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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaagatgtccaggaactcatggatttgttgtcattaaccatcgccttcctttaaccag

Basic information

species Vitis vinifera
transcript Vv03s0038g02340.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA06G00600.2 (Glycine max), 5'ss of exon 16
---AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaagatgtccaggaactcatggatttgttgtcattaaccatcgccttcctttaaccag---------------------
   | | ||||| | |   || || || |||||||| |||||||||||||| ||||| |||||||||||||||||||| || |||||||| |||||||||||||||  ||  | |     |     ||    |       | ||  |  ||  |  | |||   | | ||||  |      |                      
TTCATCTAATGGGAAT---GGACCTTCAGAATCAGCAGATGATGACTTGCCTAGTGTGATGACATGTGCTAATTACCTGAAACTTCCTCCTTACTCTACCAAGgtactgtgatatgacatacgagaaatgatttttacgtcacaatgtcttcctacctttactta-caccttgttgggggaaaatgtgtttttctaagtttcta

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA04G00530.1 (Glycine max), 5'ss of exon 16
---AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaa-gatgtccaggaactcatggatttgttgtcattaaccatcgccttcctttaaccag---------------------
   | | ||||| | |   || || || |||||||| |||||||||||||| ||||| |||||||||||||||||||| || |||||||| |||||||||||||||  ||  | | |   ||    || ||| |  | |     |||  ||      |||   |   | ||||  ||     |                      
TTCATCTAATGGGAAT---GGACCTTCAGAATCAGCAGATGATGACTTGCCTAGTGTGATGACATGTGCTAATTACCTGAAACTTCCTCCTTACTCTACCAAGgtactgtgatatggcatatgagaaatgatttttacgtcacaatgtcttccaacccatc--cttacaccttgtttggggaaaatgtgtttttttctaagtttc

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA11G11490.1 (Glycine max), 5'ss of exon 16
---AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgt---gaagatgtccaggaac-tcatgg-atttgttgtcatt-aaccatcgccttcctttaaccag----------
   | | ||||| |     || || || |||| |||||||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||||||||||    | |     | |||||    || |||  || | |  |||  |  | | |||   || |||  | |   |    |  |||           
TTCATCTAATGGGAAC---GGTCCTTCAGAATTAGCGGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTTAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttggtaatatgatcatgcatgtcaaagtgtcttttggtgttgaactgttgatatttgatttccattttaaaacag

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
---AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaagatgtccaggaactcatggatttgttgtcattaaccatcgccttccttt---aaccag
   | | || || | |   || || || |||| ||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||||||||||    | |     | |||||   | | |      |  ||||     ||     || | | | |  |||| ||   || |||
TTCATCTAACGGGAAT---GGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttg-gttatatgatcatgcatgtcaaagtgtcttttgatctttgatttccattttaaaacag

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT4G38600.2 (Arabidopsis thaliana), 5'ss of exon 16
AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaagatgtccaggaactcatgg--atttgttgtcattaaccatcgcct-tcctttaaccag
|||        |  | ||  | |||||  |||| |||||||| ||||||||||||||||| || || || ||||| || || ||||| || ||||| |||||  |  || | |   | |  |   || ||||| |      |||   || ||   | | |    | |  | |  || || |||
AGCAGCCAACGGAGCAGGGGCTTCGGAGACAGCAGATGATGATTTGCCCAGTGTCATGACTTGCGCAAACTACCTTAAACTCCCTCCTTATTCTACAAAGgtgagtcatgtcttctattcttcttga-gtccatgttagtgtggttgttggtgagcctgaggagttgtatgttattgaaacag

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S263_1V6.1 (Physcomitrella patens), 5'ss of exon 9
---AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgt-atggtatttttg-tgaa---ttgtgaaga-------tgtccaggaactcatggatttgttgtcattaaccatcgccttcctttaaccag------------------------------------------------------------------
   ||||  | | ||   |||     |    |  |||||  | ||| |||||||||| ||||||||||| || ||||| |||||||||||||||||   |||||| | | | ||  || || |   | |||  |        |||   ||    || |  | |    |  |||   || |       | || |                                                                    
GGGAGCCT-TAGCAGGGTTGGG--GACCACGTTGGCGGACAAAGACCTGCCCAGTGTGATGACATGTGCAAACTACCTGAAGCTTCCTCCGTACTCGTGCAAGgttaggatgttcgtggtggaagttggtgcggggttgcattgtttgggggtgcacgcgtgtagcctagttagttatgggtggagatgaatcgatttagttgtgacgtgttggcatggtgagtaaagttggtactgaatgggtgtgggtgatgttcacag

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|71879155|gb|DT028210.1|DT028210
EST:     GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAG                         GAAATCATGTACAAGAAACTTCTGTATGCGATCAGCGAGGGACAGGGGTCT
genomic: GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatt ... ctttaaccagGAAATCATGTACAAGAAACTTCTGTATGCGATCAGCGAGGGACAGGGGTCT
EST: gi|37185190|gb|CF604543.1|CF604543
EST:     GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAG                         GAAATCATGTACAAGAAACTTCTGTATGCGATC
genomic: GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatt ... ctttaaccagGAAATCATGTACAAGAAACTTCTGTATGCGATC
EST: gi|30126932|gb|CB912271.1|CB912271
EST:     GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAG                         GAAATCATGTACAAGAAACTTCTGTATGCGATCAGCGAGGGAC
genomic: GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatt ... ctttaaccagGAAATCATGTACAAGAAACTTCTGTATGCGATCAGCGAGGGAC
EST: gi|110684682|gb|EE062237.1|EE062237
EST:     GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAG                         GAAATCATGTACAAGAAACTTCTGTATGCGATCAACGAGGGGCAGGGGTCN
genomic: GTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatt ... ctttaaccagGAAATCATGTACAAGAAACTTCTGTATGCGATCAGCGAGGGACAGGGGTC-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaagatgtccaggaactcatggatttgttgtcattaaccatcgccttcctttaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT