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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagttttgactatcatgaatttttttgcttctgataatgctgacaaaactgccatacctcattaagacatacatgttacccttttccctctgccatt...

Basic information

species Vitis vinifera
transcript Vv19s0014g04740.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os08g08200.1 (Oryza sativa), 5'ss of exon 10
GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagtttt-----gactatcatgaat-----ttttttgcttctgataatgctg--acaaaactgccatacctcattaagacatacatgttacccttttccctctgccatt--------------------------------------------------------------------------------------
|||||||||||||| || |||||| |||| ||||| ||| |||||||||   ||||||| |||||||  | ||      |||||   || |     | |  || ||    | ||  ||    ||        ||     |   ||  | ||| |||   | |    | | | | |                                                                                      
GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctcttccttaaactattgcgagtaacactctgctgttttcccttattttgcagtaagttgattgtaaaatctatggaagttcattttatt-tctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcag

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G042398_T01 (Zea mays), 5'ss of exon 11
GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagttttgactatcatgaatttttttgcttctgataatgctg-acaaaactgccatacctcattaagacatacatgttacccttttccc-tctgccatt-
|||||||||||||| || |||||| |||| ||||| ||| ||||||||| ||||||||| ||||||  |           | |  || | |||||||  | | | ||      | |    || |||||  ||  | |      ||   ||| ||  | |  ||   
GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAGgtactgg----------aggggttctattgcttc-aacagtcctctgtgcagcctatatgcctcaccaatgcttgttacatattgtttgccaatgtttcacag

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G41190.1 (Glycine max), 5'ss of exon 10
GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtata-------gttttgactatcatgaatttttttgcttctgataatgctgaca--aaactgccatacctcattaagacatacatgttacccttttccctctgccatt-----
|| ||||||||||||||||||||||||||||| || ||||| ||||| ||||| || ||||||||||        ||||  |      |||| || |    ||    ||| ||||  |  | | | | |   ||  |    || |  |   |||   |||     ||   ||     
GACGCTGTTGATTGTCCTGAATGGATTGTCCCCTTCCATGTATTCAAGTCATTAGCTGAAGAGgtatgcatcactgtttgaaacgctgtgaaattctagattttc--taaggctggtatcagatttcaaaggcttgt----acttctagactactaatttaaacttgttgtttacag

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA08G22390.1 (Glycine max), 5'ss of exon 10
GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtat--agttttgactatcatgaatttttttgcttctgataatgctgacaaaactgccatacctcattaagacatacatgttacccttttccctctgccatt
|||||||||||||||||||||||||||||||| || ||  | ||||| ||||| || ||||||||||  |    ||  | | |   | |       ||||     | ||   | || |     |   ||   ||   |||   ||     ||  | | | |    
GATGCTGTTGATTGTCCTGAATGGATTGTCCCCTTCCACATATTCAAGTCATTAGCTGAAGAGgtatgtatcactgtttttgaaacaatgccaaatttctagcttttctaggataaatatttgattgca---aggattactcatttaaacttatcgtttacag--

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT3G20650.1 (Arabidopsis thaliana), 5'ss of exon 10
GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagttttgac-tatcatgaatttttttgcttctgataatgctgacaaaactgccatacctcattaagacatacatgttacccttttccctctgccatt
||||||||||||||||||||||||||||| || ||| | |||||||| || || || || |||||| |   ||||   |   | ||  |     | |   | | |||| | || ||||    |  |   | ||    ||||  | || |      |  |  |  
GATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAGgtaaatacttgatgcagtgttaacgtgaaaaccttcta-attgctaaaaacactggttcatatttgtgagtgtgacattgtcccatgaatttttggatag-

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|22011789|gb|BQ796823.1|BQ796823
EST:     GTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAG                         TATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAG
genomic: GTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagtttt ... gcttttgcagTATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAG
EST: gi|30124931|gb|CB910270.1|CB910270
EST:     GTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAG                         TATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAG
genomic: GTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagtttt ... gcttttgcagTATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAG
EST: gi|30125615|gb|CB910954.1|CB910954
EST:     ATTTCATGTCTTCAAATCATTGGCAGAAGAG                         GATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAG
genomic: ATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagtttt ... gcttttgcagTATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGgtatagttttgactatcatgaatttttttgcttctgataatgctgacaaaactgccatacctcattaagacatacatgttacccttttccctctgccatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccctc