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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaatttagaagcacttggggttttattcagtggtttggcagtgattataggaagtatttgtaggctttataatacttgaa...

Basic information

species Vitis vinifera
transcript Vv04s0008g04240.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g48160.3 (Oryza sativa), 5'ss of exon 5
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaatttagaagcacttggggttttattcagtggtttggcagtgattataggaa-gtatttgtaggctttat-aatacttgaa------
||||| || || |||||||||||||| || |||||||||||||| ||||| || || ||||||| |||        ||  |  | |  | |||  | |     | |||| |           |||  ||||   || || | | |    ||| | ||||  | |       
AAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAGgcatg--------ttccttaacacgttgaactattctcattattatgctactccaaaagagtccttatgaaaatgtctcttttttttttgtgaataaatcagtacaag

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g48160.2 (Oryza sativa), 5'ss of exon 5
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaatttagaagcacttggggttttattcagtggtttggcagtgattataggaa-gtatttgtaggctttat-aatacttgaa
||||| || || |||||||||||||| || |||||||||||||| ||||| || || ||||||| |||        ||  |  | |  | |||  | |     | |||| |           |||  ||||   || || | | |    ||| | ||||  | | 
AAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAGgcatg--------ttccttaacacgttgaactattctcattattatgctactccaaaagagtccttatgaaaatgtctcttttttttttgtgaataaatcag

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G481261_T01 (Zea mays), 5'ss of exon 6
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggca-gtatatttttctaaa------tttagaagcacttggggttt-tattcagtggtttggca-gtgattataggaagtatttg----taggctttataa-----tacttgaa---------
||||| || || |||||||| |||||||| |||||||| || || ||||||||||||||||||| | |    || |  ||  | | |      |  |  | |||||    |   ||| || ||     | | ||  ||    |||||| ||     ||  |  | | |      | ||| |         
AAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAGgcaagcttcgttttgttccccacacatcgttcaatcaacacttcacttccatatgcattgaaaaagaaagttgttcagtgaagtacttaaccatatacactgtcaactgtcatttgcatttttttag

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G470653_T01 (Zea mays), 5'ss of exon 5
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaatttagaa-gcacttggggttttatt--cagtggtttggcagtgattataggaagtatttgtaggctttataatacttgaa---------------------
||||| || || |||||||| |||||||| |||||||| || || ||||||||||||||||||| |  ||   || || |||   |   |    ||| |      || | |  ||   |  | | |    || |     | | |  |   |  ||||     | ||                     
AAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAGgca-agcttcattttgttccccacacatcctgcaatcaacacttcacttccatatgcattgaaaaagttgttcagtgaagtacttaaccatatacactgtcaactgtcatttgcatttttttag

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G30770.1 (Glycine max), 5'ss of exon 5
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaat---ttagaagcacttggggttttattcagtggtttggcagtg-attataggaagtatttgtaggctttataatacttgaa
||||| |||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||   |  | ||  |  ||  |    |    | |    | ||  | | ||   || |   ||   |  |||     |  |  |   ||   |  || |||  
AAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAGgtatcttacaaaatcatagtaggtgttctgtgtgtagcaagagtggtgt-cacgagtgtaagagcacagcatataccatgatcatgatctacttt-tatttg--

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA14G16070.1 (Glycine max), 5'ss of exon 4
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaat---ttagaagcacttggggttttattcagtggtttggcagtg-attataggaagtatttgtaggctttataatacttgaa
||||| |||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||||||||      | ||  |  ||  |    |    | |    | ||  | | ||   || |   ||   |  |||     |  |  |   ||   |  || ||   
AAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAGgtatctttcaaaatcatagtaggtgttctgtgtgtagcaagagtggtgt-cacgagtgtaagagcacagcatataccatgatcatgatctacttt-tattta--

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ22344 (Selaginella moellendorffii), 5'ss of exon 3
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaatttagaagcacttggggttttattcagtggtttggcagtgattataggaagtatttgtaggctttataatacttgaa
|| ||||   |||||||||| ||||||||||| ||||||||| ||||    ||  |||||| ||||  | |   ||  || ||   |    | ||| || |   | |  |   |  |||     |  || |                                
AAGCCTGGTACTTGGAGGCTGGCTTGCCAAACAATTGTTGGAGATAAGTCTAATGCTGGCAGGgta-agaaaagtaaattact---tgccaaggcaatttgatctcttgtttttcatttttttttttttctgcag----------------------------

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ25552 (Selaginella moellendorffii), 5'ss of exon 3
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggca-gtatatt--tttctaaatttagaagcacttggggtttt-attcagtggtttggcagtgattataggaagtatttgtaggctttataatacttgaa
|| ||||   |||||||||| ||||||||||| ||||||||| ||||    ||  ||||||||||| || | ||| |||  || | ||    |   |  ||   | |||| |||   |  ||  ||||                                       
AAGCCTGGTACTTGGAGGCTGGCTTGCCAAACAATTGTTGGAGATAAGTCTAATGCTGGCAAGgtaaggaaagtaaattacttgccaaggcaatttgatctcttgtttttcattttttttttctgcag---------------------------------------

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|110402342|gb|EC959914.1|EC959914
EST:     GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG                         GTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
genomic: GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagt ... tcgctttcagGTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
EST: gi|110374024|gb|EC938501.1|EC938501
EST:     GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG                         GTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
genomic: GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagt ... tcgctttcagGTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
EST: gi|351021976|gb|FQ437763.1|FQ437763
EST:     GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG                         GTTGTAGTTCAGAGATTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
genomic: GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagt ... tcgctttcagGTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
EST: gi|30134334|gb|CB919672.1|CB919672
EST:     TAAAGAGAACTCTGGCAAG                         GTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
genomic: TAAAGAGAACTCTGGCAAGgtatggcagt ... tcgctttcagGTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
EST: gi|110379568|gb|EC944773.1|EC944773
EST:     GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG                         GTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT
genomic: GGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagt ... tcgctttcagGTTGTAGTTCAGAGACTGCCCCAGTGGAAGAAGTGAACAAGGCTCAACCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGgtatggcagtatatttttctaaatttagaagcacttggggttttattcagtggtttggcagtgattataggaagtatttgtaggctttataatacttgaa

- - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaagta