Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG

Basic information

species Vitis vinifera
transcript Vv08s0007g05170.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
gttaaaatttaaattagttatatttagatgatacagcttagcataa--taatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
||   ||||||  |    | |  ||      | |  |||| | |    ||||| |  || || |    | || |   | ||||  ||   |||||||||||||||||||||||||| ||||| |||||||| ||  | || ||||||
gtgttaatttatctcctattt-cttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 5
gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcct-----ttgatcaatcttctt---cagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
            ||  | | |||    |  |||||   |    | || ||      |||       |     |  || | ||||  |   |||||| | ||||| ||||| ||||||||||||||||| || |||||||| ||||| || |||
----------gtatgcgctgtatcaccac-atacaatatgctttgatcatacatgcaatccaccattcaaagtaaatgactctttctcaacagACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 6
--------------gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG----------------------------------------
               |   |   || |||  | || | |  ||   || |||||   |||  || || || || | |   |||  | || |      ||||| | || || ||||| |||||||||||||||||||| |||||||||||| | ||||||                                        
gtactcttatcactatatcatgatacattgatcatgtgttaatc-cactgcttaatgtaa--atattatttatatatattttttttaaaac------agACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGGTAATTTGGAAGTTGGAAGATTACTGAATCTTTGCTTCTT

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G125243_T01 (Zea mays), 3'ss of exon 5
--------------gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
               |   |   || |||  | || | |  ||   || |||||   |||  || || || || | |   |||  | || |      ||||| | || || ||||| |||||||||||||||||||| |||||||||||| | ||||||
gtactcttatcactatatcatgatacattgatcatgtgttaatc-cactgcttaatgtaa--atattatttatatatattttttttaaaac------agACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G030280_T02 (Zea mays), 3'ss of exon 3
gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
||  |  ||| || |||   | ||    | || |       |||  |  || | ||  ||| | | | |  |  || ||   |||||||| || || ||||||||||||||||| ||||| || || |||||| ||||||| |||
gtgcaggtttgaaatagcattcttgttctcattc-------catgtttctgctgtttcttt-tacttatatttgattttg--cagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
--gttaaaatt-taaattagttatatttagatgatacagcttagcataat-----aatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
   ||||  || |    ||  | | | ||     ||  | ||   |  ||     |||| |  ||  | | |  |    |   | ||||| ||   ||||| |||||||| ||||||||||| || || |||||||||||  | |||||||||
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
gttaaaatttaaattagttatatttagatgataca-gcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
       | |  | || || | || | |||  | | || |    | |  |||   | | |||  |  ||| ||   | |  ||||||||||| | |||||||||||||||||||| |||||||| ||||||||| | |||||||||
---gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatt--tttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 6
gttaaaatttaaattagttatatttagatgataca-gcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
       | |  | || || | |  | ||   | | || |    | |   ||| || ||||| |   |||        |  ||||||||||| | |||||||||||||||||||| |||||||| ||||||||| | |||||||||
---gttgtatgcagtaattgtgtgcaaatagcataagccttttgttactgtgtgct-aatttttcatttt--------tcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G28400.1 (Glycine max), 3'ss of exon 1
-------gttaaaat-ttaaat----tagttatatttagatgatacagcttagcataataatgttcttaatt--tgttcctttgatcaatcttc-ttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
        | ||||  ||||||    || || | || | |||  | |    ||| |  |  |  | |  |||  | || ||||  | | | ||| ||||||||||| | |||||||||||||||||||| |||||||| ||||||||| | ||||||| |
ttgaccaatcaaaaggttaaatgcagtaattgtgttcaaatggcataagcaagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATG

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|110359279|gb|EC920517.1|EC920517
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|71884309|gb|DT033364.1|DT033364
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|33409731|gb|CF215358.1|CF215358
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|110397602|gb|EC963367.1|EC963367
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACTGC-GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATT
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTAC-GCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATT
EST: gi|161710152|gb|FC061050.1|FC061050
EST:     GTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: GTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|71885133|gb|DT034188.1|DT034188
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|71888810|gb|DT037865.1|DT037865
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|71883209|gb|DT032264.1|DT032264
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA
EST: gi|161720288|gb|FC070549.1|FC070549
EST:     TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAG                         ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAATAAGCCGATTA
genomic: TGGCCTCTGATTCGAGTGACAGATCAAAAGAAAAAGCCGGTGATCAGAAGgttaaaattt ... tcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacagcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG
                                             tcttcttc  CT-rich tract
            ataataatgttcttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaatttaaattagttatatttagatgatacagcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA