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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctacaaagtttcatcattggtggactatttttgtcttatgatgtgcaactttgtaattatatttgcctctttatttcaatgcag

Basic information

species Vitis vinifera
transcript Vv08s0007g01700.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01700.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G27120.1 (Glycine max), 5'ss of exon 4
GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctacaaagtttcatcattggtggactatttttgtcttatgatgtgcaactttgtaattatatttgcctctttattt-caatgcag
|| |||||||| ||||| |||||||||||||| || ||| |||| ||||||| ||| || |||||||||||| ||||||| |||||||||||||| |||||  | || ||    | |     ||    | ||| | |    |  || | |  |||| || || ||  || || | | |||   ||||||
GAAGGAGTTGGGGCTCTTTGGACTGGGCTTGGCCCCAATATAGCAAGAAATGGTATCATCAATGCTGCTGAATTAGCCAGCTATGATCAAGTGAAACAGgtgatttaaaag---tgactggaggctagc-attgtggagcaaacattt-ctcctttatatttgtaaatgactatgtctttgttatgcag

upper sequence: Vv08s0007g01700.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G14780.1 (Glycine max), 5'ss of exon 5
GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctacaaa-gtttcatcattggtggactatttttgtcttatgatgtgcaactttgtaattatatttgcctctttatttcaatgcag
|| |||||||| ||||| |||||||||||||| || ||| |||| ||||||| ||| || |||||||| ||| ||||||| |||||||||||||| |||||  | || ||  |         | |     |        | | |    |  |  ||||||| || ||||   ||||| |||   |||||
GAAGGAGTTGGGGCTCTTTGGACTGGGCTTGGCCCCAATATAGCAAGAAATGGTATCATCAATGCTGCCGAATTAGCCAGCTATGATCAAGTGAAACAGgtgatttaaaagtgaccggaggctagcattgtggagcaaacatttctcctttatatttgtaaata-atttatgtcttttttt--gtgcag

upper sequence: Vv08s0007g01700.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G17380.1 (Glycine max), 5'ss of exon 4
GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctacaaagtttcatcattggtggactatttttgtcttatgatgtgcaactttgtaattatatttgcct---ctttatttcaatgcag
|| ||||||||||| || ||||||||| |||| || ||  |||| || |||| |||||| |||||||||||||||||||| |||||||||||||| |||||  |  | ||      |   |   |     | |     ||| | || |      || || || | | |  |    |||  |||   |||||
GAAGGAGTTGGAGCACTTTGGACTGGGATTGGTCCCAACATAGCAAGGAATGGTATTATTAATGCTGCTGAACTAGCCAGCTATGATCAAGTGAAACAGgtaatgaaaaagacactagactgcattttggagtaaaaccttgtaatctttcctcttttatttttttataacctaacttacttttgttgcag

upper sequence: Vv08s0007g01700.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA18G42220.1 (Glycine max), 5'ss of exon 4
-GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctacaaa-gtttcatcat-tggtggactatttttgtcttatgatgtgcaactttgtaattatatttgcctctttatttcaatgcag
 || ||||||||||| || ||||||||| |||| || ||  |||| |||||||  || || |||||||||||||||||||| ||||||||||| || |||||  |  | | |   |  |     |  |||| ||   || | | ||  | | |   ||| |  ||||||   |||     |||  ||||| 
GGAAGGAGTTGGAGCACTTTGGACTGGGATTGGTCCCAACATAGCAAGAAATGGCATCATTAATGCTGCTGAACTAGCCAGCTATGATCAAGTAAAACAggtaatgaaaagacactagactgcattttggagtaaaattttgtaatctt-tcctcttttatttttatata-acctaacagttttgatgca-

upper sequence: Vv08s0007g01700.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S54_186V6.1 (Physcomitrella patens), 5'ss of exon 4
GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgt----tgtctacaaagtttca----tcattggtggactatttttgtcttatgatgtgcaactttgtaa--ttatatttgcctctttatttcaatgcag--------------------------------------------------------------------------------------------
|| ||  |   |    |||||||||||||||| || || || ||  | || ||||| || |||||||| ||||| ||||||||||| ||||| ||||||||     ||||      |  ||    |  ||| || | |  ||| ||    ||     |   || | ||  ||  | |||  |   |||  ||  |||                                                                                             
GAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAGgtgagacgtctttcctatcccagttatttttgatgaagtgcttt-gttggctgcccctccttttcggaaagtttaagttgtttgcatatc-cagggcatatacctgcaattggcgcttccattttagattgtgatttcggatgttcgaaaagcactttcagtttactaatatggcatgttgcgctttgcag

upper sequence: Vv08s0007g01700.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S15_443V6.1 (Physcomitrella patens), 5'ss of exon 5
GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgt-----ctacaaagtttcatcattggtggactatt--tttgtcttatgatgtgcaactttgtaa--ttatatttgcctctttatttca----atgcag------------------------------------------------------
|| ||| |   |    |||||||||||||||| || ||||| ||  | || ||||| || |||||||| ||  | ||||||||||| ||||| |||||||||        | |  |   | ||  ||| ||    |||  ||| | || || | |   | || | ||  ||    |||  |  ||| ||||    |||||                                                       
GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAGgttaggcgtgttccttatcctgatttttgttgataaattgttttattttctgctcttttatttaggaaagttggtgttgtattgttaattcaggaaatgcactacgcaatcgggcaggacgtttgttttactaacatgacaagttgagctttgcag

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|33407463|gb|CF213090.1|CF213090
EST:     ATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAG                         ACGATTTTGAAAATTCCAGGGTTCAAAGATAATGTTTTGACTCATCTCTTA
genomic: ATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctaca ... ttcaatgcagACGATTTTGAAAATTCCAGGGTTCAAAGATAATGTTTTGACTCATCTCTTA
EST: gi|161718697|gb|FC066335.1|FC066335
EST:     ATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAG                         ACGATTTTGAAAATTC
genomic: ATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctaca ... ttcaatgcagACGATTTTGAAAATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAGgttgtctacaaagtttcatcattggtggactatttttgtcttatgatgtgcaactttgtaattatatttgcctctttatttcaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC