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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATTGCGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctctctctctctctctctctctactcagtactctctctctctctcttctcagtactctccctctctctccatcaagtacttacaagtaccattttgccatttattttctctcattcatggaattcaag

Basic information

species Vitis vinifera
transcript Vv01s0026g00350.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00350.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G03740.1 (Glycine max), 5'ss of exon 6
ACCATTGCGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctctctctctctctctctctctactcag-------tactctctctctctctcttctcagtactctccctctctctccatca--agtacttacaagtaccattttgccattta----ttttctctcattcatggaattcaag------------------------------------------------
||||| || || ||||| || |||||||||||  ||||||| ||||||||||||||||| ||| ||||   |||||||||||| | | | |        || | |     | | | |  ||  ||         | ||   ||    |||  |||   | |  |  ||   | |||    |||| ||| |||  |    ||                                                    
ACCATAGCTCTCATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAGgttctccctcttcttctctctctctcacaattaacaaaaaattattttacaagtttttttaatcgataactattagttgtcgggattgttagtttttattggcaagagattctaacttacgacttttttcttatttctttcttttttttcaccactaaaccaatcttatatctaatttgttttgatggaactgaag

upper sequence: Vv01s0026g00350.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G03940.1 (Glycine max), 5'ss of exon 6
ACCATTGCGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctctctctctctctctctctctactcagtactctctctctctctcttctcagtactctccctctctctccatcaagtacttacaagtaccattttgccatttattttctctcattcatggaattcaag
||||| || || ||||| || |||||||||||  ||||||| ||||||||||||||||| ||| ||||    ||  |||||||| |         |||||||||| |||        || | | ||        ||| | | |  |   ||||   ||     ||   |||||||| |  |||||| | |||
ACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAGgttctccctcttctccttcctctctctat--------ttctctctctcactc--------acacacacttaacaagaatctatttcacaattgtactccttcatttttatgtttctctc-tcaatggaactgaag
















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|110422036|gb|EC988347.1|EC988347
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTAGGAGCTGTTCACAAG                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
EST: gi|110416844|gb|EC982850.1|EC982850
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTAGGAGCTGTTCACAAG                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
EST: gi|110711993|gb|EE089106.1|EE089106
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACA-G                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTT-GGTTAC
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
EST: gi|110402919|gb|EC963794.1|EC963794
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTAGGAGCTGTTCACAAG                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
EST: gi|71866843|gb|DT015898.1|DT015898
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTAGGAGCTGTTCACAAG                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTA
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTA
EST: gi|110702512|gb|EE081308.1|EE081308
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAG                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC
EST: gi|77581829|gb|DV219868.1|DV219868
EST:     CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTAGGAGCTGTTCACAAG                         GTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAATTTGGTTAC
genomic: CGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctc ... ggaattcaagGTGATTGAAGACCTGAGTTATGTCGTTCTACTAAGAAAGAAGTTTGGTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATTGCGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAGgtcctctctctctctctctctctctctctactcagtactctctctctctctcttctcagtactctccctctctctccatcaagtacttacaagtaccattttgccatttattttctctcattcatggaattcaag

- - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - -  GCTGTT