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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttattaagatgttatcccttccatatattaaaattcctgattcttttttccctccattttggcctttattcaataccaccgtatcataaattttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG

Basic information

species Vitis vinifera
transcript Vv09s0054g00890.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 15
gtgtgttattaagatg-ttatccctt--ccatatattaaaattcctgattcttttttccctccattttg-gcctttattcaatacc-------accgtatcataaattttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG
|| |||  | ||| || |||     |  ||  ||  |  |  |    |   || | | | |  | || | |  ||  ||| ||  |       |   | | |  | |||  | |||  || |  ||||| | ||| | ||||||||||||| ||||||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| ||||||||||
gtatgtcctcaagttggttactttgtaaccccattctccagctttctacatttgtatgcatatagttagtgttttggttccatgactttcctgatttttttaatattttctttttggtatctttagGCACTTGAAACCTTTTATGAGCAATTTGATCCAGATTTTATAAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 15
gtgtgttattaagatgttatcccttccatatat---taaaattcctgattcttttttccctccattttggcctttattcaataccaccgtatcataaat---tttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG
|| |||  | ||| || |  |  |   |   ||     |  || ||   | | | | |      ||||||  ||   | | |  | ||| ||  | |||   ||  | |||  || |  ||||| | ||| | ||||||||||||| ||||||||||||||||||||| ||||||||||||||||| || |||||||| ||||||||||| ||||||||||
gtatgtcctaaagttggttactttgtaactcatcctccagctttctacatttgtatgcatagtgttttgg--ttccatgactttccccgaatttttaatattttctttttggtatctttagGCACTTGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
gtgtgttattaagatgttatcccttccatatattaaaattcctgattcttttttccctccattttggcctttattcaataccaccgtatcataaattttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG
                           ||   | || ||||  | |||    ||  ||   |||       |||  |  |     ||||   |||   |   || || |||  ||||| |||||||||| |||||| | |  ||||||||||| ||||||||||||||||||||  | |||||| |||| || ||||| || || ||||||||||
-------------------------gtatgcttaaatattctcggttcaaacttgtcttggttta-----ctatctagaaatcttgtatataaaacgctgctttttgtttt--agGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG

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|110720887|gb|EE097200.1|EE097200
EST:     AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACG                         GCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAATATCAGG
genomic: AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACGgtgtgttatt ... tgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGG
EST: gi|110715176|gb|EE092929.1|EE092929
EST:     AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACG                         GCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGG
genomic: AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACGgtgtgttatt ... tgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGG
EST: gi|110707093|gb|EE083190.1|EE083190
EST:     AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACG                         GCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAATATCAGG
genomic: AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACGgtgtgttatt ... tgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGG
EST: gi|37189190|gb|CF608539.1|CF608539
EST:     AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACG                         GCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGG
genomic: AACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACGgtgtgttatt ... tgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttggcctttattcaataccaccgtatcataaattttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG
                                   ttttctcttgt  CT-rich tract
                          tatcataaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttattaagatgttatcccttccatatattaaaattcctgattcttttttccctccattttggcctttattcaataccaccgtatcataaattttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG