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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactggattctatcatcaaacttgtaccatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA

Basic information

species Vitis vinifera
transcript Vv11s0016g03200.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g09300.3 (Oryza sativa), 3'ss of exon 5
---------------gtcactggattctatcatcaaacttgtaccatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA
               ||||     |  |  | |  |   | |   |||  | |    | |||||  ||   ||  |  | | | || |||||| ||||||| || | ||  ||||     ||||| | | |||||||||||| |||||||| |||||||| || || ||  ||||||| ||||||||  | || || ||
gtggacaaaaaacaggtcatgcattcttgccgttcag--tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttc-atcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 5
gtcactggattctatcatcaaacttgtaccatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA
||||     |  |  | |  |   | |   |||  | |    | |||||  ||   ||  |  | | | || |||||| ||||||| || | ||  ||||     ||||| | | |||||||||||| |||||||| |||||||| || || ||  ||||||| ||||||||  | || || ||
gtcatgcattcttgccgttcag--tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttc-atcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 5
------------------gtcactggattctatcatcaaacttgtaccatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA
                     ||      ||   |  | |  ||   || ||| ||    | |||| | |||   |  ||  ||      | ||||    ||||||| | || ||||||||||| ||| |||||||||| || || ||| ||||||||||  | ||||| || || |||||||||||||||   || |||||
gtaaaaagtggcaaatcgcgtacacatagctggtactatatctggtacaattacaaagaaaaataatttatacaat--tgtattcatttttgtttcatgaagGTCAAGTTTCGGATCCCTTGAAAGGATTATATGGAGCTGGAGCTCATACTGACTATGGTTTAATTACACTGTTAGCAACAGATGATGTCTCGGGTCTTCA

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S180_67V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtcactggattcta--tcatcaaacttgt-accatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGT---CAAATCTCTGATC---CCTTGAAG--GGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA
      | | | ||||     || |||| ||  |    ||||  || ||     |    |       |    || |  |      |  |  |||   || ||     |||     |||||   |||||||||||| | ||||| |||||||| |||||||||||||| ||  | || || || || || |  || || ||
gattgctaattcgattgggattcttcaatctcatcgagattttgaattggtctcattaaacgatcaaaaaccttctttcacacaactctggggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTGATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCA

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|110390246|gb|EC955146.1|EC955146
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|71881554|gb|DT030609.1|DT030609
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTGAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|71887181|gb|DT036236.1|DT036236
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTGAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|77589174|gb|DV223847.1|DV223847
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTGAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|110690968|gb|EE068534.1|EE068534
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAA                         GTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCCAG-TGCACATTCT
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGC-AGGTGCACATTCT
EST: gi|71884795|gb|DT033850.1|DT033850
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTGAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|110404543|gb|EC969762.1|EC969762
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|30253270|gb|CB970821.1|CB970821
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|110421097|gb|EC987385.1|EC987385
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
EST: gi|71884047|gb|DT033102.1|DT033102
EST:     TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAG                         GTGAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG
genomic: TATTGCAACCTTGCGCCTACTGCATTATGAAGGTGGAAATCAAATTGAAGgtcactggat ... tttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA
             atataac  putative branch site (score: 3)
                                   ttttcccctttttcca  putative PPT
     aaaactgtatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactggattctatcatcaaacttgtaccatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG