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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga...

Basic information

species Vitis vinifera
transcript Vv13s0067g03320.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttcctttttacctctttttccttcattttcttccgccttttccc-acccagatctcggcgttttgtttcaaattttcaatacg--agaaacga-
 || |  |  | ||||||||||||| | || ||||||||||| |||||||| || ||||| || ||||| |||||||| |||||||||||||||||| |||||    |   |||    | |||||| |||  |  | ||  ||  | || | |  | |    || |  | |   | |   ||| | |    ||   |||  |  
GGCGGAAGGGGGGATGGACGACTACGCGCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATCAGGgta----caaatcccccatccctcttcttctcttctcttgctcacctttctgcggatctgactcactacttgcggatctcaatctccggcccgccggaattgct

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G099980_T03 (Zea mays), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttc-ctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga
|  |   || | ||||||||||||| | || ||||||||||| |||||||| || ||||| || ||||| |||||||| |||||||||||||||||  ||||   | | |    ||| ||  ||   |||||  |||   ||||     |      ||     | || |     | |  |  ||||||   |    |    
ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtacttccaacttattttcttcgtttccgccatcc-cttcattgatccggtgcctcacccacgcctcacggatctagcttttcatcccctccagttt

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgt----attttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgttt---caaattttcaatacgagaaacga
|  |    | | ||||||||||||| | || ||||||||||| || ||||| || ||||| || ||||| |||||||| ||||| |||||||||||  ||||    | || ||  | ||||    |  ||   | | | ||   |    |  |  | |||||| | | | |  | | | ||   |     | |  |  |        
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg-------

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttccttt--ttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga
         ||| |||||||| |||||  | || ||||||||||| ||||| || |||||||| || || |||||||||||||||||||||| |||||| |||  | |    | |    || ||||||     ||| |   | |    |  |||    |   |  | ||  | || || |   || |   |     |     
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatccattcaattctcaacttagggttattcttccgttttctttttgtctcag----

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga
    |    ||| ||||||||||||||  | || ||||||||||| ||||| || |||||||| || || ||||||||||||||||| |||| |||||| ||   | | |  |   ||    | |  |  |   |  | | | |   | || | ||  ||   |   | |     ||    ||||   |   ||      
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacatacc---ttagggtttcctcaccgtagatccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag------

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G55000.1 (Arabidopsis thaliana), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgt--attttcctttcctttttacc-tctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga---------------------------------------------------------------------------------------------
|  || |   | ||||||||| || ||  ||||||||||||| ||||||||  | |||||||||||||||||||||||||| |||||||| |||||||||||  |||  |  | | | | |||| |   ||     ||     ||  |  |          | |     | | || |||| ||||     ||||   |  |                                                                                               
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatac---atacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G55005.1 (Arabidopsis thaliana), 5'ss of exon 1
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaa-attttcaatacgagaaacga--
 || ||   |   |||||||| || ||  ||||||||||||| ||||||||| | |||||||||||||||||||||||||| || ||||| ||||||||||||| ||  |||   | || || |  || |  |  || | |  |    ||   ||  || ||  ||  |     ||| |  |     || | ||||||  |  
GGCGGTAAGAACAATGGACGATTATACAAGAGAGATGATGGATCTCAAGACCTTAGTCACTCGAACCCTAGAGAAGAAAGGTGTTCTCGCTAAGATCCGGgtatatttgtttttctcttgccacgattcctctggttctgtgacatactt---cattcaaattccgtagagagatttgagtacagagaagaagagaaaacata

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|110699314|gb|EE076202.1|EE076202
EST:     CCC-TGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCCAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|351043024|gb|FQ443866.1|FQ443866
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|110730208|gb|EE107028.1|EE107028
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|351029495|gb|FQ436889.1|FQ436889
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|349829621|gb|FQ421139.1|FQ421139
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|110410730|gb|EC976422.1|EC976422
EST:     GAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: GAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|110732400|gb|EE107653.1|EE107653
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|349827978|gb|FQ422846.1|FQ422846
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|110685295|gb|EE063554.1|EE063554
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|349825323|gb|FQ418055.1|FQ418055
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|349817511|gb|FQ407301.1|FQ407301
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGTT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|18458749|gb|BM437027.1|BM437027
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|110381982|gb|EC938169.1|EC938169
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|351014234|gb|FQ434823.1|FQ434823
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCTAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|351016330|gb|FQ446190.1|FQ446190
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|349827894|gb|FQ422762.1|FQ422762
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|294965188|gb|GW837019.1|GW837019
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|110710077|gb|EE086097.1|EE086097
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
EST: gi|349824073|gb|FQ417460.1|FQ417460
EST:     CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGG                         GCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT
genomic: CCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcct ... ttcttgccagGCTGAACTGCGAGCAAGTGTGTTTGAGGCAATAGAAGAGGAGGATCGGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaac