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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGCAAAAGGCACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcctttttaccaatattttctagctcatagccaccgaatctggatgcttaaatcag

Basic information

species Vitis vinifera
transcript Vv05s0077g01200.t01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: LOC_Os01g23590.1 (Oryza sativa), 5'ss of exon 23
GTGTGGCAAAAGGCACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcctttttaccaatattttctagctcatagcc--accgaatctggatgc-ttaaatcag-----------------------------------------------------------------
|||  | ||        | |      ||      || ||||||   |   || ||  | |  || ||||| |||||||||||||| ||||| |||||||||| |||    |   | |      | |  | |    || | ||  |    |   || | | | ||||    |  | |      |||  || | ||                                                                  
GTGCTGAAACGAAGTTAAGTGCCAATGTACCTGATATTAGAAAGAAAGCGGAAGAAAGAGGCCTTGAGAAGGAAGAGGAAGACTATTTCAATGAGGACAGgtttgctgtctccctctcttttttttttccactttagtcattgaatgcttcactttttgtttataggaaaatggcactcttttgcactagagcattctatttcagtgttcatgaattgcattgtggtatgtaaaatgatatgataattactctttcttag

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G087749_T01 (Zea mays), 5'ss of exon 7
GTGTGGCAAAAGGCACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcct--ttttaccaatattttctagctcata---gccaccgaatctggatgcttaaatcag----------------------------------------
| |  | |  | |    | |  |   |||      |  |||||       ||  |  | | ||| ||||| |||||||||||||||||||| |||||||||| ||  | ||||||  | |      |   ||     | |  ||||| ||||||   | || | | |    |||  |       ||| ||  || |                                         
GCGCTGAACCAAGGTTGAATGCTAGTGTGCCTGACATGAGAAAGAAGGCAGAACAAAGAGGTCTTGAGAAGGAAGAGGAAGACTACTTCAATGAGGACAGgtttgt-tattgttttcttacttcccagtgatttcttcattattttagcaatatagacgagattagatattccagggtgcaaatatgttttgattatacggtgaatttgcaagttaaatgatatttgttctttctag

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA15G15270.1 (Glycine max), 5'ss of exon 21
------GTGTGGCAAAAGGCACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcctttttaccaatattttctagctcatagccaccgaatctggatgcttaaatcag
       || ||||||||| ||   || |    | |||  | |   || |||| |||||||||||||||||||||||||||||||||||||||| || ||   |||||||  ||||| |||     |||| ||    ||| ||  ||| ||| | |    |   |    | | ||     | |||  | |  ||||||
ATAATGATGGGGCAAAAGGTACTGCTATTATGATTGACCTTCG---AAGACGACTTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTTAATGA---CAGgtatttatcttctttc----acatgtattg-taggagattttatacaactggcatggggtctcttgaca-----tttggtggtt--aatcag

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA09G04260.1 (Glycine max), 5'ss of exon 22
------GTGTGGCAAAAGGCACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcctttttaccaatattttctagctcatagccaccgaatctggatgcttaaatcag
       || | ||||||| ||   || |    | |||  | |   || |||| ||||||||||||||||||| |||||||||||||||||||| || ||   |||||||  ||||| | |     |||| ||    | ||    ||| ||| | |    |   |    | | ||     | |||  | |  ||||||
ATAATGATGGGACAAAAGGTACTGCTATTATGATTGACCTTCG---AAGACGACTTGATGAGCGTGCTCTGGATAAAGAAGAGGAAGACTACTTTAATGA---CAGgtatttatcttctctc----acatgtattgttggagat-tttatacaactggcatggggtctcttgaca-----tttggtagtt--aatcag

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA07G37040.1 (Glycine max), 5'ss of exon 20
GTGTGGCAAAAGGC---ACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcctttttaccaatattttctagctcatagccaccgaatct--ggatgcttaaatcag
||| | |||| |      ||| || ||||||||||  | | ||||   ||| |||||||||||||||||||| |||||| |||   ||||| || |||||||||||   | ||| ||| |||| |||     | ||||       ||    ||| | | |||| |  || | |  ||| |   | |  ||  |||||
GTGGGACAAATGATGATGCCACTACTGCAGTGGACCTTCGAAGAA---GAAATGATGAGCGTGCTCTGGAGAGAGAAGAAGAACGGTACTTTAATGAGGACAGgtacataccttatttcttgatcatgc--tagtagattttcagttgtttatactgt-tagcacggagtctcttaattttttgtttatttgatcag

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|351017758|gb|FQ436111.1|FQ436111
EST:     GATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAG                         TGATGAAGAAGATACAGCATCTGCATGCGTGTCACATACCAATAAAGTACA
genomic: GATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatct ... cttaaatcagTGATGAAGAAGATACAGCATCTGCATGCGTGTCACATACCAATAAAGTACA
EST: gi|351022501|gb|FQ447023.1|FQ447023
EST:     GATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAG                         TGATGAAGAAGATACAGCATCTGCATGCGTGTCACATACCAATAAAGTACA
genomic: GATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatct ... cttaaatcagTGATGAAGAAGATACAGCATCTGCATGCGTGTCACATACCAATAAAGTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGCAAAAGGCACCATTAATGCAGTGGACAGTAGTAGAAAACGAATTGATGAGCGTGCTCTGGAGAAAGAAGAGGAAGACTACTTCAACGAGGACAGgtatgcatcttgtttgttgaacatataacaatagaagcctttttaccaatattttctagctcatagccaccgaatctggatgcttaaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA