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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaataaaaatatctttattcttatttttgcctttttttatactatgcatttatgttattactcactgttgcattgatgtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGAGGACAAATAGGGCTGATAGTGC

Basic information

species Vitis vinifera
transcript Vv12s0035g00280.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 11
agaataaaaatatctttattcttatttttgcctttttttatactatgcatttatgttattactcactgttgcattgatgtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTC--ACCTGGAGGACAAATAGGGCTGATAGTGC
            |||| |  ||| ||||   ||  ||| |  || | || |  |  | ||             ||||    ||| | |    ||||  ||| |||||||||||| ||||||||||  | || || ||||||||||||||||| ||||| || |||||        || |    | |  | | ||  |     
-------gtgagtcttcaaacttgttttcatctaatttcagtct-tacagtggtcgtgtt-------------ttgacacctttctatgtgtatatgtagGTGCTGTTGGATATTTGGGCTCCACCCTATTTGTGAGGAGGATCTACAGAAATATCAAATGCGACTAAACTTGGTCTAGGCTGCTAGCATGTCTTGTCAC--

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 11
------------------------------agaataaaaatatctttattc--ttatttttgcctttttttatactatgcatttatgtta--------tta--ctcactg-ttgcattga--tgtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGAGGACAAATAGGGCTGATAGTGC
                              ||||     ||| |||  ||   |  |   | ||||||||||   | |  ||| ||| ||        |||  || |    ||| ||||   |  |||| ||| ||||| | |||||||||| || ||||| || || | |||||| || |||||||||||||||||||||||||||||||| | |   || ||||     ||  | ||      
gtaagtcttcagtttaattgtaatctctgcagaaatgggataccttagttaagtgctgaatacctttttttaatatttatattaatgctagagtgttcttaatcttatcacttgaattggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------agaataaaaatatctttattcttattt--ttgcc--------tttttttatactatgcatttatgtta----------ttactcac--tgttgcattgat-gtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGAGGACAAATAGGGCTGATAGTGC
                                                    |||||    ||| |||  | |||| |   |||||         ||||||||| ||   ||| ||| ||          ||  | |   | |   || |||   |||| ||| ||||| | |||||||||| || ||||| || || | |||||| || |||||||||||||||||||||||||||||||| | |   || ||||     ||  | ||      
gtaagtcttcagtttaattgtaatctctgtttggattgtgtgttcactctgcagaattgggatacctt-gtccttagtcaattgccaaatacctcttttttatatta-atattaatgctagagtagagtgttcttaatcttatcatatggattaaatttttctccaaatgtgcagGAGCTGTGGGTTATCTTGGTTCGAATTTGTTTGTGAGGAGGATCTACAGAAACATCAAGTGTGACTAAGGCTTTTGTAGGAGTCTGAGACCAGAGCACTT

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 11
-----------------agaataaaaatatctttattcttat----ttttgcctttttttatactatgcatttatgttattactcactgttgcattgatgt--------atttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTA-GGTCACCTGGAGGACAAATAGGGCTGATAGTGC
                  || | | | | ||    | |||||    ||     | || |  |    ||  |       | | ||  || |||   |||  |        ||||||||| |||| | |||||||||| || | ||| || || | ||||||||| |||||||||||||||||||||||||| || || |||   |||    | |  |  |        |  
gtaagtcttcttcaatttgatttagattttcaccctgcttatgtgattggatatcttatcgtgtgctgattaagccccacttctttctattgtcctgaattgggttataatttatctttaaatgtgcagGAGCTGTGGGTTTTCTTGGTTCAAATTTGTTCGTGAGGAGGATCTACAGAAACATCAAGTGCGATTAAGGTTTTCTGAGTCAGACCTGAGCACTTCCATA-

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------agaata----aaaatatctttatt----cttatttttgcctttttttatac-tatgcatttatgttattactcactgttgcattgatgtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGG--AGGACAAATAGGGCTGATAGTGC
                                                |||||    |   | |    |||    |  | || | ||| || |  | | ||     || |||  |||    |||   |   | | || |  |  |  ||| | |||||||||| || | ||| || || | ||||||||| ||||||||||||||||| |||||||| || || |       |  ||  |  |        ||||   
gtaagtcgtcttcaatttgatttagattttcaccctgcttatgtgattgaatatcttatcgtgtgccaattaagccccacttcttcctattgtcctgcataaagccttgtgtccttatctcctgaatcgg-gctataatgtttctttaatgtgcagGAGCTGTGGGTTTTCTTGGTTCAAATTTGTTCGTGAGGAGGATCTACAGAAATATCAAGTGCGATTAAGGTTTTGAGTCAGACCTGAGCACTTCCATAGG--

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 11
agaataaaaatatctttattcttatttttgcctttttttatactatgcatttatgttattactcactgttgcattgatgtatttatcttcaaatatt-cagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGA-GGACAAATAGGGCTGATAGTGC
              |    ||    | ||  || | || | ||||   | |  |||||||  |      |  |     ||   ||| |  |||| || ||||||||||||| || ||||| || | | |||| || |||||||||||||||||||||||||| ||||||   |  |  | ||| ||| || |   | |    
-------------gtgagctcactctcttcactctcttcaaactagcgagtggtgttattgatt-tgactaaaccttcgt---tatgtgaaaattttgcagGAGCTGTTGGCTACCTGGGATCAAATCTGTTTGTAAGGAGGATCTACAGAAACATCAAGTGCGACTAGAAGAGGTAAACGGAAAAAAAGAGAAAACAAAT-

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|110427641|gb|EC994090.1|EC994090
EST:     CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTG                         GAGCTGTTGGATATCTGGGCTCTACTTTGTTCGTCAGGAGGATCTACAGAA
genomic: CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtttct ... aaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAA
EST: gi|110426337|gb|EC992743.1|EC992743
EST:     CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTG                         GAGCTGTTGGATATCTGGGCTCTACTTTGTTCGTCAGGAGGATCTACAGAA
genomic: CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtttct ... aaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAA
EST: gi|28958732|gb|CB339359.1|CB339359
EST:     TTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTG                         GAGCTGTTGGATATCTGGGCTTTACTTTGTTCGTCAGGAGGATCTACAGAA
genomic: CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtttct ... aaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAA
EST: gi|110404372|gb|EC969330.1|EC969330
EST:     CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTG                         GAGCTGTTGGATATCTGGGCTCTACTTTGTTCGTCAGGAGGATCTACAGAA
genomic: CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtttct ... aaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAA
EST: gi|110428100|gb|EC994561.1|EC994561
EST:     CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTG                         GAGCTGTTGGATATCTGGGCTCTACTTTGTTCGTCAGGAGGATCTACAGAA
genomic: CTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtttct ... aaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttatgttattactcactgttgcattgatgtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGAGGACAAATAGGGCTGATAGTGC
                               atgtatttatcttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaataaaaatatctttattcttatttttgcctttttttatactatgcatttatgttattactcactgttgcattgatgtatttatcttcaaatattcagGAGCTGTTGGATATCTGGGCTCCACTTTGTTCGTCAGGAGGATCTACAGAAACATCAAGTGTGACTAGGTCACCTGGAGGACAAATAGGGCTGATAGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - -aaaaata
- - - - - - - - - - - - - - tgccttt
- - - - - - - - - - - - - - - - - - - - - ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg