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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

Basic information

species Vitis vinifera
transcript Vv09s0002g01800.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 16
gtaaaaattatgtttca-atgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
        ||||  ||  ||| ||     | |  ||| | ||   | |   |||  | | |||||| |    | || ||  |  |||||||| ||||| ||  | || || || ||||| || || || ||||| ||||||||||||||||| ||||||||||||||||  ||  | ||||||||  
-----gtatatggatcgcatggtagctaatataagcatgagacaac-atcatttttcct-tgaaaatt---ctggtgctttt--cagGGAGGCACATTCACCATATCAAACCTAGGAGGTCCTTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATCTTGGCCATTGGTA

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
     |  |   ||  |  ||  ||| || ||| || |  |   | ||  |||  |  |||| ||||   |  ||  |  || |||||||| ||||| ||  | || ||  ||||||| || ||||| || |||||||| ||||||||||| |||||||||||||| |  ||  | |||||||| |
---gtatatggattgtatggtagttaatttttg-catgaaacaac-agcatttttc-catgagaactt-ttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
           || |       ||   |  |||        ||| |||  |||  | | ||| || | |  |       ||||||||| || || || |||||||| ||  ||||||| || ||||| || |||||||||||||||||| | |||||||| || ||||  ||| | || ||||| |
-----------gtataggccgaatatatatttgat------tcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 11
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
||| |   |   |   |    |  ||   |  || |||        ||     ||   |||| |  | | | |  | |  || ||||| || || || ||  | || ||  ||||||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||  ||| | || ||||| |
gtatatcgtgcatactaggtgtgctaa--gcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcattttt-cagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
---gtaaaaattatgtttcaatg--ttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcct-ccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
    | | | ||   | || ||   |||||  |   ||   |  || | || ||| |     ||||||   | |  | | | | | || |||||||| |||||||| ||| |||| |||||||| || |||||| |||| ||||||||||| |||||||||||||||||| |||||||||| ||| |||| |
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggct-ggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA07G03930.2 (Glycine max), 3'ss of exon 16
---gtaaaaattatgtttcaatg--ttattagttgttggcaagtgatcgctagggtttaacatatgaaaact-ggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
    |   | ||   | || ||   |||||  |   ||   |  || | || ||| |     ||||||   | |||||      | || |||||||| |||||||| |||||||| |||||||| || |||||| |||  ||||||||||| |||||||||||||||||| | |||||||| ||| |||| |
gtaattggagtttcatgtccattctttattcatctgtgaataacgacctcttgggct-ggtttatgaatttttggcttgaattgcattacagGGAGGTACATTTACAGTGTCTAACCTGGGAGGGCCATTTGGTGTCAGACAATTCTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGAT

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 16
gtaaaaattatgtttcaatgttattag-ttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
          ||    ||| | ||||  ||  |  | | | ||  ||     | |||||   ||   |    ||||  ||    |||||||| ||||||||||| |||||  |||||||||| ||||| |||||||||||||||||  || | ||||| |||||  | | |||||||||  |||| |
---------gtgagagaat-tcattatcttactcactaatcatatctttcagtaaacatgctaa---taatctcgttttct---cagGGAGGAACATTTACTGTCTCTAACTTGGGAGGACCTTTTGGCATCAAGCAATTCTGTGCAGTCGTTAATCCACCTCAAGCCGCCATTCTAGCAGTTGGAT

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 3'ss of exon 14
------------------gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
                   | || |||||| ||     |||||  ||  |  ||  |   |       ||||  | |||     |  || |  |     ||||||| || ||||||||  | || ||| |||||||||| ||||| || || ||||| ||||| |||||||||||||||||  ||| |||||| ||  ||||| 
attccgtgtttctgtgatttgaagattatgattt----ttattttttagtttcatttttccttcgttttttactaaatgttttttaactgcaacaattctgcagGGTGGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGA

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctcc----ttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
                                 | ||| | | |||  |   | | |  |||||      |  ||||       | |||||| || || || || || || ||  |||| ||||| ||||||||||| ||||| ||||| ||||||||||| || |||||  ||||||| ||| | ||  
---------------------------------gtaagcgtttgctttg-catgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA

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|22008294|gb|BQ793328.1|BQ793328
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|110407843|gb|EC973460.1|EC973460
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCTGTAGATTATGAG                         GGAGGGACATTTACTGTGTTTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|22009486|gb|BQ794520.1|BQ794520
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|33405959|gb|CF211586.1|CF211586
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCTGTAGATTATGAG                         GGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|34363482|gb|CF405067.1|CF405067
EST:     TAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: TAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|161714484|gb|FC064459.1|FC064459
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCATAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|32250355|gb|CD716174.1|CD716174
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|22009599|gb|BQ794633.1|BQ794633
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
EST: gi|30132039|gb|CB917378.1|CB917378
EST:     AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAG                         GGAGGGACATTTACCGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA
genomic: AGTTGGCCCAGAAAGCCAAGGAGAACAACTTGAAGCCCGTAGATTATGAGgtaaaaatta ... ctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT
                  gtttaac  putative branch site (score: 3)
                                      cttcgtcctccttgc  putative PPT
                   tttaacatatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC