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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgattataaaatcttaaatataaagggtaatcaggattgagtgcacaaacatcctcaagaatgcctattttcaatccaatatt...

Basic information

species Vitis vinifera
transcript Vv10s0116g00940.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os05g51630.1 (Oryza sativa), 5'ss of exon 10
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgattataaaatcttaaatataaagggtaatcaggattgagtgcacaaacatcctcaagaatgcctattttcaatccaatatt-----
|||||| ||||| ||||||||||||||||||||||||||  |  | |||||||||||| | || |||||  | ||||||||||| || | |||||| |||||||  |          |  ||   | |  || | | |     ||  | ||   ||| |      |  | || ||  | || |  |||  ||  | ||||     
ATATTTCTTACTTGGCCTTGTCTATGCTGTGGTGACACCGTTATTGCTTCCTTTCATATTGGTATTCTTCGGGCTGGCATATGTTGTCTACCGCCACCAGgtaaggaccactgcagctacttgcgagaattttattgtgttaagttttaag---tgattatgatgaactactaaatta-gcttgctttgtatg-actatttagac

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os01g35050.4 (Oryza sativa), 5'ss of exon 10
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaag---ttgacattttgattataaaatcttaaatataaagggtaatcaggattgagtgcacaaacatcctcaagaatgcctattttcaatccaatatt--
 ||||| || || || |||||||||||||||||||||||| |  | |||||||||||| |  | |||||| |  | |||||||| |||| ||| || ||||||| ||    |||  |   |  || | |  | |   |  |   |  |||||| || |  || ||      |  |   |  |||| | |   | |  |||  |  
CTATTTCTTGCTCGGACTTGTCTATGCTGTGGTGACACCATTTTTGCTTCCTTTCATATTAATATTCTTTGGGTTAGCATATGTGGTATACCGTCACCAGgtaataaccctttggaacact--ttgtgatttttagcactttgtgattaatcatgaatctgtccatcttt-tgttttggggtgccaagtgaaagt--aattcttg

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA13G10490.1 (Glycine max), 5'ss of exon 10
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgattataaaatcttaaatataaagggtaatcaggattgagtgcacaaacatc-ctcaagaatgcctattttcaatccaatatt----
 || |||||  |||| || || |||||||  |||||||| |   | |||||||||||||| ||||||||| ||||||| ||| | || ||||| ||||||||| | || ||  |  || ||  | ||     | ||  || |   | | | | ||   |||||    ||   ||  |      |    | ||||     ||    
GTACTTTTTGTTGGGTCTAGTATATGCTGCAGTGACACCTGCTGTTCTTCCTTTCATAATAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCGTCATCAGgtacagagatgtaaaatttatagtgaa----cagat-caatgatgattgaagtttatatgcacgtttatgattctggtgccagtgccattaatcattcgttaaaa

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G01400.1 (Glycine max), 5'ss of exon 9
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgattataaaatcttaaatataaagggtaatcagga---ttgagtgcacaaacatcctcaaga-atgcctattttcaatccaa-tatt------------
 || ||||| ||||| || |||||||||   || |||||     | |||||||||||||| ||||||||| | || || ||||| || ||||| |||||||||       ||  ||   ||||||  || | |  |  ||||| | ||        |||||| | | |   |  |    | ||   ||  || ||  ||  || |            
GTACTTTTTGCTGGGTCTAGTCTATGCTTCAGTTACACCTACTGTTCTTCCTTTCATAATAGTTTTCTTTGGGCTCGCCTATGTTGTGTTCCGTCATCAGgtagttccaagatgttagaattatattat-tcatgt-caaaggatgattgtattatttgagtcccctatttttgttgccatatatataagttgaagacacctactttccaattgcag

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA20G16230.1 (Glycine max), 5'ss of exon 5
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgat---------tataaaatcttaaatataaagggtaatcaggattgagtgcaca-aacatcctcaaga--atgcctattttcaatccaatatt---------------------------------------------------------------------------
 || |||||  |||| || || |||||||  |||||||| |   | |||||||||||||  ||||||||| ||||||| ||| | || ||||| ||||||||| | || ||  |  || ||         | ||  ||  |      |      | |||  |   | |||||| ||||   | || |  ||      ||  |    |||                                                                              
GTACTTTTTGTTGGGTCTAGTATATGCTGCAGTGACACCTGCTGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCGTCATCAGgtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcag

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA20G16230.3 (Glycine max), 5'ss of exon 5
--------ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgat---------tataaaatcttaaatataaagggtaatcaggattgagtgcaca-aacatcctcaaga--atgcctattttcaatccaatatt---------------------------------------------------------------------------
         || |||||  |||| || || |||||||  |||||||| |   | |||||||||||||  ||||||||| ||||||| ||| | || ||||| ||||||||| | || ||  |  || ||         | ||  ||  |      |      | |||  |   | |||||| ||||   | || |  ||      ||  |    |||                                                                              
ATACAATTGTACTTTTTGTTGGGTCTAGTATATGCTGCAGTGACACCTGCTGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCgtcatcaggtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcag

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA07G39320.1 (Glycine max), 5'ss of exon 10
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgattataaaatcttaaatataa-agggtaatcaggattgagtgcacaaacatcctcaaga-atgcctattttcaatccaa-tatt------------
 || ||||| ||||| || |||||||||   || |||||     | |||||||||||||| ||||||||| | || || ||||| || ||||| |||||||||       ||  ||   ||||||  ||       | |  | | |  |     |||||| | | |   |  |    | ||   ||   | ||  ||  || |            
GTACTTTTTGCTGGGTCTAGTCTATGCTTCAGTTACACCTACTGTTCTTCCTTTCATAATAGTTTTCTTTGGGCTCGCCTATGTTGTGTTCCGTCATCAGgtagttccaagatgttagaattatattatacacgtcaaagtatgattgtattatttgagtcccctatttttgttgccatatatataaggtgaagacacctactttccaattgcag

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|34550981|gb|CF519185.1|CF519185
EST:     CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAG                         ATAATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
EST: gi|110363926|gb|EC927558.1|EC927558
EST:     TTTCATAATTG-TTTCTTTTTGCCTGGCATATGTTGTATTCCGCCATCAG                         ATAATTAATGTTTATAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: TTTCATAATTGTTTTC-TTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
EST: gi|30251320|gb|CB969053.1|CB969053
EST:     CGTATTCCGCCATCAG                         ATAATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: CGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
EST: gi|351028550|gb|FQ444831.1|FQ444831
EST:     CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTTGTATTCCGCCATCAG                         ATAATTAATGTTTATAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTTTTTACTGGGCCTTGTCTATGCTGTGGTGACACCAGTGCTACTTCCTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagttgacattttgattataaaatcttaaatataaagggtaatcaggattgagtgcacaaacatcctcaagaatgcctattttcaatccaatatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agggtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacaaa