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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgccttcttggttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatctttttctctttg...

Basic information

species Vitis vinifera
transcript Vv14s0081g00200.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G40930.2 (Glycine max), 5'ss of exon 2
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgccttcttggttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaata-atcaatctttttctctttg------
||||| ||||| |||||||| || ||||||||||||||||| |||||||||||||| ||  | |  || ||||| ||||||| ||       | |  ||  | | ||  || |||  |  | | ||   |     |    | ||  | |    ||  | || | | | |   |||  |      
TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAATTCAGGCAAGCTTAGCGAGTGTGCCGAgtaagaat-------tagacttattcttctgttacgtttgaaatgaatttagtgtgtcatttctttatttcttgtcaagcatattagtgtctcgatctgggtacata

upper sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G30650.1 (Glycine max), 5'ss of exon 2
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgccttcttggttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatcttttt-----ctctttg----
|| || ||||| |||||||| |||||||||||||||||||| ||||||||||| || ||  |||  || ||||| ||||||| ||     |||  ||   |  || |  | ||  | | |||  ||  |       | ||  ||  || | |  | | || |  | || |     ||  |||    
TACCTGGATGAGAACAAGTCCTTGATTCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCCGAgtaag-atttagacttaattgcaacatcatcttttgaaa-attttgtttttc-------atatcttaatttggtaacagtgatgaccccttctggtggctagttggaag

upper sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G43580.1 (Glycine max), 5'ss of exon 2
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgccttcttggttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatctttttctctttg-----
||||| ||||| |||||||| || ||||||||||||||||| ||||||||||| || ||  |||  || ||||| ||||||| ||  |  |||  | ||   |||  | |   ||  | ||    |  ||||       || |  |||  ||   |||||   |||   |||   ||     
TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCCGAgtaagaattaca-cttattcttttgttctgtttgaattgaatttagtgtttctcatttct--ttattacttgtcaagcataat--gtctccatctgggtgcctgg

upper sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G36960.1 (Glycine max), 5'ss of exon 2
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaag---tatgccttcttgg------ttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatctttttctctttg
|| || ||||| |||||||| ||||| |||||||||||||| ||||||||||| || ||  |||  || |||||||||||||   |   |    |||       |||| |     |||| | | |||  ||| ||  || || ||| ||     |||    |   || |        |        
TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttggactaaattgcaacatcttttgaaaaatttgtttctcatatcttagtt-tcttaacaaacatgcccccttctggtggctagttggcagagt--------

upper sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G28640.1 (Arabidopsis thaliana), 5'ss of exon 2
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtat--gccttcttggttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatctttttctctttg
||  | || |||||||| || |||||||||||||||||||||   || || || |||||  | |  ||||| || |||||||      | |   |  |||    || |   | |||| | ||| | | ||   |||  |   |  |  |    |||                       
TACTTGGACGAAAACAAATCGTTGATTCTGAAGATTGTTGAGTCTCAAAACTCTGGAAAGCTTAGCGAATGCGCCGAgtaagagacaacatatctcctttatgatttcacttgtgttct-gttgagtaacaagaaatgatgattaaaatggttatag----------------------

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|110400803|gb|EC967383.1|EC967383
EST:     CTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGA                         GAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCAGCAATTGCTGA
genomic: CTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgc ... cttttttcagGAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGA
EST: gi|110733165|gb|EE109120.1|EE109120
EST:     CTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGA                         GAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGA
genomic: CTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgc ... cttttttcagGAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGA
EST: gi|37187930|gb|CF607281.1|CF607281
EST:     GGAAAATTGACTGAATGTGCAGA                         GAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGA
genomic: GGAAAATTGACTGAATGTGCAGAgtaagtatgc ... cttttttcagGAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGA
EST: gi|77581760|gb|DV219834.1|DV219834
EST:     CTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGA                         GAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATTGCTGA
genomic: CTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgc ... cttttttcagGAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaagtatgccttcttggttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatctttttctctttg

- - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcataaa