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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttgaatgccacataatattttagatgctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG

Basic information

species Vitis vinifera
transcript Vv19s0085g00720.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
-taaatttgaatgccacataatattttagatgctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG
     ||||||  |||  | |   |          |     | | | ||     ||  | |     |   |        ||   |  | | |||   | |||| || || ||||||||||| ||||| ||  | || ||| | ||||||||||| || |||||  | |||||||| ||||| ||||| ||||||||||||
agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttgtgcaagtagacggttgtcaaattgtgcatatttggttctcttttgta-agCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
-taaatttgaatgccacataatattttagatgctgagccatt-ttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG
 |   |   |||  || |      ||  ||||   |   ||| ||   ||  |              | | |    |   |    || | || ||     |||| || || ||||||||||| || || || || || ||| | ||||| |||||||| |||||  | ||||||||||| || ||||| ||||||||||||
tttcgtcacaatttcagaactagcttatgatg--aatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 10
-taaatttg--aatgccacataatattttagatgctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaa---acagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG
 | | ||    | | | |  |  ||  | |  | ||||       ||||       | |    |||||      |  ||  ||||  |||  |||       | || |||| || |||||||| || |||||||||||||| ||| ||||||| |||||||| |||||||||||||| |||||||||||||| || |||||||||
ctgacttctgtagttctagcttttaaataactttctgaaatgacctttcc------acatcttacacctggttcgttgaattaaaattctgctttcttgtgtatagTTGGATGGAGGAGGTGTGGCAAGTGGAGGTCTTCGAGAACTGATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAG

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
taaatttgaatgccacataatattttagatg-ctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctattttt-caaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG-
   | ||   |    |    | ||  | ||  ||     |  |   |||  ||||    | ||   | | ||   |   ||||  |||  |||    |  || |||| || ||||||||||| |||||||||||||| ||| | ||||| |||||||| |||||||||||||| |||||||||||||| || ||||||||| 
-tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcatt--ggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
taaatttgaatgccacataata-ttttagatgctgag---ccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG
                || ||  ||||| |   | |      ||||| | || |    |  || |  |  ||  |    |    ||       || | |   || |||| || || |||||||| |||||||| ||||| || || |||||||||||||| || ||||| || || ||||| || ||||||||||||||||||
--------------gtatgatccttttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G16340.3 (Arabidopsis thaliana), 3'ss of exon 10
taaatttgaatgccaca-taatattttagatg--ctgagccattttttcttaac--aaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG
    | ||      | |   ||  | |   |    | ||  | |  ||  |     |||   ||| ||    || |  | |   |||  |   || || | | || | || || || |||||||| ||||| || ||||| ||||| ||||||||||| || || || || || |||||||| || ||||||||||||||||||
---gtatggtcattagaacgatgctctgagtaatttaagaaaatgcttggtgttttaaagctaaatcagaattggtctaaactcaaacataccttgtttatatagTTAGATGGTGGGGGTGTTGCTAGTGGTGGCCTTCGCGAATTAATACCATGCATAGCAAGAACCGCCGTAGCTGTTGGTGTCGATGGAATTTTCATGGAG

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|30127062|gb|CB912401.1|CB912401
EST:     GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAA                         CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
genomic: GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAAgtatggactt ... tttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
EST: gi|110388217|gb|EC952948.1|EC952948
EST:     GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAA                         CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
genomic: GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAAgtatggactt ... tttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
EST: gi|30252497|gb|CB970048.1|CB970048
EST:     GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAA                         CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
genomic: GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAAgtatggactt ... tttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
EST: gi|110360517|gb|EC923683.1|EC923683
EST:     GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAA                         CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
genomic: GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAAgtatggactt ... tttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
EST: gi|30128204|gb|CB913543.1|CB913543
EST:     GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAA                         CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC
genomic: GTGGCAGATGTCACACATTCACTACAACAGCCTGCGGGGAGAAAAgtatggactt ... tttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG
                                       tctatttttc  CT-rich tract
      aaaaaaaaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatttgaatgccacataatattttagatgctgagccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - ccacata
- - - - - - - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa