Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA

Basic information

species Vitis vinifera
transcript Vv04s0008g02670.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G07870.1 (Glycine max), 3'ss of exon 11
gtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
                | |   |    ||||  |   |||   | ||    |||| | | | |     |  | |  || |  |    || ||| ||      || | ||   |  | ||| ||||||||||| || ||||||||||| ||||||||||||||||| |||
----------------ccagattcataatatgcc---atgccctcattactattttgttcatatttttctaaacaatgaaaatcacaatccatattctctgtctgttcttcctgttcagGAGTTGGGAATGATCCCAGAGAAGATCGTTATTTCAGCATCCCAAAACAA

upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ18278 (Selaginella moellendorffii), 3'ss of exon 11
gtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
                                                             | |   |||| | |  |      | || | |  || | |  |     | ||     ||| ||||||||||| ||| ||||||||||||| |||||||| || || || 
-------------------------------------------------------------gtaactacatttttacgttcaagtttaagaagcttgacacgccgagtttttgctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG

upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ22017 (Selaginella moellendorffii), 3'ss of exon 11
gtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
                                                             | |   |||| | |  |      |  | | |  || | |  |     | ||     ||| ||||||||||| ||| ||||||||||||| |||||||| || || || 
-------------------------------------------------------------gtaactacatttttacgttcaagttgaagaagcttgacacgccgagtttttgctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG

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|110367735|gb|EC931686.1|EC931686
EST:     CCTCGATTACGACCCTTGTTCCAATTATGGAAATTGGACCTATGGAGCAG                         GTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
genomic: CCTCGATTACGACCCTTGTTCCAATTATGGAAATTGGACCTATGGAGCAGgtgattcaca ... gttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
EST: gi|110389719|gb|EC954579.1|EC954579
EST:     CCTCGATTACGACCCTTGTTCCAATTATGGAAATTGGACCTATGGAGCAG                         GTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
genomic: CCTCGATTACGACCCTTGTTCCAATTATGGAAATTGGACCTATGGAGCAGgtgattcaca ... gttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA
                            ttttaat  putative branch site (score: 3)
                                    tcctatcctgtttt  CT-rich tract
               atctatatatgcattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA