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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgttttctagttcttgttatagaaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact...

Basic information

species Vitis vinifera
transcript Vv15s0048g02350.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattg---ttttctagttct-tgttatagaaaatgt--tgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact
|||| | ||||| ||||||||||| |||||| | || |||||||||||||| || ||  |||| |||||||||||||| || ||| | || ||||||||||||   |||    ||| || |||| | || |      ||   ||||  |||  | || |||   || |      |     |  ||  |   |||    ||      
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt------

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 2
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgttttctagttctt---gttatagaaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacat-agctgcaactttcagact
|||| | |||||||| ||||| || |||||  | ||||| |||||||| || |||||  | || || ||||| ||||| || |||||||| ||||||||||||| ||| | | || |  |||   |||   ||  | ||  || |  |   | |||| || |||       |  | ||||    |  | ||  | || |     
TCACTTCATGATCCCGTGGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAAGCCGTGATCTCCAGATGgtaaaattctgtccttgcacttggggtttctgactaggtcatg-tcgttgagatgatgatttgtagcatgtagaaggtgatttgttggttgtgatttgcga---

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgt----aatattgttttctagttcttgt-tatag--aaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact
|||| | || || || |||||||| ||||| ||||||||||||||||||||||| || ||||| || |||||||| || ||||| ||||| || ||||||||    ||||    || ||||   |||  | |||  | |  |   ||||| || |    |  ||  ||  |       ||  ||    |  |   ||   |      
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggtatcaa--attcgtagaaccctaaaaaagaattctgaccttaatcata-----

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaa-tattgttttctagttcttgt-tatag--aaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact
 ||| | ||||| || |||||||| ||||| ||||||||||||||||||||||| || ||||| || |||||||| || || || ||||| || |||||||||| ||   ||| |||   |||   | |||  | |  |   ||||| ||||    |  ||  || ||  |||  ||   | |  |  |    |  ||      
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatcaa--attcgtacaactgaaaaaaaaaaatctgaccttcatattgtat--

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 3
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgttttctagttct--tgttatagaaaatgttgtgg--ttatgttgctgatcatgtgttcaggtga-tgaagtgagacatagctgcaactttcagact
 ||  | ||||| || ||||| || ||||| || ||||| ||||| ||||||||||||||| | || |||||||| |||||||||||||| ||||| |||||||   | |||  | || ||  |  | |    | | ||  |   | || |||| |      ||     |||  || |  ||| || |   |  | |        
ACATATTATGATTCCTTGGTTCGAGAGGCCTGTGATCTACGATGTACGTGCACGCCCTCATTTAGTAGAGAGTACATCAGGGAGCCGTGATCTCCAAATGgtaagtctttttgtttgtcctatttcttttcttattcttaagacctgatattgcagtatgcttgaatttgtggctgcaaggagtcaaacaggttattcat-----

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G01850.1 (Glycine max), 5'ss of exon 2
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgttttctagttct--tgttatagaaaatgttgtgg--ttatgttgctgatcatgtgttcaggtga-tgaagtgagacatagctgcaactttcagact
 ||  | ||||| || | ||| || ||||| || ||||| || || |||||||| |||||| | || |||||||| |||||||||||||| ||||| ||||||| | | |||  | || ||  |  | |    | | ||  |   | || |||| |      ||     |||  || |  ||| || |   |  | |        
ACATATTATGATTCCTTTGTTCGAGAGGCCTGTGATCTACGACGTACGTGCACGACCTCATTTAGTAGAGAGTACATCAGGGAGCCGTGATCTCCAAATGgtaaaactttttgtttgtcctatttcttttcttattcttaagacctgatattgcagtatgcttgaatttgtggctgcaaggagtcaaacaggttattcat-----

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 4
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgtt--ttctagttcttgttatagaaaatgttgtggttatgttgc-tgatcatgt-gttcaggtgatgaagtgagacatagctgca--actttcagact-----
|||||| ||||| |||||||| ||||||||| | |||||||| || ||||||   ||| |||| || ||||| || || ||||||||||| |||||||||||| |    ||  ||  |   ||| | |||  ||  | | |  | | || |  || |  ||| ||       |     | ||     | ||       || | ||      
TCACCTTATGATTCCATGGTTCGAAAGGCCAATCATCTATGACGTTCGTGCAAAGCCTTATCTAGTTGAGAGCACATCTGGGAGCCGTGATCTCCAGATGgtattccgcttcatttcatcacttctaatactaatgggtataatcaggtcgtgtggttttgtcgtgtgaactacatgataagcttatgttgtgtggtatttaaacattcag

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 3
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgttttctagttcttgttatagaaaatgttgtg--gttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact----------------
 ||||| ||||| || |||||||||||||| || |||||||| || ||||| || ||| | || || |||||||| || || |||||||| || ||||||||| | |  || |     ||   || |     || ||||   || |  ||  |||   ||   ||    | |  |     | |       || |||                      
ACACCTTATGATTCCTTGGTTTGAAAGGCCGGTCATCTATGACGTTCGTGCTCGACCTTACCTTGTTGAGAGTACATCCGGAAGCCGTGATCTTCAGATGgtactctgcttctactcctcccattttcagtcattttgttttgtgaatttagtgaatgtgaagtcgttcgcttcaacatcataagctcttaagttttttgtggttttaaaactttcag

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G03860.3 (Arabidopsis thaliana), 5'ss of exon 3
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgta-atattgttttctagttcttgttatagaaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact-----
 ||  | ||| | |||||||||||||||||| | |||||||| || |||||||| ||| | || || ||||| ||  | || || | ||| || ||||||||   | ||| |||||   |||| || | |    | || ||  | ||||  ||  ||  | || ||   | | | | |    ||  ||    |     |       
ACATTTTATGGTGCCATGGTTTGAAAGGCCAATCATCTATGACGTTCGTGCACGACCTTACCTTGTAGAGAGCACCACTGGTAGTCATGATCTTCAGATGgtgcgttttggtttct---tcttcttttggcttcttttctgtgtgtgtt--tgtaca-atatttagcccagggatttaattttaaatgatgttactgaatgtggtg

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|110711108|gb|EE087281.1|EE087281
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|161716355|gb|FC066866.1|FC066866
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|22013946|gb|BQ798980.1|BQ798980
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110414101|gb|EC979926.1|EC979926
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110708454|gb|EE086015.1|EE086015
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|30297423|gb|CB974217.1|CB974217
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110421504|gb|EC987802.1|EC987802
EST:     AGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: AGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110720744|gb|EE096932.1|EE096932
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTCCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|18459675|gb|BM437953.1|BM437953
EST:     CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110699664|gb|EE076859.1|EE076859
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|71862826|gb|DT011881.1|DT011881
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|161720129|gb|FC065124.1|FC065124
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110729989|gb|EE106553.1|EE106553
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
EST: gi|110718347|gb|EE095076.1|EE095076
EST:     CGCGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATG                         GTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT
genomic: CACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgt ... tactgcacagGTAAAGATTGGTCTTCGAGTTCTTACCCGTCCTGTGCCAGACCAGTTACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattgttttctagttcttgttatagaaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagaaaa