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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactaacagtggaggatgagttggaggtctcattatggggatgaatcaggcttcttttcattgatgatgtgattctgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT

Basic information

species Vitis vinifera
transcript Vv11s0016g02270.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 3'ss of exon 10
----ttactaacagtggaggatgagttggaggtctcattatggggatgaatcaggcttcttttcattgatgatgtgattctgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT---
     || ||| | |  |   ||        |||||||  ||  | ||||  |   |  ||  |||  |     |   ||| |||  | || || |      ||||||   | ||  |||| || ||||||||||| || || ||||| ||||||||  | |||||||||||||||||| | || ||| | || || || |||    
acaacta-taataatttattctgttcatatagtctcatcttgctgttgaacgacagta-ttcacatcaaaatcata--tctttttctttctgttctacttctagGATG---ACTCCTTGGTCGCCCATTTTGAATACCACAAGCACCCAATTACATCTGTGGAATGGAGCCCACATGAACCGTCAACACTAGCTGTATCATCAGCTG

upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g03822.2 (Oryza sativa), 3'ss of exon 1
----ttactaacagtggaggatgagttggaggtctcattatggggatgaatcaggcttcttttcattgatgatgtga-ttctgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT---
     || ||| | |      ||        |||||||  ||  | ||||  | | |  ||  |||  |     |   || ||||||||  |||  ||     ||||||   | ||  |||| || ||||||||||| || || ||||| ||||||||  | |||||||||||||||||| | || ||| | || || || |||    
acaacta-taataatttcttctgttcatatagtctcatcttgctgttgaacgacggta-ttcacatcaaaatcatatcttttgttttattttctacttc---tagGATG---ACTCCTTGGTCGCCCATTTTGAATACCACAAGCACCCGATTACATCTGTGGAATGGAGCCCACATGAACCGTCAACACTAGCTGTATCATCAGCTG

upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G28040.2 (Glycine max), 3'ss of exon 10
-ttactaacagtggaggatgagttgga-ggtctcattatggggatgaatc-aggcttcttttcattgatgatgtgattc-tgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT
  |    | |||          |||   | | |  || ||   || |||  |   || || | |  | |||| |||    ||  ||||    |||| ||||||||| ||||||||||||||||||||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||  |||| |||||||||||||
gatttagaaagtaactttcacattgtctgatttttttctgcttattaatttacttttgttattaaagctgatatgacaagtgcattat----ttttgtgggcagGAAGGAGATTCTGTGGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTAGCAGTTTCTTCAT

upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G11020.1 (Glycine max), 3'ss of exon 10
ttactaacagt-ggaggatgagttggag---gtctcattatggggatgaatcaggcttcttttcattgatgatgtgattc-tgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT
 || ||  | |  ||   | | ||  |    |||| ||| |   | | | | |   ||  |   |  | ||||||||    ||  ||||    |||| ||||||||| ||||||||||| ||||||||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||  ||||||||||||||||||
-tattatgatttagaaagtaactttcacattgtctgatttttctgcttatttacttttgctacgaaagctgatgtgaaaagtgcattat----ttttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTGGCAGTTTCTTCAT

upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G19540.1 (Arabidopsis thaliana), 3'ss of exon 9
ttactaacagtggaggatgagttggaggtctca-ttatggggatgaatcaggcttcttttcattgatgatgtgattctgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT
                 | ||||  |   |  |  |||     |   | ||   ||| || |   |   | ||||   ||   ||     | ||     ||| ||||||| ||||||||||||||||||| || ||||| || || ||||| || |||||||||||| | |||||||| || ||| | |||||  ||||  
----------------gtaagttaaaaaccgtagctatatattttccttagcaatctcttaac-aagattctgatatggtggcatataaatcttgaactagGGTGGAGATGCTGTGGTAGCACATTTTGAGTACCATAAGCATCCTATTACGTCAATTGAATGGAGCGCTCATGAAGCTTCGACACTTGCAGTCACTTCCG

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|110369277|gb|EC933431.1|EC933431
EST:     CTGGAAGTGATGATGGGACGTTTTCTATTCGTGATCTTAGGTTGCTCAAG                         GATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
genomic: CTGGAAGTGATGATGGGACATTTTCTATTCGTGATCTTAGGTTGCTCAAGgtatgcattt ... ttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
EST: gi|110410877|gb|EC976571.1|EC976571
EST:     CTGGAAGTGATGATGGGACGTTTTCTATTCGTGATCTTAGGTTGCTCAAG                         GATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
genomic: CTGGAAGTGATGATGGGACATTTTCTATTCGTGATCTTAGGTTGCTCAAGgtatgcattt ... ttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
EST: gi|110362753|gb|EC926305.1|EC926305
EST:     CTGGAAGTGATGATGGGACGTTTTCTATTCGTGATCTTAGGTTGCTCAAG                         GATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
genomic: CTGGAAGTGATGATGGGACATTTTCTATTCGTGATCTTAGGTTGCTCAAGgtatgcattt ... ttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
EST: gi|110389219|gb|EC954039.1|EC954039
EST:     CTGGAAGTGATGATGGGACGTTTTCTATTCGTGATCTTAGGTTGCTCAAG                         GATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
genomic: CTGGAAGTGATGATGGGACATTTTCTATTCGTGATCTTAGGTTGCTCAAGgtatgcattt ... ttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
EST: gi|110714196|gb|EE090829.1|EE090829
EST:     CTGGAAGTGATGATGGGACGTTTTCTATTCGTGATCTTAGGTTGCTCAAG                         GATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA
genomic: CTGGAAGTGATGATGGGACATTTTCTATTCGTGATCTTAGGTTGCTCAAGgtatgcattt ... ttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaggcttcttttcattgatgatgtgattctgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT
              cattgat  putative branch site (score: 4)
                            ttctgttttatgctct  putative PPT
          ttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactaacagtggaggatgagttggaggtctcattatggggatgaatcaggcttcttttcattgatgatgtgattctgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - gagttgg
- - - - - - - - - - - - - - - - - - -ggggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctc