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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG

Basic information

species Vitis vinifera
transcript Vv05s0020g03880.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gttaggacataattcttgccttgtgttta-tacagaaaatctgaactgctagttaccctgttaagtgaggttt---tctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
  ||||   |  ||  ||  | || | || |||    |  |   | | | | |||    ||   |  |   ||   |   |||||||| || |||| ||| |||||||||||||| ||||| || ||||||||||| |||||||| ||||| || || |||||||| || ||||||||||||
-gtaggcgctttttgctggatagtctgtactacttctagccctcatttccatttatgtggtgctgaaatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G153754_T01 (Zea mays), 3'ss of exon 6
---------------------------gttaggacata-attcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
                            ||  ||  ||  | | ||  |||    | |||    |  | |   ||||   |||  | |  | |||  |        |||||| || |||| ||| ||||| ||||| || || ||||| ||||||||||| || ||||| ||||| || || |||||||| || |||||||| |||
gtatggcgttgcgtacttctgttggagattgagatgtatgtacgtgtgttggccatttactcccagaccgtggtgct---tacattctacaatgaaatc-------gcagGAAGATCCTAACAACACTCCGGCTTCGGCTCGTCACAAGAGAGGATGCAATTGTAAGAAGTCAAGCTGTCTCAAGAAATACTGTGAATGCTACCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G366584_T01 (Zea mays), 3'ss of exon 5
gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctc-ttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
|| || ||  |      |    |    |||       || |  | |  |        || | |  |       ||| ||  |||||||  ||| ||||||||| ||||| || ||||| |||||||||||||| |||| ||| ||   ||| || || ||||| ||||| |||| ||||
gtaagaactaagaa---gaacagatcctattagttgcatttttatttttttcactattgctcatggcatcccgctcattatagGATGATTCTAACAAAACTCCTGCTTCTGCTCGACATAAAAGAGGATGCAATTGCAGGAAGTCTTCTTGTCTTAAAAAATACTGCGAGTGCTTTCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
gttaggacataattctt--gccttgtgtttatacaga--aaatctgaactgctagttaccc---tgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
|| || | || | | ||   | || | ||   ||     || | | |||   |  ||   |   | |||| |    ||||  |||||||||||| |||| |||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||| ||||| ||||||
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattat--tttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
gttaggacataattctt--gccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
|| || | || | | ||   | || | |||        ||| | |||      ||  | | |         |||| ||||||||||||| | || |||||||||||| ||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||| ||||||||||||
gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccc-tgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
||||| | ||||      | | || |||   |  |  |  ||||       |||    | |||| |    | || |  || ||||||| || |  |||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||| ||||||
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatctttt--tgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
gttaggacataattcttgccttgtgttt-atacagaaaatctgaactgctagttaccc-tgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
||||| | ||||   |  | | || ||| |   |   |||   |||  |   |||    | |||| |    | || |  |||||||||| || |  ||||| |||||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||| ||||| ||||||
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaattattatctttt--tgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
gttag-gacataattcttgccttgtgtttata-----cagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
|| || |   | | | || |||| |  ||||      ||  | || |       |    |  || | || |   |  ||   |  ||||| ||  | || ||||||||||||||||| ||||||||| |||| || ||||||||||||||||  || || |||||||| || ||||||||||||
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaggacataattcttgccttgtg-----tttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
||  |    |  | |  | | | ||     | |  |      ||||    |||| |      |  ||| |   ||  |  |   ||||||||  | ||||||||||||||||| || || || ||| | || |||||||||||||||||||  || || |||||||| || ||||||||||||
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataa-tattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgag---gttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
                   |      ||    |   ||           |  |   |||          |||  ||      |||    ||| |||    ||||||||  | || ||||| || ||||| |||||||||||| | || |||||||||||||||||||  ||  | |||||||| || ||||||||||||
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG

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|110702530|gb|EE081350.1|EE081350
EST:     CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGG                         GATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC
genomic: CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacat ... tctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC
EST: gi|351044072|gb|FQ452745.1|FQ452745
EST:     CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGG                         GATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAA-GAGGATGCAAC
genomic: CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacat ... tctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG
                                          ttttctcttgc  CT-rich tract
     agaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA