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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG

Basic information

species Vitis vinifera
transcript Vv02s0012g01850.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 2
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaat-tgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
| || || | | |  |  |  |     | ||  ||   |   || |  |  |   |  ||        ||| ||  ||||  |       |  |||| ||||||||||| |||||||| ||||| || || ||||| ||||| ||||||||| | ||||| |||||||| ||||||||| | || | |||||| ||| | |
tatgaatctatgatcattactattttaaggaacatttctat-gttccatttttgctgatgtattacacaatgtgtgttgatgacctcgtttggaactacagGCCAGCAAAAAGATTGCTGATGCGAAGCTAGCAAAGGATTTCCAAGCAGTTCTGAAAGAATTTCAGAAAGCTCAACGGTTAGCGGTAGAAAGAGAAGCTG

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G017329_T01 (Zea mays), 3'ss of exon 2
tttggatatgttagaaaaaggaaacagaagaggatgcttccag-tgctg--tgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
      |    ||  |   ||  |     |    | |||   | ||     || |||||| |      |  | |||   | |  ||     ||  |  ||||||| | |||||||||||| ||||| || || || |||||||| ||||||||  ||||||| || ||||| || |||||  | |||||||| || ||| | |
gcccattcctctattatctggggattttcgtttttccttgtggatgacaattggtcttttctttt---tacatttgtggtcatgatctcatattgacttgcagGCTACCAAGAAGATTGCTGATGCAAAGCTAGCTAAAGATTTCCAAGCAGTCCTAAAAGAATTCCAGAAAGCCCAACGATTAGCAGCAGAGAGAGAAGCTG

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 2
tttggatatgttagaaaaaggaaacagaag-aggatgcttccagtgctgtgatcttttttgagg---ggtgtaatt-gccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
     |||   |  |||   |    |   | |   |  ||   |   | |    ||   |||       |||  || ||||  || |   | | | | | ||||||| |||||||||||||||||||||||||| || ||||||||||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||| |
-----atactgtgaaaacttgtgttacgggcaatgtctttattgcattttagggttccatgaccttccatgtcttttgcctcaaaaacatttcttattattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 2
----tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
    | || ||   ||    || | ||||||   |   |  || |||    |  || | |||| ||        ||||||  || |   | | | |   ||||||| ||||||||||| |||||||||||||| || ||||||||||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||| |
ttaatctgcatcatttttttaatgaaaacagtgaaaacttgttacag----gcaatgtctttttagtatgtcttttgcctcaaaaacatttcttatttttgcagGCAAGCAAGAAGATAGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatctttt---ttgaggggtgtaa---ttgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
       ||||| |    ||   |   |      |  |    | |   |  | ||||   ||||||   | ||   |  |||| ||  |  |   | ||  ||||| | || |||||||| |||||||| || || |||||||||||||| || || || ||||| |||||||||||||| || ||  |||| || |||||||| |
------aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 2
-tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
   |  || |  |  |  |  |     |  ||   ||  |  | |  | |   | ||   ||  |    | |  |||| ||  |  |   | ||  ||||||| || |||||||| |||||||| || || |||||||||||||| || || || ||||| ||||||||||| || || ||  |||| || |||||||| |
agctttatgtactgaattattggtggcgc-gatcttgaatttatttgtttttcccttgaggaaagaaaaagtgaccttcaatgtattggttgtatttgcagGCAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCACAGCGTCTTTCAGCGGAGAGGGAAACTG

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgc--agGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
                         | |   | ||  ||    |  |||    |||||    |  | |   |    ||     |     | ||| ||   || | || |||||||||||||||||||| || ||||  || |||||||| |||||||||||||||||||| |||||||     || || ||||| |||||  
-----------------------gtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------tttggatatgttagaaaaaggaaacagaaga------ggatgcttccagtgctgtgatcttttttgaggggtg-taattgccttgaac-attctccatctaac--tgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
                   |  | |||  ||||||| | |  | |   |       | |  | ||   | ||||||  ||| || |    || |  ||  |||  |  | |    || |     |||||   || ||||||||||||||||||||||| ||||| |||||| ||||||  || |||||||||||||| || || |   |  |||  ||||| |||||  
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
         || ||  |      | | | || ||| |||    | ||        || ||       | |||     |||  |  |   |      |||    |  ||||||||||  |||||||| || ||||| || |||||||| || || ||||||||||| |||||||| || || || || ||||| ||||| |
---------gtgagtcatttatgataaaggaagattcttgttcttcttctgctacttctgt------tgattaataggaatttgattggttggttagCAA---AAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG

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|349814672|gb|FQ400310.1|FQ400310
EST:     CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|349807660|gb|FQ402051.1|FQ402051
EST:     CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|110690731|gb|EE068149.1|EE068149
EST:     CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|349828272|gb|FQ416225.1|FQ416225
EST:     CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|349823620|gb|FQ415030.1|FQ415030
EST:     CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|349821234|gb|FQ404366.1|FQ404366
EST:     CTGCTAAACTTAAGCAAGCCAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|351021992|gb|FQ437779.1|FQ437779
EST:     CTGCTAAACTTTAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
EST: gi|349817337|gb|FQ405341.1|FQ405341
EST:     CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT                         GCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT
genomic: CTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc ... ctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG
                                           atctaac  putative branch site (score: 2)
                                     ttctccatct  CT-rich tract
     atctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG

- - - - - - agaaaaa
- - - - - - - - - -ggaaaca
- - - - - - - - - - - - - -aagagga
- - - - - - - - - - - - - - - - - -gcttcca
- - - - - - - - - - - - - - - - - - - - - gtgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctc