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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg...

Basic information

species Vitis vinifera
transcript Vv15s0021g01580.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtatt------catcaagc--tggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg
|| || || ||||||||||| ||||| ||||| |||||| | |||||| | ||||| |||||||| || |||||||||||||||||  ||||  | |||      | | | ||  |  | |||  ||    |||   | ||  ||   |    |||  | ||| ||   |   | ||  || | |  | | |      
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaatttttttgccttaggcacttaaatctctatttt-ccatcttctaacctccctaacaaaaaccatgtcattacaaatatatc-ttgtgtggattat------

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 3
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattca---------tcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg-------------------
 |||| || |||||||| || ||||| || ||||| ||| |||||||| | ||||| |||||||| || |||||||||||||||||| ||||  ||  | |         | ||  | |  ||||        |  | | |     ||||| |  | |||| ||  |||    |  ||  ||    | |    |  |                     
ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgttacatcctctttaaattttggctctggtatttttcttattttcagtggtttttaatacttctagtgttgcctaaagtatttttgacatcatatccataatattctgcatgttcatgcag

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G027551_T01 (Zea mays), 5'ss of exon 2
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg
 |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| ||||||||||||||||||||   || |         | ||  | |  | |   |  ||  |  ||| | |      |  ||| ||||                                  
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCAagagttg--------gatgtttccaacgtaagag-aacttgaagattatgc----atgttcatgtag---------------------------------

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G152100_T02 (Zea mays), 5'ss of exon 2
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg
 |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| ||||||||||||||||||||   || |         | ||  | |  | |   |  ||     ||| | |      |  ||| ||||                                  
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCAagagttg--------gatgtttccaacgtaagag-aactcgaagattatgc----atgttcatgtag---------------------------------

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G115277_T02 (Zea mays), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcat---caagctggattctgcatccaaccaaactatagactgtt-ttgagaaattcttg-----------taatgctag-gaaaataattattttaactgtcccagg-----------------------------------------------------------------------------------
 |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | ||  ||  | |    |    |  |||    |   ||      |||| ||  || ||| || | || |            ||   |||  |  | || || || |   | |     |                                                                                   
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgttacatcctctttaaattagatacttaatatttgtataaaccattcttgtgagactcgtaaatgtgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtatctagtgttgcttaaagtatttttggtatcatatccataatattatgcatgttcatgtag

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G085670_T06 (Zea mays), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcat---caagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg
 |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | ||  ||  | |    |    |  |||    |   ||       ||| ||  ||                                                  
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACgtaagagaactcgaagattttctaatcaatgagtgcatgtattcagtgagttgttacatcctctttaaattagatacttaatatttgcataaaccattcc------------------------------------------------

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G152805_T01 (Zea mays), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggta--------ttcatcaagctggattct--gcatccaaccaaactata-----gactgttttgagaaattcttgtaatgctag-gaaaataattattttaactgtcccagg-----------------------------------------------------------------------------------
 |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | ||  ||          || | ||  | ||| ||    ||      |||||||      ||   || | |     || | ||   |||  |  | || || || |   | |     |                                                                                   
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgttacatcctctttaaattagatacttaatatttgtataaactattcctgtgagacttgtaaatgtgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtatctagtgttgcctaaagtatttttggcatcatatccataatattatgcatgttcatgtag

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G085670_T03 (Zea mays), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggta--------ttcatcaagctggattct--gcatccaaccaaactata-----gactgttttgagaaattcttgtaatgctag-gaaaataattattttaactgtcccagg-----------------------------------------------------------------------------------
 |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | ||  ||          || | ||  | ||| ||    ||      |||| ||      ||   |  | |     || | ||   |||  |  | || || || |   | |     |                                                                                   
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgttacatcctctttaaattagatacttaatatttgcataaaccattcctgtgagactcgtaaatgcgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtttctagtgttgcctaaagtatttttggcgtcatatccataatattatgcatgttcatgtag

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G25690.1 (Glycine max), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgc-taggaaaataattattttaactgtcccagg---
||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||||||||| || |||     |  |    |  |  |   |||   || |   || | | | |     | | |   |  |  | | ||| |   |||     | ||   
GTACTACCCTATGACCAACTGATGCAGGAGTTAGATGTGACAAATGTTCGTGAGCTTGAAGATTTTCTAATTAATGAATGCATGTATGCGgtaggcat-cattcccttccagagagtgtttacataaa---tatatgattgtaatacacatacgcagtctgtttgtgattgattctggcaacataatctggttt

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G35760.1 (Glycine max), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgag-aaattcttgtaatgctaggaaaataattattttaactgtcccagg--
||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||||||||| || |||  |      | |||  |      ||   ||  |||| |   |    |   ||  |     |  |  |   ||||  | | |||    |   
GTACTACCCTATGACCAACTGATGCAGGAGTTAGATGTGACAAATGTTCGTGAGCTTGAAGATTTTCTAATTAATGAATGCATGTATGCGgtaggcat-cattcattcccttcctgagtgt--ttaatgcatttactgctcaaaatgtacatttacaccatcattatcactgttatgattattgttattgcta

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G48710.1 (Glycine max), 5'ss of exon 4
-GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtat-----tcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgc----taggaaaataattattttaactgtcccagg
 ||||| |||||| | |||||||||||||| |||||  | |||||||| |||||||||||||||||||| || | ||| ||||||||  ||||||| ||     || |||||   || | |   ||    ||||||  |   ||    |  |||||  || ||||     |   | |||  ||||| | | | |      
GGTACTACCCTATAACCAACTGATGCAGGAGTTAGACATGACAAATGTTCGTGAACTTGAAGATTTTCTAATTAGTGAATGCATGTACTCggtagggatcattctcttcaag--agaatatatttctgctcaaactcaaatgtg----gcaaaattaatggaatgtgcatttacacaattgttattatgattattt----

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G02090.1 (Arabidopsis thaliana), 5'ss of exon 4
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg
||| | |||||||||  ||| |||   || ||||||||| | ||||| || ||||| || || |||||||||||||| ||||||||||||||  ||| || | | || |  ||||     | |    || |   |||||   || ||   |   |  ||||   |   |  || |||||    |  ||| 
GTATTGCCCTATGATACACTAATGGTCGAGTTAGATGTTTCCAATGTTCGCGAACTCGAGGACTTTCTTATCAATGAATGCATGTATGCGgtgagtactcttta-gcagtcttctaatctctatttgacaactaactgt---gacaa---cgcatggtgctc--attttttttcttttacactttgcag-

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|351022721|gb|FQ428630.1|FQ428630
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|351024207|gb|FQ423630.1|FQ423630
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|351030256|gb|FQ432194.1|FQ432194
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGTATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|161721497|gb|FC069725.1|FC069725
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|351028781|gb|FQ433211.1|FQ433211
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|352798513|gb|FQ480538.1|FQ480538
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|351039449|gb|FQ461316.1|FQ461316
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|351029115|gb|FQ435315.1|FQ435315
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|352791342|gb|FQ479729.1|FQ479729
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
EST: gi|351025041|gb|FQ433458.1|FQ433458
EST:     CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG                         GGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG
genomic: CAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattc ... cttttgttagGGCATAGTAAGAGGGAAGCTGGATCAGCTGCGACGGTGCTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtattcatcaagctggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa