Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGTGGTTGATGAGCGTGCATATATAGAACTCTTCCTCTCAACCCGATGCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatcttttctgtcagctacaacattctttaatggtgattataatcccaagattagacttgtttaagcttcatccgtcccaattcacatgggtcag...

Basic information

species Vitis vinifera
transcript Vv07s0031g02170.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02170.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G32980.1 (Glycine max), 5'ss of exon 6
TGCAGTGGTTGATGAGCGTGCATATATAGAACTCTTCCTCTCAACCCGATGCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct--tttctgtcagctacaacattctttaatggtgattataatcccaagattagacttgtttaagcttcatccgtcccaattcacatgggtcag
||||   |||||||||||||| || ||||| |||||||| |||| ||| || || |  | |||||||||||||||||||||||  |  ||||||||||||||||||||||  || |     |    || |||||||| |  |  || |  |   ||  | |          ||| |  |     ||   |    |    |  
TGCATATGTTGATGAGCGTGCTTACATAGAGCTCTTCCTTTCAAGCCGGTGTGATTATAGCATTGTAGGTCAAGAGTTTACCAGAAATGGTTGGGGATTTgtaagtatctccttaccaatggtcctaatattctttagttttt-ttgtcttttaaatgtaatttggaacctagcatacttttctccttcttttctattcct-

upper sequence: Vv07s0031g02170.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G21470.1 (Glycine max), 5'ss of exon 6
TGCAGTGGTTGATGAGCGTGCATATATAGAACTCTTCCTCTCAACCCGATGCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct--tttctgtcagctacaacattctttaatggtgattataatcccaagattagacttgtttaagctt-catccgtcccaattcacatgggtcag--
||||   ||||| |||||||| || ||||| |||||||| |||| ||| || || |  | |||||||||||||||||||||||  |  ||||||||||||||||||||||  ||||  |  |     | ||||||||   ||  || |  ||   | ||   | |||   || ||  ||| | |  | ||||   |    |    
TGCATATGTTGACGAGCGTGCTTACATAGAGCTCTTCCTTTCAAGCCGGTGTGATTATAGCATTGTAGGTCAAGAGTTTACCAGAAATGGTTGGGGATTTgtaagtatctcctttccattggtccagatattcttta---gttttttttgtctttaaatgtaatttgg--aacctggcattcttttctattctttttttcctaaa

upper sequence: Vv07s0031g02170.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G09230.1 (Glycine max), 5'ss of exon 7
TGCAGTGGTTGATGAGCGTGCATATATAGAACTCTTCCTCTCAACCCGATGCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatcttt--tctgtcagctacaacattctttaatggtgattataatcccaagattag--acttgtttaagcttcatccgtcccaattcacatgggtcag
|||     ||||||||||||| || |  ||  ||||||| || | ||| || || || ||  |||||||||||||||| ||||  | ||||||||||||||||||||||| |    |||    |||||  | | |   |  |  || ||     | |  ||   || |||||     |||    | |   |     ||      
TGCTTACATTGATGAGCGTGCCTACACTGACATCTTCCTTTCCAGCCGTTGTGATTTAACTGTTGTAGGTCAAGAGTTCACCAGAAACGGTTGGGGATTTgtaagtatctctaacatgttctttacaatttacatgggttttttttctataagtatgtgtaactacatgttttcctctcaaatattctggtctgtgtgca----

upper sequence: Vv07s0031g02170.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G36210.1 (Glycine max), 5'ss of exon 6
TGCAGTGGTTGATGAGCGTGCATATATAGAACTCTTCCTCTCAACCCGATGCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatctttt--ctgtcagctacaacattctttaatggtgattataatcccaag--attagacttgtttaagcttcatccgtcccaattcacatgggtcag
|||     ||||||||||||| || |  ||  |||||||||| | ||| || || || ||  || ||||||||||||| ||||  |  |||||||||||||||||||||| |    |||    |||||  | | ||  |  |  || |  |  |      ||   ||| | ||||    | | ||    |   |||||  |   
TGCTTACATTGATGAGCGTGCCTACACTGACATCTTCCTCTCCAGCCGTTGTGATTTAACTGTTATAGGTCAAGAGTTCACCAGAAATGGTTGGGGATTTgtaagtatctctcacatgttctttacaatttacattggttttttttctcttttcttttccttttccttctataagaaataactgt----aactacatgttttcc

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|110413449|gb|EC979235.1|EC979235
EST:     GCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: GCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
EST: gi|71867053|gb|DT016108.1|DT016108
EST:     AGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: AGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
EST: gi|32458902|gb|CD800076.1|CD800076
EST:     AGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTC
genomic: AGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCC--TTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTC
EST: gi|110692604|gb|EE072042.1|EE072042
EST:     GTGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: GCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
EST: gi|87585438|gb|DY474156.1|DY474156
EST:     GCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: GCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
EST: gi|110421176|gb|EC987466.1|EC987466
EST:     GTGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: GCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
EST: gi|51052486|gb|CO819584.1|CO819584
EST:     AGCGG-TGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: AGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
EST: gi|71867349|gb|DT016404.1|DT016404
EST:     CATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTT                         GCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA
genomic: CATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatct ... atcttttcagGCCTTTCCACGTGACTCTCCGTTAGCAGTTGACATGTCTACTGCCATTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGTGGTTGATGAGCGTGCATATATAGAACTCTTCCTCTCAACCCGATGCGAATTCACCATTGTAGGTCAAGAGTTTACCAAGAGCGGTTGGGGATTTgtaagtatcttttctgtcagctacaacattctttaatggtgattataatcccaagattagacttgtttaagcttcatccgtcccaattcacatgggtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgtccc