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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggcttttagtatctatatgagaagttctgctcttttaaatgacctacattcaattgaaatatatatgtatctctagacttaccaataacttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGTGCTAAAGTAGTTGGGCAAGCCCTTGCTGGTGTTCCCTTGTGGCAGCTAG

Basic information

species Vitis vinifera
transcript Vv17s0000g02140.t01
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 31
lower sequence: GLYMA07G11610.1 (Glycine max), 3'ss of exon 29
ctggcttttagtatctatatgagaagttctgctcttttaaatgacctacattcaattgaaatatatatg--tatctctagacttaccaata----acttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGTGCTAAAGTAGTTGGGCAAGCCCTTGCTGGTGTTCCCTTGTGGCAGCTAG
    | |  |     ||    | ||   | ||    | | ||        ||  ||||     |   |   ||    || ||| |  ||||    || |   ||||||||| || || || || || |||||||||||||| || |  |||||| |||| ||| ||||||| ||||| ||||||||| |||||||||||||  |||
---tcgtgcaaatcatagccaaaaaacccagcc---tcatattcttcctttttgattgtgtcctgagttcttaatcatacactgaaaaatatagtaccttttttagGGTGGTATTACGTCTTCAGATCTTGCTACAAAAGCCCTTGGTGCAAGATGTGCGAAAATAGTTGGTCAAGCACTTGCTGGTATTCCCTTGTGGCAATTAG
















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|71860468|gb|DT009523.1|DT009523
EST:     TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAG                         GGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
genomic: TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAGgtacttctat ... cttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
EST: gi|30253243|gb|CB970794.1|CB970794
EST:     TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAG                         GGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
genomic: TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAGgtacttctat ... cttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
EST: gi|37190316|gb|CF609665.1|CF609665
EST:     TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAG                         GGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
genomic: TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAGgtacttctat ... cttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
EST: gi|26257761|gb|CA808824.1|CA808824
EST:     TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAG                         GGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
genomic: TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAGgtacttctat ... cttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
EST: gi|37190358|gb|CF609707.1|CF609707
EST:     TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAG                         GGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT
genomic: TGGAAATTGTTAGGCGGATAACTACAAGACCTCGATATATCCTTGCAAAGgtacttctat ... cttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacattcaattgaaatatatatgtatctctagacttaccaataacttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGTGCTAAAGTAGTTGGGCAAGCCCTTGCTGGTGTTCCCTTGTGGCAGCTAG
                                       caataac  putative branch site (score: 2)
     ttcaattgaaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggcttttagtatctatatgagaagttctgctcttttaaatgacctacattcaattgaaatatatatgtatctctagacttaccaataacttggcttagGGTGGAATCACATCATCTGACCTTGCTACAAAAGCTCTAGAAGCAAGACGTGCTAAAGTAGTTGGGCAAGCCCTTGCTGGTGTTCCCTTGTGGCAGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
-tggcttt
- - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - -acctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaataa