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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttggaagatcttctataatgacattcttttttgtgctttgggaaaataccaaaatcttctggaataccatgacttctcctgaggctttgacata...

Basic information

species Vitis vinifera
transcript Vv18s0001g02550.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA06G12110.1 (Glycine max), 5'ss of exon 7
GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttggaagatcttctataatgacattcttttttgtgctttgggaaaatacc------aaaatcttctggaataccatgacttctcc---tgaggctttgacata
|||| || ||||||||||||||||| |||||  |||||||||||||||| || |||||||| |  ||   ||| |||||   |  |||   | |  ||  |    ||  |        || || | ||| || ||  ||| | |      | |||| ||      
GAGTTATTATGAATGATGAGACAGTTCATCAGCTATGTAAACAAGCTGTAGCCCAGgtaatat--gactgtctgctatacacattttcaactgtaggcagttaccaatcattttttttaagatttactg-aacacattgattgccttaagtaaggcctt------

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA04G42670.1 (Glycine max), 5'ss of exon 8
GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttggaagatcttctataatgacattcttttttgtgctttgggaaaatacc-----aaaatcttctgga-atacc-atgacttctcctgaggctttgacata
|||| || ||||||||||||||||| |||||  |||||||||||||||| || ||||| || |  ||   ||||||||||  |  |||   | |  ||  |    || ||       || || | ||| | |||   || || |    |  ||| |||     
GAGTTATTATGAATGATGAGACAGTTCATCAGCTATGTAAACAAGCTGTAGCCCAGgtcatat--gactgtcttctataaacattttcaactgtaggcagttaccaattatttttttaagatttactgaacatattgatcaccttcagtatggccttg-----

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: EFJ10919 (Selaginella moellendorffii), 5'ss of exon 7
GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttggaagatcttctataatgacattcttttttgtgctttgggaaaataccaaaatcttctggaataccatgacttctcctgaggctttgacata
| || || ||||| ||||| || || |||||| |||| ||||||||||||||||||||  ||||           | |  |  |  | ||| | ||    || |                                                    
GCGTGATCATGAACGATGAAACTGTCCATCAACTATGCAAACAAGCTGTTGCTCAGgttttttt---------cttgttctttctctttttctggtttgctgag----------------------------------------------------

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: EFJ25898 (Selaginella moellendorffii), 5'ss of exon 7
GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttggaagatcttctataatgacattcttttttgtgctttgggaaaataccaaaatcttctggaataccatgacttctcctgaggctttgacata
| || || ||||| ||||| || || |||||| |||| ||||||||||||||||||||  ||||        |||| |  |    |  |||  || | ||| |     || ||                                           
GCGTGATCATGAACGATGAAACTGTCCATCAACTATGCAAACAAGCTGTTGCTCAGgtttttttcttgttctttctct--ttttctggtttgctgaggtttcgtg--ctatcag------------------------------------------

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|349830570|gb|FQ416868.1|FQ416868
EST:     TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG                         GCTAAGGCAGGAGCAGATGTTGTTAGTC
genomic: TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAAGGCAGGAGCAGATGTTGTTAGTC
EST: gi|351036615|gb|FQ457328.1|FQ457328
EST:     TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG                         GCTAAGGCAAGAGCAGATGTTGTTAGTCCCAGT
genomic: TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGT
EST: gi|110379323|gb|EC944509.1|EC944509
EST:     TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG                         GCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGTGACATGATGGATGGTCGT
genomic: TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGTGACATGATGGATGGTCGT
EST: gi|351052784|gb|FQ456511.1|FQ456511
EST:     TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG                         GCTAAAGGCAGAA-CAGATGTTGTTAGTCCCA
genomic: TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAA-GGCAGGAGCAGATGTTGTTAGTCCCA
EST: gi|351044566|gb|FQ443097.1|FQ443097
EST:     TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG                         GCTAAGGCAAGAGCAGAT
genomic: TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAAGGCAGGAGCAGAT
EST: gi|110373793|gb|EC938150.1|EC938150
EST:     TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAG                         GCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGTGACATGATGGATGGTCGT
genomic: TAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGTGACATGATGGATGGTCGT
EST: gi|351055179|gb|FQ440518.1|FQ440518
EST:     AATGAATGATGAGACAGTGCATCAATTATGTAAAACA-GCTGTTGCTCAG                         GCTAAGGCAGGAG
genomic: AATGAATGATGAGACAGTGCATCAATTATGTAAA-CAAGCTGTTGCTCAGgtaattttgg ... ttataaacagGCTAAGGCAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCATAATGAATGATGAGACAGTGCATCAATTATGTAAACAAGCTGTTGCTCAGgtaattttggaagatcttctataatgacattcttttttgtgctttgggaaaataccaaaatcttctggaataccatgacttctcctgaggctttgacata

- - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctcc