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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagttctagcttagactc...

Basic information

species Vitis vinifera
transcript Vv00s0282g00040.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 5'ss of exon 12
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccctttccctttctgtcagctagataatcctactaatgtttc-tagtttcccacatcatttatgtaaagaaaacagttctagct-tagactc
||| |||||||||||||| ||  |||||||||||||||| ||||||||||| || || ||||||||||| ||||| ||||| ||||||||| |||| |||||     | |   | |   ||      |  |   ||||  |   ||| ||   || ||  | |  |     || |      || |  || |  | |  | | 
TGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtaatgttgtttgtgtttgttcacactaaatttgtaattttg--aatattgaataattgtctaattgccgaatttcccatgaataaatccatttgttcattt

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA13G32670.1 (Glycine max), 5'ss of exon 14
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagttctagcttagactc---
||| |||||||||||| | || ||||| |||||||||||||||||||  ||||| || ||||| ||||| |||||||| || |||||||| |||||||||||  ||||||    ||   ||| | | ||||   |||       |||     ||   |  ||  || |||    | ||  |   ||  | || | |       
TGTTAAACCAAGTTTGAGGCCTCTATCTATGGCTATGTCTACTGTTGTTATTCATATCTTTGGCGATGTACCTTCCTCGCCTCTTGTTGGAGTTCTCCAGgtcagcctttatacttttatttgt-tgagctcattaacatggggaat--cagtatcatggcaattcttttgccaacagttacttgtagtggcatggctgaaca

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA07G30370.1 (Glycine max), 5'ss of exon 14
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagttctagcttagactc------
||| |||||||||||| | ||||| || |||||||||||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||  || | |||||| || |||    ||   ||    |||     ||  |       | ||   || ||| ||||| |||       |     | |||     || ||  ||      
TGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTACCTTCCTCACCTCTTGTTGGACTTATGCAGgttagctttt----ttaagttgtattcattacaatttttaagtggaagtaattacttttccacaacatgatgaccagatttatagtctc--ctcaggttcaagggg

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G06880.1 (Glycine max), 5'ss of exon 13
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccc---tttccctttctgtcagctagataatccta---ctaatgtttctagtttcccacatca-tttatgtaaagaaaacagttctagcttagactc
||| |||||||||||| | ||||| || |||||||||||||||||||| ||||| || ||||| ||||| ||||||||||| || |||||  || |||||||| || |||      ||    |   |      |   |   |  |     || |     |||||  || || |  | |||      |  || |  |   |       
TGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTGCCTTCCTCACCTCTCGTTGGACTTATCCAGgttagctttttttaagttgtattcattacagatttagtgtcctcaggttcaagggaaaaagtttggcaaatgagctgatgcctttgaggcattattttgt-------

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA15G06660.1 (Glycine max), 5'ss of exon 14
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagttctagcttagactc---
            |||| | || ||||| |||||||||||| ||||||| ||||| || ||||  ||||| |||||||| || |||||||| |||||||||||  ||||||    ||   |||  | ||  |  || | | |  | | ||   |   ||  ||  || |||    |  |  |   ||  | || | |       
------------TTTGAGGCCTCTATCTATGGCTATGTCTGCTGTTGCTATTCATATATTTGTAGATGTACCTTCCTCGCCTCTTGTTGGAGTTCTCCAGgtcagcctttatagttttattt--gacaagttcattaacatggtga-gtcaatgtcttggcaattcttttgctaacggttacttgtattggcattgctgaaca

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G64500.1 (Arabidopsis thaliana), 5'ss of exon 12
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttcc--ctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagt--tctagcttagactc-------------------------------------------------
||| ||||||||| || | || ||  ||||||| |||||||||||  | || || || ||||| ||||| |||||||||||||| ||||| ||||| ||||||||  ||  |  || |  |           |   | |     ||||||| | || |       | | |   |  || |  |  | |  ||||| ||||  |                                                  
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctcagctgtatccacaaaattcttgattcagagctctaatgtct-taatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag

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|22011957|gb|BQ796991.1|BQ796991
EST:     TTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAG                         GATAGTGTTAACAACTGGAGAGAGACTGCTCTTATTCTAACATCTATACTA
genomic: TTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgccttt ... gatcctacagGATAGTGTTAACAACTGGAGAGAGACTGCTCTTATTCTAACATCTATACTA
EST: gi|110376483|gb|EC941548.1|EC941548
EST:     TTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAG                         GATAGTGTTAACAACTGGAGAGAGACTGCTCTTATTCTAACATCTATACTA
genomic: TTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgccttt ... gatcctacagGATAGTGTTAACAACTGGAGAGAGACTGCTCTTATTCTAACATCTATACTA
EST: gi|32460991|gb|CD802165.1|CD802165
EST:     TTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAG                         GATAGTGTCAACAACTGGAGAGAGACTGCTCTTATTCTAACATCTATACTA
genomic: TTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgccttt ... gatcctacagGATAGTGTTAACAACTGGAGAGAGACTGCTCTTATTCTAACATCTATACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttccctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagttctagcttagactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa