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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctacaagttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG

Basic information

species Vitis vinifera
transcript Vv14s0068g00220.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G28080.2 (Glycine max), 3'ss of exon 6
gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctacaagttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG
      | |  |||| | ||  |  || || ||  |   | ||| |   |||  |      ||| |  | || ||    ||   || |||||  | ||||||||||||||||| ||||||||||  | | ||||||  || ||||| || |||||||||||||||||||||||||||||  |||| ||
------gtaaatttgtttttggtgtctatgtttgcatttg-tgttcttcctagca------taattgaaatgttgtggcttccctt-cagATCAACGATGATGAGGTGGAACTATGGGTGGTTAGAGGATTAACTGCTAAGTTAATTGACTGTAAGATGGACCAAATGAATCAAGTTGTAGTTGTCAG

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 7
gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctacaagttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG
      | |  |||  | ||  || || || || ||   | ||| |   |||  |      ||| |  | || ||  |  |   || |||||   |||||||||||||||||| ||||| ||||  | | ||||||  || ||||| || |||||||||||||||||||||||||||||  |||| ||
------gtaaatttatttttggtttctatgtttgtatttg-tgttcttcctagca------taattgaaatgttgtgacatccctttcagATCAGTGATGATGAGGTGGAACTATGGGTAGTTAGAGGATTAACTGCTAACTTAATTGACTGTAAGATGGACCAAATGAATCAAGTTGTAGTTGTCAG

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G06410.1 (Glycine max), 3'ss of exon 7
gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctacaagttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG
      |    ||||   |   || || || || |    | ||  |   |||  |      ||| |  | || || ||   |  || |||||  |||||||||| |||||||| ||||||||||  ||||||||||  || ||||| || |||||||||||||||||| |||||   ||  |||| ||
------gtgaatttgtattcaatttctatgtttgtgtttg-tgctcttcctagca------taattgaactgttggaacgctcctttcagATCAATGATGATGAAGTGGAACTATGGGTGGTTAGAGCAATAACTGCCAAGTTAATTGACTGTAAGATGGACCAAATGCATCAATCAGTAGTTGTTAG

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G15610.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctaca--agttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG--
     ||| ||||| ||       |  |      |         |   | | |     ||  | | |   || |      |   |  ||||| |  |||| || ||||| ||| | ||||||||||||||||||||||  |||||  | | |||||||||||| || ||||| ||||||||  |||| ||  
--gttagcttcttttctacgaacaatacattaaatgttgataaccttttttgcgttgctttctcagactcatcgaatttgtcgggggtgcagGTAAATGACGAGGAGGTTGAATTGTGGGTGGTTAAGGCAATAACTGCAAAATTGGTTGCTTGTAAGATGGATCAGATGAACCAAGTTGTAATTGTCAGGC

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G15610.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctaca--agttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG
     ||| ||||| ||       |  |      |         |   | | |     ||  | | |   || |      |   |  ||||| |  |||| || ||||| ||| | ||||||||||||||||||||||  |||||  | | |||||||||||| || ||||| ||||||||  |||| ||
--gttagcttcttttctacgaacaatacattaaatgttgataaccttttttgcgttgctttctcagactcatcgaatttgtcgggggtgcagGTAAATGACGAGGAGGTTGAATTGTGGGTGGTTAAGGCAATAACTGCAAAATTGGTTGCTTGTAAGATGGATCAGATGAACCAAGTTGTAATTGTCAG

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|30326179|gb|CD009441.1|CD009441
EST:     CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGG                         ATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
genomic: CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGGgtaaaagcat ... ttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
EST: gi|37187675|gb|CF607028.1|CF607028
EST:     CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGG                         ATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
genomic: CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGGgtaaaagcat ... ttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
EST: gi|87586086|gb|DY474543.1|DY474543
EST:     CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGG                         ATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
genomic: CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGGgtaaaagcat ... ttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
EST: gi|110421499|gb|EC987796.1|EC987796
EST:     CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGG                         ATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA
genomic: CTGATGAATCTTGTCAAATTCCATATTCTCTCATCAAAGACACACTTAGGgtaaaagcat ... ttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaggtgtcccatctacaagttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG
                                           ttttgttt  CT-rich tract
                     ttggttaaatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagcatctttgctctttcttactctgcttctaccaggtgtcccatctacaagttggttaaatatattggtgcaattttgtttgcagATTGATGATGATGAGGTGGAACTCTGGGTGGTTAAGGCAATAACTGTGAAATTAATGGATTGTAAGATGGACCAAATGAATCAAGTTGTGCTTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA