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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgacatccacacacaaatccgtttaatgtagctgtgaattcatgttgttttcttcagcatatgcttatatatgtgtacttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG

Basic information

species Vitis vinifera
transcript Vv10s0003g04900.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------atttgac-atccacacacaaatccgtttaatgtagctgtgaattcatgttgttttcttcagcatat---gcttatatatgtgtacttgaac-aatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
                                                                || ||  | |        |||  |    ||  ||||||       |      || |  |  ||||   |    | |   |  ||||  || ||    ||||||||||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgac--ataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG

upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 3
-------------------------------------------atttgacatccacacacaaatccgtttaatgtagctgtgaat------tcatgttgt-----------tttcttcagcatatgcttatatatgtgta-------cttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
                                           | ||| |||   || || | |     |   ||   |||||||      | | | |||           |   |  |  ||||  | |   |  |||         || |  ||    ||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG

upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 1
---atttgacatccacacacaaatccgtttaatgtagctgtgaattcatgttgttttcttcagcatatgcttatatatgtgtacttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
    ||  |     | |   | ||   |||     |  ||  |||      ||  |  | |  | ||   || |  ||   |  ||  | | ||| | |||||||| || ||||||||||| ||| ||||||||||||||||||||||||||||||| |||||  | || || ||||||
taagttgtagggtaatagctacatgaattttcctaaattgataatgtggaatgcatattacttcttag--ttgtgaatccatttttcta-actgcttcttcagGTCAGCCAATATTGGAGTTTTTGTATGCTTAAAATGTTGTGGTGTGCACAGAAGTCTTGGCTCTCAAATATCAAAG

upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 1
------atttgacatccaca-cacaaatccgtttaatgtagctgtgaattcatgttgttttcttcagcatatgcttatatatgtgtacttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
       |  || |    || ||  |||     |||  |     ||      ||   |     | | |   |  || |  ||   |  ||  | | ||| | |||||||| || ||||||||||| ||  ||||||||||||| ||||||||||||||||| |||||  | || || ||||||
taagttgtaggaaactagcaacatgaattttcctaaaatgataatg------tggaatgcatattacctcttagttgtgaatccatttttcta-actgcttcttcagGTCAGCCAATATTGGAGTTTTCGTATGCTTAAAATGCTGTGGTGTGCACAGAAGTCTTGGCTCTCAGATATCAAAG

upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------atttgaca--tccacacacaaatccgtttaatgt---agctgtgaattcatgt---tgttttcttcagcatatgcttatatatgtgtacttgaacaatgcat---------tttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
                                     |||| |    ||   |  ||  |   || |||||        ||  | | |     ||  || ||  |  | |     | |  ||  ||    | ||  | |         || |||||| || ||||||||||| |||||||||||||||||||||||||| |||||||||||||| |  ||||||||||||
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgattgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG

upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
atttgacatccacacacaaatccgttta-atgtagctgtgaattca-tgttgttttcttcagcatatgcttatatatgtgtacttgaacaatg---cattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
       || |      |  | | | || ||||   ||||  || | |  ||| |  ||  |  | | ||||||| ||  || |     | |      ||||||| || |||||||| ||||| || || |||||||||||||| ||||||||||| ||||| || || ||||| ||||||
----attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatat-tgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG

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|161708530|gb|FC061280.1|FC061280
EST:     ATCGCACTTGTGCCGATTGTGGTGCTCCAGATCCCAAATGGGC                         GTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: ATCGCACTTGTGCTGATTGTGGTGCTCCAGATCCCAAATGGGCgtaagtttca ... gcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|161719936|gb|FC066718.1|FC066718
EST:     AGTGATAATCGCACTTGTGCCGATTGTGGTGCTCCAGATCCCAAATGGGC                         GTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGCACTTGTGCTGATTGTGGTGCTCCAGATCCCAAATGGGCgtaagtttca ... gcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttttcttcagcatatgcttatatatgtgtacttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG
                                              cattttc  CT-rich tract
                atatgcttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgacatccacacacaaatccgtttaatgtagctgtgaattcatgttgttttcttcagcatatgcttatatatgtgtacttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - -ccacaca
- - - - - - - - caaatcc
- - - - - - - - - - - - - - -tgtagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatgc