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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaaatgaaaaatttatttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT

Basic information

species Vitis vinifera
transcript Vv11s0052g01480.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 4
gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaaatgaaaaatttatttcctgtggaatgtgac---aattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
                                                                                       ||||   |  |  | | |    |    ||  | ||   |  |||  || ||   | ||   ||   || || | ||  |||  ||||||||| ||||| |||||||||   ||  |||| ||||||||| ||||||| ||||||||||| ||||| |||||||| || ||||||||| | ||||||
--------------------------------------------------------------------------------------gtact---atatattgaatccaagaaataagaatatttgatcttttatttctcctgtatcgaactctaaattaaagcgcttgtgcagGACAATTGATCGCCGGAAGAGAGTAATATTAGCCATGGATGCTGCATTTGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGT

upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 3
gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaaatgaaaaattta---tttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
                                                                                             | | | |   || |      | ||  ||  | | ||||    ||   | |    | |  |||  | | ||  |||  ||||||||||||||| |||||||||   ||  |||| ||||||||| ||||||| ||||| ||||| || || |||||||| || ||||||||| | || |||
---------------------------------------------------------------------------------------------gcactacattttctaaagcaagaaataagaatatatttggtcttctatttctcctttatcaaaataaagcacttgtgcagGACAATAGATCGCCGGAAGAGAGTAATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCACGGGAAGAATATAGTCCATTTTGACCTGAAGTGT

upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 10
gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaa--atgaaaaatttattt-cctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
                         | | |    |  |||  |    |||  |||| ||  | ||     ||| ||| ||| |||    || | | ||||    ||    ||||||      ||| |   || || |   | |  |   ||   ||| |  || ||| ||||| |||||||||||||| ||||| | ||| ||||| ||||||||| ||||||| ||||||||||| ||||| || || ||||| |||||||| || ||||||
-------------------------gtaatttgatgcatgcatgggcttatatttcatcaatatttaatagtatgctttaaggca----ctgaaatgtgcagccttccatctgaaagccctcatggactgttgatgtatttatttatgctgtttattctgagcaatttaacagAACAATAGATCGTCGTAAGAGGCTCATTATAGCCATGGATGCTGCATTTGGGATGGAGTATTTGCATGGAAAAAACATTGTGCATTTTGATTTGAAATGT

upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 7
gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaa--atgaaaaatttatttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
                         | |      |  |||  |    |||  |||| ||  | ||      || | | ||| |||    || | | ||||    ||     ||||||     ||| |    | || |  | |  |   ||   ||| |  || ||| ||||| |||||||||||||| ||||| | ||| ||||| ||||||||| ||||||| ||||||||||| ||||| || || ||||| |||||||| || ||||||
-------------------------gtaacttgatgcatgcatgggcttatatttcatcaatatttaa---tatgttttaaggca----ctcaaatgtgcagccttccatatgaaaaccctcatggactggtgatgtattatttatgctgtttattctgagcaatttaacagAACAATAGATCGTCGTAAGAGGCTCATTATAGCCATGGATGCTGCATTTGGGATGGAGTATTTGCATGGAAAAAACATTGTTCATTTTGATTTGAAATGT

upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaaatgaaaaatttatttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
                                                                            || |||   |  || ||    |||  ||| | | ||        | ||  |    |||  |||    |  | ||| |  |   ||  |   ||| || || |||||||| || |||| ||||||||| |||||| || ||||||| ||||||||||| || || ||||| ||||| ||||| || || || |||
---------------------------------------------------------------------------gtaaaaaagtttcacctattcatgc--attatatactattttccta-gagtatccaattatctg----acatcacattggttgactcctc--cagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT

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|71881847|gb|DT030902.1|DT030902
EST:     GAATTCATGGTTAATGGTTCTTTGAAACAATTTTTGCAGAAAAAGGACAG                         GACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGG
genomic: GAATTCATGGTTAATGGTTCTTTGAAACAATTTTTGCAGAAAAAGGACAGgtaattgttt ... tattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGG
EST: gi|71883412|gb|DT032467.1|DT032467
EST:     GAATTCATGGTTAATGGTTCTTTGAAACAATTTTTGCAGAAAAAGGACAG                         GACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGG
genomic: GAATTCATGGTTAATGGTTCTTTGAAACAATTTTTGCAGAAAAAGGACAGgtaattgttt ... tattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGG
EST: gi|71882459|gb|DT031514.1|DT031514
EST:     GAATTCATGGTTAATGGTTCTTTGAAACAATTTTTGCAGAAAAAGGACAG                         GACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGG
genomic: GAATTCATGGTTAATGGTTCTTTGAAACAATTTTTGCAGAAAAAGGACAGgtaattgttt ... tattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaatgaaaaatttatttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
     atgaaaaatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaaatgaaaaatttatttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA