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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT

Basic information

species Vitis vinifera
transcript Vv18s0041g02080.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G44600.1 (Glycine max), 3'ss of exon 3
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
 || |   ||    | |   ||    | |||||||||||       || |  | |||| | |  |  |  |    ||| |  |   ||| |||  |||||| |||||||| ||||||||||||||||||||||||||||| ||||| || || ||||||||  | || || || ||||| ||  ||||||| ||||||||
gtaatttcccccaccttt--tgctcctgccaaatactaa----tgtttcaaataccctgccaaatact-aacatcatatccatggctgtgcaaattgtagGTTTTGATGGGGTTGAGATCCATGGGGCTCATGGCTACCTGCTTGAGCAATTTATGAAAGATAAAGTGAATGACCGAACAGACGAATATGGTGGATCCCT

upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
ctattgaaccatttcgtggatgtaattcc-----caaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgt---tcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
    | |      | |   |   |||| |     ||  ||||||           ||| |     |     | | ||| ||  |  | || |     || || |||||| |||||||| ||||||||||| || |||||||||||| ||||||| || ||||| |||||| | || || ||||||| ||||  |||||| ||||||||
---gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT

upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
     | |   |  | |   | |   |||    ||| ||    |  |  | |||   | |||   ||    |   ||| |  |  |||| |||  | |||| |||||||||||||||||||||||||||||||| |||||  |||| || ||| |||||||  |||| || || ||||| ||  ||||||| ||||||||
-----gtaatttcccttcccttttgctcc----tacaaatgttctttcaaattgttttacaaa--ctagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT

upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
-------ctattgaaccatttcgtggatgtaattccca-aatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
          ||| ||  |   ||  |||  ||   ||  ||  ||||| |     ||||| |   | || ||| |  || |  ||||   | |||  |||| |||||| |||||||||||||||||||||||||| ||||| |  ||| |||| || ||  |||||||||| || |||||  |||| || ||||| || |||||  |
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgg----gattttcgaattaagttcatcaattcc-taaccacaattg--caat-tgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT

upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G35410.1 (Glycine max), 3'ss of exon 4
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttg---atgcaataac--attacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
   |   |    |  ||||| ||    |   ||||  | |  |   |    ||   ||   |||         || ||||  |  |   |   | |||| |||||| ||||||||||||||||| |||||||| ||||| |  ||| |||| |||||  ||||||| || || |||||  |||| || |||||||| ||||||  
---tcatatacctgagtgga-gtttcactttaatatgatatagtcatgatgttaaactgtgattctcaaagatattcaattcctaaccgcaattgcaat-tgtagGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTTTCTAATTGATCAGTTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCCAC

upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ20558 (Selaginella moellendorffii), 3'ss of exon 4
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
                                 |  |||||    |||   || |  |  | |||| | |    |  || |  ||| |       |||||| |||||||| |||||||||||||||||||| ||||| ||  | ||||| ||| ||||| |    ||||||||| |||| ||| | ||||| || ||  |
--------------------------------gtgttaaactatgctt--ctttctttctagtttcatgggctaacgaaaa--actgg------gtgtagGCTTTGATGGTGTTGAGATCCATGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAAATGGTGTCAACGATAGAACGGATGAGTATGGTGGTTCTTT

upper sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ28624 (Selaginella moellendorffii), 3'ss of exon 4
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
                                 |  |||||    |||   || |  |  | ||||   |    |  || |  ||| |       |||||| |||||||| ||||||||||| |||||||| ||||| ||  | ||||| ||| |||||||    ||||||||| |||| ||| | || || || || ||
--------------------------------gtgttaaactatgctt--ctttctttctagtttcacaggctaacgaaaa--actgg------gtgtagGCTTTGATGGTGTTGAGATCCACGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAGATGGTGTCAACGATAGAACGGATGAGTACGGTGGTTCTCT

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|110418337|gb|EC984484.1|EC984484
EST:     TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTG                         GATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
genomic: TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTGgtatgtgata ... caatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
EST: gi|33404250|gb|CF209877.1|CF209877
EST:     TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTG                         GATTTGATGGAGTTGAGATCCA-GATCGCTCATGGCTACCTACTTGACCAG
genomic: TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTGgtatgtgata ... caatatgtagGATTTGATGGAGTTGAGATCCATGGG-GCTCATGGCTACCTACTTGACCAG
EST: gi|110375633|gb|EC940640.1|EC940640
EST:     TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTG                         GATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
genomic: TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTGgtatgtgata ... caatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
EST: gi|33404329|gb|CF209956.1|CF209956
EST:     TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTG                         GATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
genomic: TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTGgtatgtgata ... caatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
EST: gi|27581933|gb|CB004628.1|CB004628
EST:     TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTG                         GATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
genomic: TCAAGTTGTAAATGATTTTAGACTTGCTGCAAGGAATGCTATTGAAGCTGgtatgtgata ... caatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
                            caataac  putative branch site (score: 2)
                                       cttgttc  putative PPT
                             aataacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT

- - - - ccatttc
- - - - - - - -gtggatg
- - - - - - - - - - - - - -cccaaat
- - - - - - - - - - - - - - - - - -ctaaacc
- - - - - - - - - - - - - - - - - - - - - gcacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataac