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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctatagtctggcactttatac...

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 13
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagat--gtgattcctattatggaaaacttcttttctcctttggaggctatagtctggcactttatac-
||||| || ||  ||||||| || ||||||||||| |||||||||||||| ||||| || || |||||||| |||||||| || |||| | |   ||    ||      | |    ||| ||||  |  |    | ||     ||| |||||||  || ||       |||  ||   |  | ||   
GTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACGgtaggtt--tctacagttccgttgtttgcacttggagattagctagctatgtttcattaaatttcttttgaccgtttattcaaata-cctactatgtgattaa

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 13
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctc-actttgcagatgtgattcc-tattatggaaaacttcttttctcctttgga--ggctatagtctggcactttatac---------------------------------------------------------------------------------------
||||| || ||  | |||||||||||||||||||||||||||||||| || || || ||| | |||||||| |||||||| || ||||  ||   ||  |||   | | | || |  |    | |    | |  | || | |  |  ||||| ||    ||       | |  || || ||    || |                                                                                       
GTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgta--attttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccggagtgtaacttttgacgttgttctctgcaatcag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 6
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctata-gtctggcactttatac----
||||| || ||  | |||||||| ||||||||||||||||||||||| || ||||| ||| | |||||||| |||||||| || ||||    |   |||   ||  |  | | ||    | ||||      ||| ||||    |      |||| ||||  |   |||     | |||    ||      
GTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACGgta----attttcttgcttcactttgttacca-actgatggctactctactatgctctagcagcattcttctttacactttattcaagtagcaaccaatgtgtga

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 11
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatg---------atagcctct-ctttttccca--tctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctatagtctg--gcactttatac--------------------------------------
||||| ||| ||| |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| |||||||||||||||||||||           ||| | | ||||  ||||   |  | |||    ||||   | | ||||    | | ||  | |||   |||     | || |     |  |||| |                                        
GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatctattggagcttttgctttgccccaatacctattttctgaatgtttattc-attacatgacattttgtctctatgttgttacatttatttgaatgtgctttctctgatgttctgctattaatgaattgtgattttctttttag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctatagtctggcactttatac-------------------------------------------------------------
||||| ||| | | |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| ||||||||||||||||||||         |||        | |  ||||||     | || |||||| |  |||  ||  ||  |    ||     |    ||       ||| |                                                              
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgctttgccccaat-atacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 13
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatgga--aaacttcttttctcctttggaggctatagtctggcactttatac
||||||||| | | |||||||||  |||||||||||||||||||||||||  | || ||| | ||||||||||||||||| |||||||          |||||    |      |||| |    |||| |  | || || |  |   ||| |       |     |   |  | | | | |||    
GTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactttgatctttgggaccgtgtgctttaccccagtgactatt-ttctgaattagtgttcatgcgatactctattgtgttgctgtagtattttgat-

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 13
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctatagtctggcactttatac-
||||  ||| | | |||||| || ||||||||||||||||||||||||||  | || ||| | ||||||||||||||||| |||||||          |||||    | |    |||| |     ||| |  | |  |    |   |   | |     |  |   | | | |||     || |   
GTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATGgtacacactttcatctttgagaccttatgctttaccccattgactattttctttattagtgttcatgcaatactctatagtgttg-ctgatgtattttgat

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|87583926|gb|DY473286.1|DY473286
EST:     TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG                         GTAAGTTTCA-GCCTGTGATC
genomic: TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagc ... ctgcttgcagGTAAGTT-CAAGCCTGTGATC
EST: gi|161717766|gb|FC066590.1|FC066590
EST:     TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG                         GTAAGTTCAAGCCTGTGATCAAGAA
genomic: TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagc ... ctgcttgcagGTAAGTTCAAGCCTGTGATCAAGAA
EST: gi|110699977|gb|EE077493.1|EE077493
EST:     TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAAGAGACATG                         GTAAAGTTCA-GCCTGTGATCAAGAAG-CAATGGGTGAACTTGATG
genomic: TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagc ... ctgcttgcagGTAA-GTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
EST: gi|110419896|gb|EC986150.1|EC986150
EST:     GCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG                         GTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
genomic: GCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagc ... ctgcttgcagGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
EST: gi|77584856|gb|DV221506.1|DV221506
EST:     TGTTGGTGGAACTGCCTTGACTTCATTAACGGATGTGGAGAGGAGACATG                         GTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
genomic: TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagc ... ctgcttgcagGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
EST: gi|110720557|gb|EE096583.1|EE096583
EST:     TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG                         GTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
genomic: TGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagc ... ctgcttgcagGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctatagtctggcactttatac

- - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaaaa