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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGTGTAGTAACACAACGTGGTTTTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttataattctcttacaagcacactttttgtgtggcttagccgattgttactgacatggaactttttttattag

Basic information

species Vitis vinifera
transcript Vv05s0077g01210.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 9
ATCAGTGTAGTAACACAACGTGGTTTTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttataattctcttacaagcacactttttgtgtggcttagccgattgttactgacatggaactttttttattag----------------
|||| ||| || ||||| |||||||||||||||||||||||||| |||||||| || ||||| ||||| ||| |||| ||||  ||       |  | ||  |||| |           |   |  |  ||   |||| |  |    |   |                 
ATCAATGTTGTTACACAGCGTGGTTTTATTCCTGTTGATGAGCGAATGCGAGTCATGGATGCAGATGGCAATGTGgtatgttgaaacaaatgaattaccatgctttgttcagaataatcctcttcctggcttgtatgggatctaacatgccatgcatttttatttgtag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 9
ATCAGTGTAGTAACACAACGTGGTTTTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttata----attct-cttacaa-gcacacttt-ttgtgtggc---ttagccgattgt--tactgacatggaactttttttattag----------
 |||  || || |||||||| |||||| |||||||||||||||| |||| ||| || || || ||||| |||  |||  ||||      || || | |||||  ||  |||| |||  || |   |||| |  | |    |||  ||  | ||   |||   ||           
GTCAACGTTGTTACACAACGCGGTTTTGTTCCTGTTGATGAGCGGATGCAAGTTATGGACGCAGATGGCAATGCGgtacgttaagttgcatactacctacaatacattctttgttgcttgccattttagacattggcacaactaccaatgcacacctttggctaataatcttcct

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 9
ATCAGTGTAGTAACACAACGTGGTTTTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttataa-ttctcttacaagcacacttttt---------gtgtggcttagccgatt----gttactgacatggaactttttttattag
|||| ||| || ||||||||||||||| | ||||||||||| || |||||||| || ||||| | ||| ||| |||| ||||  || || | || || | |  ||||           ||||  | |      ||     | | | ||||  | | || ||    ||
ATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTGgtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacag

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|110398357|gb|EC964660.1|EC964660
EST:     TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTG                         GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCT
genomic: TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttata ... tttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCT
EST: gi|34544811|gb|CF513043.1|CF513043
EST:     TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTG                         GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCT
genomic: TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttata ... tttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCT
EST: gi|351031178|gb|FQ445005.1|FQ445005
EST:     TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTG                         GTTCCTCACTTGTATTGCATAGGTGATGCAA
genomic: TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttata ... tttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAA
EST: gi|34549728|gb|CF517960.1|CF517960
EST:     TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTG                         GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCT
genomic: TTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttata ... tttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCT
EST: gi|351023248|gb|FQ432631.1|FQ432631
EST:     TATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAAATCTG                         -TTCCTCACTTGTATTGCATAGGTGATGCAAATGG
genomic: TATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAA-TCTGgtctgttata ... tttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAGTGTAGTAACACAACGTGGTTTTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTGgtctgttataattctcttacaagcacactttttgtgtggcttagccgattgttactgacatggaactttttttattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA