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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttttattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG

Basic information

species Vitis vinifera
transcript Vv00s0445g00020.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0445g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G071714_T01 (Zea mays), 3'ss of exon 2
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttttattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
                                                            |   ||    ||      | |  |||     | || |  | |  |  ||     |  |||||    |       |||||      ||   | |  | ||| | |    ||     ||| |   |||| || ||| ||||| ||||| ||||| ||  |||| || || || ||| | |  ||||||||  |||||||||| ||||| ||||| || || ||||||||||||||
------------------------------------------------------------gtaagagacatgtacctcactgtatgcttggctacttgaatgttagtatggagttggtcacc----ggccctgtcagtta-----atacattaaccattccatatgctgtaccc-ttgctactaattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTGGATTGCATGTTTTTGCGCACAACATTGAAACTGTGGAAGAGCTTCAAAG

upper sequence: Vv00s0445g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G32890.1 (Glycine max), 3'ss of exon 2
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttt--tattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggttttt--attgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
                                                                                                |  | ||||  ||  |  ||| || |  || | |  |   ||  | |     |     |||  |||      || || ||  | | ||     || |  |||||| || || ||||||||  ||| |||||| || || ||| | ||||| ||||||||||| ||||| ||||| |||||||| |||||||||||||| ||
------------------------------------------------------------------------------------------------tctagggaactatgctagtatgcttaattcaaaaccttttcaaatacagct-taaaaaatttcttcctgtgatgattgttgcactatttttgtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACACAACATTGAGACAGTTGAAGAGCTTCAGAG

upper sequence: Vv00s0445g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G37570.1 (Glycine max), 3'ss of exon 2
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttttattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
                                                                    |    ||  |||   |        ||      |  |||| |||| | |    | ||   ||||      || || | ||| ||  | |  |||         ||||||||||           |||||| || || ||||||||  ||| |||||| || || ||| | ||||| ||||||||||| ||||| || || |||||||| || ||||||||||| | 
-------------------------------------------------------------------tgacaattattatgctagtatgcttaatt----aaaaatctttttaaatacagcttcacaaattt----attcctgtgatgattgttgcactct---------ttttattgtta---------cagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACATAACATTGAGACAGTCGAAGAGCTTCAGAA

upper sequence: Vv00s0445g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G20860.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttttattctcacctc-tagaattccccagttgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
                                                                                                             |  |||  | | ||  | | |||   ||       |||||  |  |  ||| |||   ||  |||| ||||| |  ||  |||||||||||| ||||| |||||   ||| ||||| || || ||||| || || ||  | ||||| || |||||||| |||||||| |||||||||||||| ||
------------------------------------------------------------------------------------------------------------gtaatataatgatctggtgggattgatca-------tcatgagttttggtttttaa-tttg--ttttgttgtttg--atgatgtagTTCCTGATTTCCGCGGAGATGGTGGATGTGTTGAGAAGGTTTCCAAGTCAGGGCTTGATGTCTTAGCTCACAACATTGAGACAGTTGAAGAGCTTCAGAG

upper sequence: Vv00s0445g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S70_295V6.1 (Physcomitrella patens), 3'ss of exon 2
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttttattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
                                                                                    | ||| |||     | ||   |    ||  ||  |  |   |||| |    |||   |||   || |  |    ||   |||||     | |    | |   |    |||||| || ||||| || || || |  |||||||||| |||| | | ||| ||  | ||||| || |||||||||||||| || |||||||||||||||||
----------------------------------------------------------------------------------tttagaatcca-----ctagtttttgccttggtttgcttcaacagaaatagtgagtg--tcttgcggatgttcaaatcattacctgaaacatgt----gcgtgcttcacagTTCCGGATTTCCGTGGTGATCCGGCGTGTGTGGAAAGAGTTGCAACATCGGGGCTTGATGTGTTCGCTCACAATATTGAAACTGTTGAAGAGCTTCAAAG

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|77585571|gb|DV221879.1|DV221879
EST:     GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTG                         TTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
genomic: GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTGgtagtaatct ... aattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
EST: gi|110360592|gb|EC923821.1|EC923821
EST:     GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTG                         TTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
genomic: GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTGgtagtaatct ... aattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
EST: gi|77581729|gb|DV219812.1|DV219812
EST:     GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTG                         TTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
genomic: GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTGgtagtaatct ... aattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
EST: gi|110390977|gb|EC955927.1|EC955927
EST:     GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTG                         TTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG
genomic: GGTGCAGAAATTGAAGATTCTGAAGCCCAATATGCTGATTGAAGCCCTTGgtagtaatct ... aattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
                   ttctaaa  putative branch site (score: 2)
                               tttttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttttattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggtttttattgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT