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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatccaagggtcccacttttttctgctaattttgagtaagataatgattcatccaaatagttacttatttggatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA

Basic information

species Vitis vinifera
transcript Vv04s0008g03810.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G157332_T05 (Zea mays), 3'ss of exon 2
------------------tttcatccaagggtcccacttttttctgctaattttgagtaagataatgattcatccaaa---tagttacttatttg-gatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA
                     ||        || ||  ||||      | ||||   |   | ||||    || |||    ||||     |  || |||||  || ||   ||     ||||| || || || || ||  |||| || || || ||||||||| ||||| ||||||| ||  |||| |||||||| ||||||||||||||| ||||  | ||
gttggacaaactacaaagagacaatattatatcacaaattttggcttcattttttcttgcaagaatgtggaatacaagctgtagtccggcacatgtgatgat-ttcttcatttttggtgcagGTAATAAAGTCAATAACATTGATGTAGTTTATACTCCATGGTACAATTTGAAGAAGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAA

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G08640.1 (Glycine max), 3'ss of exon 2
tttcatccaagggtcccacttttttctgctaattttgagtaagataatgattcatccaaatagttacttatttggatgacattatttgctta--catggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA
    |   |   ||   | |||||  |   | |  ||  |    |    ||| |   || |   |   | |   | | ||  | |||  |||  ||||||||| || || |||||||||||||| || || |||||||| |||   ||| | |||||||||||||| ||||||||||| |||||||||||| |||| |||||
-gatacatatatgtagtaatttttcttcagattcatgtatttccttccaatt-acaaaattctatgtgtgtagtgctcaccatttttctttattcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGGCAAGTTGGTTTTCACAACTCAAA

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 3
tttcatccaagggtcccacttttttctgctaattttgagtaag-ataatgattcatccaaatagttacttatttggatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA
     | ||||   |  |  | |   |  |  || |    |   ||     | | ||||| || | | || | ||  |  || |   |   | ||||||||| || || ||||||||||| || || || ||||| || |||   ||| | |||||||||||||| |||||||||||||||||||||||| |||| |||||
-aggtttcaagatacatatatgtagttaatttttcttcacattcatgtatttccttccaattactaaattctgtgtctaccaattactttattcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G11500.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------tttcatccaagggtcccacttttttctgctaattttgagtaagataatgattcatccaaatagttacttatttggatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA
                                              ||  ||  || || ||| ||| || |    |    | | |  |||  | ||  | |   |  || ||||   |  ||   |  |  | |||  || ||||||||||||||||||| ||||| || || |||||||| |||  |||  ||||||||||||| || ||||||||||| |||||||||||  ||||||||||
gtaatctttttttctacctgtcgtgaacttaacatttgcataaccattagtcttagagtaccagtttgttttttagaaggagggcac-atataggttttttc---tgttttcttacc-gactggtgtc-tgggattatgtgccagGCAACAAGGTGAACAACGTTGATGTTGTGTACACTCCGTGGTCCAACTTGAAGAAAACTGCCTCCATGGATGTTGGTCAAGTTGGTTTCCACAATTCAAA

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|161720775|gb|FC070283.1|FC070283
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA
EST: gi|34549359|gb|CF517591.1|CF517591
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACGATC-ATGGCACAATCT
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACAC--TCCATGGCACAATCT
EST: gi|110715789|gb|EE094238.1|EE094238
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA
EST: gi|110710049|gb|EE086042.1|EE086042
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA
EST: gi|30128520|gb|CB913859.1|CB913859
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA
EST: gi|161721392|gb|FC070768.1|FC070768
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA
EST: gi|110357353|gb|EC920834.1|EC920834
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA
EST: gi|27583079|gb|CB005774.1|CB005774
EST:     AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAG                         GCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTAA
genomic: AGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatg ... tacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgattcatccaaatagttacttatttggatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA
                                         tgcttac  putative branch site (score: 2)
                                       tttgctt  CT-rich tract
            aaatagttacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatccaagggtcccacttttttctgctaattttgagtaagataatgattcatccaaatagttacttatttggatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- tcatcca
- - - - - - -tcccact
- - - - - - - - - - - - -ctgctaa
- - - - - - - - - - - - - - - - - - - - aagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatga