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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagtttctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgtgtgtattgtgtattgcgtattt...

Basic information

species Vitis vinifera
transcript Vv13s0106g00620.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 5'ss of exon 5
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgta-----acaatcattagtttctgcacttataga-------ttcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgt--gtgtattgtgtattgcgtattt----------------------------------------------------------------------------
|||||| |||||||||||||| || || ||||| || || || || || || ||| |||| ||||| || ||||| ||||| ||||| ||||| ||||||||| | | || |||||| | | || || ||| | || | | | | | ||| ||| | || | | | ||||
AGTTAAGCTAAAAATGCAAGGTGCCTGCAGTGGATGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttctgtgctttatttctgtttcctcaaaacctccactccttttggctcattatataaggtgttttatctgataagtaaaatgttgaaagaagttgcaattcctattagtttgttcagactgcttaaagcagtaatttatcctttgatctagcgaaattttaatatttcacacttctttggcag

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G131249_T03 (Zea mays), 5'ss of exon 5
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagttt-ctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgtgtgtattgtgtattgcgtattt
|||||| || ||||||||||| || || || ||||| || || || || || ||| |||| ||||| || ||||| ||||| ||||||||||| |||||||| ||| | | ||| | || ||| | | | | || | | ||| | || || | || | | ||||
AGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCACTATGTGCCTGAGgtgacatgaagcaatttattctgtttgctgatgtttcctaatgct-cgtggttcaaaaaattgttctctatttgataactagaatgcgaagtggtttattc

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G38630.1 (Glycine max), 5'ss of exon 4
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagtttctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgtgtgtatt-gtgtattgcgtattt--
||| ||||| | ||||||||| ||||| ||||||||||| || ||||| || || |||||||| ||||||||||||||||||||||| ||||| ||||||||||||| || | | || || | | | | | | || ||| | | | || | | | ||| | | ||| |||
AGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaa--gtttgacaatatctttttatgatgagtataatgcatttattattt-tcattatacttgatagaagtagaattgattagaatcttgaacattatc

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G20970.1 (Arabidopsis thaliana), 5'ss of exon 5
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagtttctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgtgtgtattgtgtattgcgtattt--------------------------------------------------------
||| || || | ||||||||||| |||||||| || || |||||||||||||| ||||||| || || ||||| ||||||||||| |||||| | ||||||||| || | | | | | | ||| | | | ||| | || || | |||| | ||| | |||
AGTGAAGCTGAGGATGCAAGGAGCTTGTAGTGGTTGTCCGAGCTCATCTGTTACTTTGAAATCGGGAATCGAAAACATGCTGATGCATTATGTATCCGAGgtaacagagatcctcctaacatttcttttactacatatggataattctagacctatctgtctgtgttcaagttttggtgttaactgttaagcaaccattggagaatcaagaacttgttaccgtcacattcttctaatgaaagttttttttgtgtag

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G51390.1 (Arabidopsis thaliana), 5'ss of exon 5
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagtttctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatca-aattgtgtgtattgtgtattgcgtattt---------------------------------------
||| || || | |||||||||||| ||||| || || || || ||||||||||| ||||||| || ||||| |||||||| ||||| ||||| | ||||||| | || || || || | || || | ||| || | || | |||| || ||| || || || | | | ||
AGTGAAGCTTAGAATGCAAGGAGCTTGTAGCGGTTGTCCAAGTTCATCTGTTACTTTGAAATCCGGAATTGAGAATATGCTTATGCATTATGTTTCCGAGgtaaagctgataaggagatgtcctacca--tttatcatt-tctgttattcttttgctgttgagggagaatcatgatcttgttaatagtctact-cttgttctctaatcattactcaccaaagcgtttgtgcaaaacacag

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|30128878|gb|CB914217.1|CB914217
EST:     TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAG                         GTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
genomic: TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatca ... atttttacagGTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
EST: gi|110417947|gb|EC984052.1|EC984052
EST:     TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAG                         GTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
genomic: TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatca ... atttttacagGTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
EST: gi|110413185|gb|EC978962.1|EC978962
EST:     TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAG                         GTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
genomic: TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatca ... atttttacagGTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
EST: gi|349824783|gb|FQ414641.1|FQ414641
EST:     TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAG                         GTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTG
genomic: TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatca ... atttttacagGTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTG
EST: gi|110426203|gb|EC992603.1|EC992603
EST:     TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAG                         GTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA
genomic: TTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatca ... atttttacagGTCAAAGGTGTAGAGCAAGAATTAGATGCTGAAGATGAAGATGTTGCACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagtttctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgtgtgtattgtgtattgcgtattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatgaa