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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgtctagagttcgctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag

Basic information

species Vitis vinifera
transcript Vv02s0012g01850.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcat----ctgactctcttgtctagagtt---cgctattcccttt-ctgattcaggctgctgactctcatttcaatttctcttttcag--------------------------
||||| ||||||||||||||||| |||||||||||| || || ||||| || ||||||||||||||||| || ||||| || |||||| |||||||||| | | || | | | | || |||||| | ||| || | |||| | | | | | | || |
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G015509_T01 (Zea mays), 5'ss of exon 4
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgac----------tctcttgtcta--gagttcg--ctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag------
||||| |||||||||||||| || |||||||||||| || || || || ||||||||||||||||||||||| || |||| ||||||| |||||||||| | | ||||| ||| || | | ||| | | || ||| | ||| | | | ||| ||| | || |||| | |
AGGGATCAGGGAATACAAGAGATTCAGCACCAAATTACTGAAGTAAACGAAATTTTCAAAGATCTTGCTGTGCTAGTTCATGGTCAAGGAGCAATGATTGgtatgtgacctgacgtatgaaatttctgcagtttgatgggtttgagcacttgattttgttatttcatcaattta-tctaattatatttcttcttgtttggttcag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgtctagagttcgct--attccctttctgattcaggctgctgact--ctcatttca----atttctcttttcag-------
||||| |||||||||||||| || || |||||||| || || ||||| || |||||||||||||||||||| |||||||| ||||||| ||||| |||| | | || || | | | | | | | || | | | |||| ||| | ||| | | |||||| |||
AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttgcaaattggatatacatttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G017329_T01 (Zea mays), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgt----aactcatctgactctcttg-tctagagttcgctattccctttctgattcaggctgctgactct-catttcaatttctcttttcag---------
||||| |||||||||||||| || ||||||||||| || || ||||| || ||||||||||| |||||||| |||||||| ||||||| ||||| ||| | ||||| | | |||| | || | ||| ||| | | | | | || | | | | | |
AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcctttctgaaaaattggatctacattttgaaatttcctacgccacatggattatttttacggcacatgattggatgggattggaaaatttta

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA09G33950.1 (Glycine max), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgt--ctagagttcgctattccctttctgattcaggctgctgactct---catttcaatttctcttttcag-----------------------------
|| || || || || |||||||| ||| |||||||| || || ||||||||||||||||||||||||||||| |||||||||||||||| ||||||||||||| | || ||| || | | || | | |||| ||| || || | | | | | || | ||||
AGAGATCAAGGTATTCAAGAAATTCAGTCGCAAATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtgttttcccttcatgcttttgctaattacacacattctagttctaact-ctatttttaaatgtctagacttgtttttttttatttgatgtaaaatatttccattttgtag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G13410.1 (Glycine max), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgt-ctagagttcgctattc-cctttctgattcaggctgctgactctcatttc------------aatttctcttttcag
|||||||| || || |||||||| ||||| |||||||| || || |||||||| ||||||||||||||||| || |||||||||||||||| ||||||||||| | || | || ||| | | | | || | | | | || | | | ||| |||| | |||||| ||| ||
AGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTACTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccattcccttttgttcttcctggttacttgtatctttattttactgtacctgctcacattacctagtgccactaaatttcattttgtag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgt-ctagagttcgctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag--------------------------------
|||||||| || || |||||||| || || |||||||| || || |||||||| |||||||||||||||||||| |||||||||||||||| ||||||||||| | || | | ||| | | | || | | | | ||| ||| | | |||| | | || ||||
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaattt-atttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G01960.1 (Glycine max), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgtctagagttcgctattccctttctgattcaggctgctgactctcatttc--aatttctcttttcag----------------------------------
|| ||||| || || |||||||||||| || ||||| || || ||||||||||||||||||||||||||||| |||||||||||||||| ||||||||||||| | | | || || || |||| | | | | || | || || | || | |||| |
AGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtt---tttcccctcccagttttgctaattacacacattcttgtactatatttttaaatgtctagacttttttttttaattttaaactttgatgtaaaatttccattttgtag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G46860.1 (Arabidopsis thaliana), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgtctagagttcgctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag
|| ||||| ||||||||||||||||| || |||||||| ||||| || ||||| |||||||||||||| || ||||| | || |||||||| ||||| ||||| | | | || | | || ||||| | | ||| | |||| | ||| || | || |||
AGAGAGCAAGGAATACAAGAAATCCATCAGCAAATTGGTGAGGTTAACGAGATATTCAAAGATCTTGCGGTTCTGGTTAACGATCAAGGAGTCATGATAGgtaa---agacaatctattaaacttaattagaacatgcccttgaagctgcagttagagaactcactttt---ttctttcttgcag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G17730.2 (Arabidopsis thaliana), 5'ss of exon 5
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgta--actcat-ctgactctc-ttgt-ctagagtt--cgctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag
|| ||||| || ||||||||||| ||||| ||||||||||||||| | ||||| |||||||| | || ||| |||| || || |||||| ||||| |||| ||| || | ||||| || | ||| | | | || | ||| | | | | | | | |||| | |
AGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAGGTGCACGAGATCTTCAAAGACTTGGCAGTGTTGGTGCACGATCAAGGAAACATGATAGgtaaaactgattccaactcttgttatgctaaaactctcacttatgtcttcaaaacctaagacg-taagacctatttttgtgtag--------

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|349814626|gb|FQ399266.1|FQ399266
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|349814672|gb|FQ400310.1|FQ400310
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|349807660|gb|FQ402051.1|FQ402051
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|110690731|gb|EE068149.1|EE068149
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCNAGGAGTTATGATTG                         ATGATATTGGCTCCAACA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACA
EST: gi|110403262|gb|EC964685.1|EC964685
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCGACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|349828272|gb|FQ416225.1|FQ416225
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|349823620|gb|FQ415030.1|FQ415030
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|349821234|gb|FQ404366.1|FQ404366
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|110369733|gb|EC933900.1|EC933900
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
EST: gi|349817337|gb|FQ405341.1|FQ405341
EST:     GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTG                         ATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA
genomic: GATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatc ... ctcttttcagATGATATTGGCTCCAACATTGATGGTGCCCAGGCTGCAACAGCACAGGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgtctagagttcgctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG