGAGGAACAATATGGTGGTGAAGAAGAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 3
--aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgctgtataaaaagaataacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
   |  |  |  | | |  |     |      |||   |||    |  ||   || |     || ||| |  |||     ||||| || |        ||||||| |||||||||||||| |||||||||||||||||    || || || ||||||||||||||||||||||| ||||||
tgcaactgggagtcactttaccttcttttcactgtttttaattcccttttggcccgtgtccctgccattcactatttgt-gaatatct-gactggcactcagGTACAAATTTGATGATGAGAGGGTGACAAAAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 11
--aatgtatggatgagtacatgcaatgccatttgtagctaagctacaat-tttaccctacagttgtcatgctgtataaaaagaataacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
  ||  |   || |||| | | ||     |||| | | ||   |  | |   |  | ||| | | |  ||     |  |  | ||   ||       | | |||||||||||||||||||| |||||||| |||||||||   ||  |||| || |||||||||||||||||||| ||||||
gcaacattctga-gagtcctttcacc-ttattttt-gttattttgtattgcatttcttactgctttactgagcacttcactgcatgctttaattgaatattagGTATAAATTTGATGATGAGAGGGTGACTAAAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 11
aatgtatggatgagtacatgcaatgccatttgtagc--taagctacaatttt----accctacagt-tgtcatgctgtataaaaagaat-aacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
           |||| | | ||    | |||||     | |  | || || |     |  ||| |         ||| ||     || | ||          | | |||||||||||||||||||| |||||||| |||||||||   ||  |||| || ||||||||||||||||| || ||||||
--------tgagagtcccttcaccttcttttgttattttgaattgcatttcttgctgctttactgagcacttcactgcatgctttgattgaatgcatatgactattagGTATAAATTTGATGATGAGAGGGTGACTAAAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAG

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|110388155|gb|EC952874.1|EC952874
EST:     CATGGTGGACATTATTATGCCTTTATAAGACCCACCCTTTCTGATCAGTG                         GTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTT
genomic: CATGGTGGACATTATTATGCCTTTATAAGACCCACCCTTTCTGATCAGTGgtatggactg ... aatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaccctacagttgtcatgctgtataaaaagaataacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG
                                 gaataac  putative branch site (score: 2)
                                               tttttc  putative PPT
                         tataaaaagaataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgctgtataaaaagaataacttgggaatttttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- tgtatgg
- - - - - - -gtacatg
- - - - - - - - - - caatgcc
- - - - - - - - - - - - - - - tgtagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataac