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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagtgcatgctgcatctgatcaaactctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG

Basic information

species Vitis vinifera
transcript Vv03s0038g01780.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G852968_T03 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------------ttgga--tgtcaaatgtagttttatactctg-tgtctgaatgttctggttttctggagatgctgtccagtgcatgctgc-atctgatcaaactctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
                                                                                       |||||   ||    || |||||  ||   |  | |  | ||    || ||  |  |   || || ||     |||   | ||||       |||| | |||||||||| |||||||    ||| ||| ||||||| || ||  |||||||||| ||||| ||||||||||| ||||| ||||| |||
gttggtttctcgtttcacataagctgtcaggataacgtgtttcgcgtgtttctttttccattaaatttgaaaatggaaagattgaacttggaaccgtggtttgcagtttgctaaattactatgaggataacgtgtttaacatggcttgatggccctgtgatgtgaccatcttcatttgctctgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 7
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagt--gcatgctg-catctgatcaaactctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
|  ||  |  ||| |   || | |       | | |||   |  ||     | ||  ||  |  |||    |||||  |||   |  || || || ||  |||| || || |||| ||||||  || | |||||||| || ||||| ||||||||||||||||||||||| |||||||| ||||||
tcaga-atttaatttttcttcaaatgaaagattttaatcagccagtacagcgcagcagcattgtagtagatatgctaacattgaagtaatctgtcctt--cagGGTCTGTAAATGCGAGCAACAGTGCTGAGCTCGCGAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
ttggatgtcaaatgtagttttatactctgtgtctgaatgtt-ctggttttctggagatgctgtccagt-gcatgctgca----tctgatcaaac---tctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
    || ||| |  | ||| |        | | |||||||   |  |||| |    || | || |||  |||| ||  |    |   ||||||    ||| | || |||| || || ||||  |||||  || | ||||| || || ||||| ||||||||||||||||||||||| |||||||| ||||||
-accatctcagaattggttct--------tatttgaatgtaattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 7
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagtgcatgctgcatc--tgatcaaac--------tctct-tttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG-----------------
          | | || ||    ||| || |  |  | ||     |||| || | ||  | ||||   |  ||  ||||  |   |||||        | ||| ||| |||| || || |||||  | ||  || | ||||| || || ||||| ||||||||||||||||| ||||| |||||||| ||||||                 
---------cagtatatttgaccact-tgagattataagtctcatttttatgtaaattttttccatcacg-gcaacatcgatacccaaacattaaatttatctgttttcagGGTCTGTAAATGGAGGGAACAGTGCTGAGCTAGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAGGTACATGGTTTCTTCAA

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 7
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctg--tccagtgcatgctgcatctgatcaaactctctttt---gcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
       | | |  |      ||| |     | |||| ||     |||||  |  | || |  ||| |     |   |||   ||  | || | ||||    |||| || || |||||  ||||  || | || || || || ||||| ||||||||||||||||| ||||| |||||||| ||||||
-----cttgagaaatgagaaaatagttctcatttgaaggtaaaatttttccagcaaagcagcatccggatacagtaacattaaattcatcttttttttttttcagGGTCTGTAAATGGAGGCAACAGTGCTGAACTGGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G36990.1 (Glycine max), 3'ss of exon 7
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagtgcatgctgcatc--tgatcaaac--------tctct-tttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
          | | || ||    ||| || |  |  | ||     |||| || | ||  | ||||   |  ||  ||||  |   |||||        | ||| ||| |||| || || |||||  | ||  || | ||||| || || ||||| ||||||||||||||||| ||||| |||||||| ||||||
---------cagtatatttgaccact-tgagattataagtctcatttttatgtaaattttttccatcacg-gcaacatcgatacccaaacattaaatttatctgttttcagGGTCTGTAAATGGAGGGAACAGTGCTGAGCTAGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAG

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagtgcatgctgcatctgatcaaactctcttttgc-agGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
                           || ||  || |  | |   | ||   | |||           ||| ||  | |   |    ||||  |||| |||||| || |||||  ||||  || ||||||| |||||| |||| || |||||||||||||||||||| ||||| ||||| |||
--------------------------gtgcgttagattagt-tatctgtcgcaaaatgaaactt----tatgttgattattgcc---ttctcaattgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG

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|34545318|gb|CF513550.1|CF513550
EST:     AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAG                         GTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG
genomic: AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAGgtattttatt ... tcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG
EST: gi|110692798|gb|EE068468.1|EE068468
EST:     AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAG                         GTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG
genomic: AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAGgtattttatt ... tcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG
EST: gi|30297140|gb|CB973934.1|CB973934
EST:     AAAGAATGTCTCAGCTGAAGTTGCTTCTAGAACACGAATTATTTATGGAG                         GTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG
genomic: AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAGgtattttatt ... tcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG
EST: gi|110705429|gb|EE082267.1|EE082267
EST:     AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAG                         GTTCAGTGAATGGGAGCAATTGTTCAAAGCTCGCCCAACAAGAGGAAATTG
genomic: AAAGAATGTCTCAGCTGAAGTTGCTTCTAAAACACGAATTATTTATGGAGgtattttatt ... tcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctggagatgctgtccagtgcatgctgcatctgatcaaactctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG
                               atctgat  putative branch site (score: 4)
                                          ctctcttttgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggatgtcaaatgtagttttatactctgtgtctgaatgttctggttttctggagatgctgtccagtgcatgctgcatctgatcaaactctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
-tggatgt
- - - - - - - - - - - - - - -tgtctga
- - - - - - - - - - - - - - - - - - - gttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaactc