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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC

Basic information

species Vitis vinifera
transcript Vv06s0004g01310.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaa--aaataagattacctcttcaacta---aaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
    ||| |   || ||   |  |||  |||     ||   | ||    |||||   |||  | |||   || | || |    ||  ||       | | |  |||||| ||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||| ||||||| || || ||||| || ||||||||||| ||
--aagtgctactaactt---gtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 2
gtttgtgatttcaaatttaagatatttgtgaccttga--ttattgataagacacaaaaaataagattacctct--tcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
    | |||||    || || | |   | || || ||   ||||  ||  ||| |         ||| |  |   ||  ||||   | | || | | |||  |||||| || || || |||||||| ||||||||||||||||| ||||| |||||||| || ||  ||||||| ||||| |||||||||||||||||||| ||
--gagagatttttttttcaaaaaaacagagaactcgagcatattagtagtacaaatccttctcaattgctgccactcttctaatgtttgtat-gatctct-cagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 2
gtttgtgatttca-aatttaagatatttgtg--accttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggattgcta-tctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
||   |||| |   |||||    ||| | ||  | ||  | || ||     ||| |   |||||    |  | ||||   |  | |    |||| | | |  |||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||||||||| || ||  ||||||| ||||| |||||||| ||||||||||| ||
gtacatgatctggcaattttttttatctatgggatctgaactaatgc----acatattcaataactgcaagttttcagacatcaattatcttgcaagttttcagGTAAAAGAGCATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 2
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaacta-aaactgggattgcta----tctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
  ||||  |||   |       ||||       |  |    | | | ||  |      | || || | |||  ||||  ||  |   ||  |||    | | ||||||| || || || |||||||| ||||||||||| ||||| ||||| |||||||| || ||  | ||||| || || ||||||||||||||||| || ||
--ttgttgtttggtagcctt--tattcaaagaatgaaaacataaaaggaacctttttgtcagtttgc-tctctaactgtaagttttaatcactacaattttttagGTAAAAGGGCATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
--gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaa--aataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
   ||||| |||| |    | |  | ||  |     ||  | ||| || || | |  |  |  |  | || | ||| |   ||||  |  ||    || ||||||||| || || ||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| || || || ||||||||||||||||||||
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaat----atatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 2
--------gtttgtgatt-tcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
         ||||| |||  ||| | |||  | ||| | ||     || ||      | |      ||  | |      ||| ||| ||  |     ||  || || |||||| || || || ||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||| ||||| |||||||||||||| |||||
tctcataaatttgttattgccaagtgtaacttttttcttactacctttttt------atatctttgattcgttgtggcattccactgaatgtta---tgtgatgtgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggat-tgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
  |  | | ||     ||   |  | |      ||  |||    |        | |  |  ||||   | |   | |  |       | ||  ||  | |||||| || || || ||||||||||| |||||||||||||||||||| ||||||||||| |||||||| ||||| ||||| |||||||||||||| |||||
-ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G03060.1 (Glycine max), 3'ss of exon 3
--gtttgtgatttcaaatttaagatatttgt-gaccttgattattg----ataagacacaaaaaataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
   ||||| |||| |    | |  | ||  | ||  | |||| ||     |||    |  ||||  || ||| | |     ||| ||| | | | |   || ||||||||| || || ||||||||||||||||||||||||||||||||||| |||||||| || ||| ||||||| || ||||| ||||| || |||||||||||
aattttgtaatttgattggttatcttttcatagatatggatttttctgtcatagagtatgaaaacaaatattgcttt----actgaaaatagcaat---atatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAAGCTCTTGCTGCAGCAGGAGCTGAGATCCTTGTTGGCAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaa--aactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
                    | |  |||  |  |   |  ||||  |  || | || |   | |  |    | ||||||  || ||  | || ||     ||| || ||||| || ||||||||| | |||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || ||||||||  | ||||| ||
--------------------gttggttggcatatctttctttga--attcagagaagacttggt-gctatctgaactaagcaagtgtaaatggtac----agGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC

upper sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 2
gtttgtgatttcaaatttaaga-tatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
||   |||            || ||  |    | | | || || |  |  | |      ||  |    ||| |  |||  || | | ||     | |||||| || ||||| |||||||| ||||| || |||||| | || | ||| ||||| || |||||| |||| ||||| || || |||||||||||||| || ||
gtacctgacaatggcgcagcgactaagtagagcatagcttttttaggaaccgcttgctgtaccacatgctcatttacttcaatttgtat-----tttgtagGGAAAAGAGCGTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAAC

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|351029554|gb|FQ427394.1|FQ427394
EST:     TGAAGCTAGTGNNNNNNNGCCTACTTCAGGGTTGCCAATTGACTTGAAGG                         GTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
genomic: TGAAGCTAGTGAAAAAAAGCCTACTTCAGGGTTGCCAATTGACTTGAAGGgttagttttt ... ctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
EST: gi|349827600|gb|FQ422468.1|FQ422468
EST:     TGAAGCTAGTGNNNNNNNGCCTACTTCAGGGTTGCCAATTGACTTGAAGG                         GTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
genomic: TGAAGCTAGTGAAAAAAAGCCTACTTCAGGGTTGCCAATTGACTTGAAGGgttagttttt ... ctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
EST: gi|351014663|gb|FQ437665.1|FQ437665
EST:     TGAAGCTAGTGNNNNNNNGCCTACTTCAGGGTTGCCAATTGACTTGAAGG                         GTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
genomic: TGAAGCTAGTGAAAAAAAGCCTACTTCAGGGTTGCCAATTGACTTGAAGGgttagttttt ... ctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
EST: gi|349828693|gb|FQ418428.1|FQ418428
EST:     TGAAGCTAGTGNNNNNNNGCCTACTTCAGGGTTGCCAATTGACTTGAAGG                         GTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
genomic: TGAAGCTAGTGAAAAAAAGCCTACTTCAGGGTTGCCAATTGACTTGAAGGgttagttttt ... ctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
EST: gi|351043798|gb|FQ431350.1|FQ431350
EST:     TGAAGCTAGTGNNNNNNNGCCTACTTCAGGGTTGCCAATTGACTTGAAGG                         GTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG
genomic: TGAAGCTAGTGAAAAAAAGCCTACTTCAGGGTTGCCAATTGACTTGAAGGgttagttttt ... ctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagacacaaaaaataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
                            aactaaa  putative branch site (score: 2)
     acaaaaaataagatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - -gaccttg
- - - - - - - - - - - - - - - - - - - - - - -aagacac
- - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa