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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtattatctgaattctcag

Basic information

species Vitis vinifera
transcript Vv18s0001g02700.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagctt----aagttttgta-ttatctgaa----ttctcag----------------------------------
| |||||||| ||||| ||||||||||| || || || |||||||| ||||| ||||| ||||||||||||||||||||||| || ||||| || || |||| | | | |    |||||    ||||  |  || | | |       |     ||    ||  |   ||   || || |    |  ||||                                  
TACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTAGATCTTGCTCATGCTCCTTTTACTCATACATCCACCTTTGCCAAGGGTTGGAGTGTTCCAAGgtatttacatacatatatt----ttcacagccatgtggaattcttttttttttttttagaaaatggatagccatgtggaaatgtcttcagaaatcatcatgctgatgctatgttcatttcccag

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgttt----gttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtattatctgaattctcag---
| || ||||| ||||| ||||| ||||| || || || ||| |||| ||||| |||||  ||||||| |||||||||||||| || ||||| || || |||| |     | | | ||||    | |   | |||  |||    |     ||   | | | |   |  |  ||| |  ||  |      
TACCGGTGGAGCATGGACTTCTGCTGGACAATCTATTAGATATTGCTCATGCTCCTTTTGCTCATACGTCCACCTTTGCCAAGGGTTGGAGTGTTCCAAGgtatttacatacatatcaactaaggacaac-tggccattgaaaatttttcacaaatcatcatgctgatgctatattcatctttgtcag

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G038487_T01 (Zea mays), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgcatttcatggttattttg-gagggcccatccagcttaagtt-ttgtattatctgaattctcag------------
| ||||| |||||||| || || ||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||||||||| || ||||| || || |||| ||| ||| |  || |  | | | |    ||  |   ||     ||      | |  |     |  |  ||||  ||                
TGCCAGTTGAACATGGACTACTCCTGGATAACCTCTTGGACCTTGCTCATGCTCCTTTTACACACACATCCACCTTTGCCAAGGGCTGGAGTGTTCCAAGgtatgtacctttgcatctcacttgtgaaaactaactgacgaatatacacttccataatatcaccatggtggctgatgtcgtgttgtttctgtcag

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G082527_T01 (Zea mays), 5'ss of exon 2
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgcatttcatggttattttggag---ggcccatccagcttaagttttgtattatctgaattctcag-----------------
| ||||| |||||||| || || ||||||||||| ||||| ||||| ||||| ||||| || || |||||||||||||| || || ||||| || || |||| |||  || |  || | |   | || || || |  |        |  ||| |  |  ||||  |       || ||  || |                 
TGCCAGTTGAACATGGACTACTCCTGGATAACCTCTTGGACCTTGCTCATGCTCCTTTTACACACACATCCACCTTTGCTAAGGGCTGGAGTGTTCCAAGgtatgtatctttgcatctag-gctccaagggtactgggatccttacctgatcgacatggagttccgaccgccatgcatggtctgcttgcctgggaagctag

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G11920.1 (Glycine max), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgc---atttcatggttattttggagggcccatccagctt--aagttttgtattatctgaa-----ttctcag---------
||||  | ||||||||| | ||| |||| ||||||||||||||||||||||||||||| ||||| || || || ||||| || |||||||| || || |||||||||    |  |||       || | |  || ||||     |  || |  |   |  ||    | | | ||   ||     || | |          
TTCCCATCGAACATGGGTTACTTTTGGACAACCTTTTGGATCTTGCACATGCCCCTTTTACTCACACTTCAACTTTTGCTAAGGGATGGAGTGTTCCCAGgtttgttttcttttataccctgagatctgaaagtcatttgcattgtaccctagaaactgaaaaccatttgtcattcaaaagagattttaaaaaaaatatt

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G42840.1 (Glycine max), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtt---tgttcctgtcaatatt---gcatttcatggttattttggagggcccatccagcttaagttttgtattatct----gaattctcag---------
||||  | ||||| ||| | ||| |||| ||||||||||||||||||||||||||||| ||||| || || || ||||| || |||||||| || || |||||   ||||  | | ||||       |  | |  || ||||  |  |  || |  |   | |   |  |   ||      ||  | | |          
TTCCCATCGAACACGGGTTACTTTTGGACAACCTTTTGGATCTTGCACATGCCCCTTTTACTCACACTTCAACTTTTGCTAAGGGATGGAGTGTTCCCAGgttttgtgttttttttaatacccagagaactgaaagtcatttgtgttgtaccctagaaactgaaaatcatgccattctaaagagatttaaaaaaaaaaaa

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G03430.1 (Glycine max), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttc--------ctgtcaatattgcatttcatggttattttggagggcccatc--cagcttaagttttgtattatct----gaattctcag-----
||||| | ||||| ||  | ||| |||| || |||||||||||||||||||||||||| ||||| || || || ||||| || |||||||| || || |||||||||         |  | || | || |    || || |||  | ||||   | |        | |  |   | |  ||    |   | | |      
TTCCAATTGAACACGGTTTACTTTTGGACAATCTTTTGGATCTTGCACATGCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAGgtttgtttggtttataccattaaaactgaaagcaattgtcattcagaaggggtaaccagtgatgaagggatcaaaatgccttttggggatgttacaattt

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA14G23860.1 (Glycine max), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttc--------ctgtcaatattgcatttcatggttattttggagggcccatc--cagcttaagttttgtattatctg----aattctcag-----
||||| | ||||||||  | ||| |||| || |||||||||||||||||||||||||| || || || || || ||||| || |||||||| || || |||||||||         |  | || | || |    || || |||  | ||||   | |        | |  |   |||  |||    |  | | |      
TTCCAATTGAACATGGCTTACTTTTGGACAATCTTTTGGATCTTGCACATGCCCCTTTTACGCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAGgtttgtttggtttatacccttaaaactgaaagcaattgtcattcagaaggggtaaccagtgatgaagggataaaattgcctgttggagatgttacaattt

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G44446.2 (Arabidopsis thaliana), 5'ss of exon 7
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtattatctgaattctcag
| || |||||||| ||  | ||||| ||||| || ||||||||||| |||||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||| ||         ||| |  |    | | | |    ||     |    | ||||| ||| | || |  | | |  |||
TCCCGGTGGAACACGGTTTACTTCTAGATAATCTCTTGGATCTTGCTCATGCCCCATTCACTCATACATCCACTTTTGCAAAAGGCTGGAGTGTCCCAAGgtttcttttaactctcattactct----gttcagtgctaagatgaaacttggtttaagctttctgtttttggtactg-cag

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|110712590|gb|EE090383.1|EE090383
EST:     GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAG                         CTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
genomic: GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcct ... gaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
EST: gi|351052221|gb|FQ452375.1|FQ452375
EST:     GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAG                         CTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
genomic: GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcct ... gaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
EST: gi|349827565|gb|FQ422433.1|FQ422433
EST:     GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAG                         CTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
genomic: GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcct ... gaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCAGTGGAACATGGGCTTCTTCTGGATAACCTTTTGGATCTTGCACATGCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtattatctgaattctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA