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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattctattcctcttatgtagcttatgcacaaagatacattgtaagcatagaatcccttttattatgatttaacttaaccatggtctgtatgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGACCTTAGATATG

Basic information

species Vitis vinifera
transcript Vv05s0077g02310.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 12
------ggattctattcctcttatgtagcttatgcacaaagatacattgtaagcatagaatcccttttattatgatttaacttaaccatggtctgtatgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGACCTTAGATATG
       ||   | |||||  |   | | |  |      | |      |||   |  |  | | || | | |  | ||||  | |     || | | ||  || |||||||||||||||| || ||||| || ||  |||| || |||||||||||||||  |  ||
cacttttgaggttgttccttgtgc-tggatagtttcttgacaactgaagtacatactggcttcattctttgaaaagttaatcttat----gtttatttgtctc-agGATCCACAAGTTGTCACGGGCTCACATGATTCAACTATCAAGTTCTGGGACCTTGTAGCTG

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 11
ggattctattcctcttatgtag-cttatgcacaaagat---acattgtaagcatagaatcccttttattatgatttaacttaaccatggtctgtatgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGACCTTAGATATG
   |     || | | || | | ||| |    |  | |     |||    ||  |   |   | | ||  | | |  |  | ||  || ||||| |  || ||||| ||||||||||| || || ||||| ||||| |||||||| || ||||||||| ||||||
--gtaagtctcttttaatatggacttgttgttatggtttttggatttcttgctgaatctttttataatagtaactggaactcactttgatctgtgttgttgcagGACCCACAAGTTGTCACCGGATCCCATGACACGACCATTAAATTTTGGGACCTTCGATATG

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 10
ggattctattcctcttatgtagcttatgcacaaagatacattg--taagcatagaatcccttttattatgat-ttaacttaaccatggtctgtatgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGACCTTAGATATG-
 | |   | | ||| | || |   |    | ||   | ||  |  ||| |||  || |    ||| || | | || ||||         |  ||   ||||||||||||||||||||||| || || ||||||||||| |||||  | ||||| ||| | |    
tggtcaaagtactcat-tgcaaagtgaagataactttgcagagaataaacatt-aaccatcgttactaggttattgacttttttgcacccattaca-ttccagGATCCACAAGTTGTAACAGGATCACACGACACAACTATTAAACTTTGGGATCTT-GCTGCAG

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|110416775|gb|EC982779.1|EC982779
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|77578499|gb|DV218043.1|DV218043
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|254917683|gb|GR903335.1|GR903335
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|349818063|gb|FQ408838.1|FQ408838
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|351038798|gb|FQ464664.1|FQ464664
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|110384526|gb|EC948969.1|EC948969
EST:     TCTGGACATGATAATACAGTTTGCTCAGTTTTTCCCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: TCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|110724126|gb|EE099691.1|EE099691
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|110418288|gb|EC984425.1|EC984425
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
EST: gi|161707291|gb|FC057696.1|FC057696
EST:     CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACG                         GATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC
genomic: CACTGTCTGGACATGATAATACAGTTTGCTCAGTTTTTACCCGACCTACGgtatgtggat ... atgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatagaatcccttttattatgatttaacttaaccatggtctgtatgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGACCTTAGATATG
                            acttaac  putative branch site (score: 3)
                                              tgcttcc  putative PPT
             ttttattatgatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattctattcctcttatgtagcttatgcacaaagatacattgtaagcatagaatcccttttattatgatttaacttaaccatggtctgtatgcttccagGATCCACAAGTTGTAACTGGCTCCCACGACACAACCATTAAGTTCTGGGACCTTAGATATG

- - - - ttcctct
- - - - - - - - - - - cttatgc
- - - - - - - - - - - - - - -acaaaga
- - - - - - - - - - - - - - - - - - - - - gtaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatggt