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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtatagttgatttttgtaacatcttcattacattttcatactggtctgagtaattggttgatgtaagatttactctcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG

Basic information

species Vitis vinifera
transcript Vv07s0005g00880.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 2
----------------atgtatagttgatttt---tgtaacatcttcatta------cattttcatactggtctgagtaattggttgatgtaagatttactctcaattg------cattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
                     |  |  | ||    || ||||| |||  |        |||||  |  | |  |  |   ||| ||  | |   ||   || |||||||        || || |  || |||| |||||||| ||||||||||||||  || | || ||||| || |||||||| || ||||||||| | |||||||||||||| || |||||||| ||||
gtcaacattcattttttcacttcttctacttccactgcaacattttctatgtttaggtattttggtcgtagatttcgattttgattattattccatcctctttcaattgatcaatggttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAAGCGGCACAAGAAGTGGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 2
atgtatagttgatttttgtaacatcttcattacattttcatactggtct---gagtaattggttgatgtaagatttactc-tcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
 | | |  |  | || | | | |   | ||    |||||| | ||||||    | | |||  |  ||      |  | |  ||||||  |   || || || |||| |||||||| ||||||||||||||   | | ||  ||||||||||||||||||| ||||||||  | |||||||||||||| || |||||||| ||||
-tttctgctaaaattatatcaaaagattatatttttttca-attggtctcttaaattattattccatcctccttcaattgatcaattata--gttttaatgcagGTGAACATGGAGTATGGTCTTGATCCCAACGTCGGAGAAGCAATAATGCAAGCAGCACAAGAAGTAGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 2
atgtatagttgatttttgta-acatcttcattacattttcatactggtctgagtaattggttgatgtaagatttactctcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
       ||  |  ||  || | ||||||| |    | |  ||||    ||    ||    |  |  || | |||   |||||||  || || |  || |||| |||||||| ||||||||||||||   | | ||  |||||||||||||||| || ||||||||  | |||||||||||||| || |||||||| ||||
-------gtcaacattcatatatatcttcact----tcttctact----tgcactatcctct--ttcaaaaatta---tcaattg--ttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCATCGTGGGAGAAGCAATAATGCAAGCGGCACAAGAAGTAGCCGAGGGAAAACTAAACGAACATTTTCCTCTCG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 3
atgtatagttgatttttgtaacatcttcattacattttcatactggt-ctgagtaattggttgatgtaagatt-tactctcaattgcattattcta---ttgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
  |||   ||     |       |     ||| |||| |||     | || | |   |   |  | |  | || |    | |||||  ||| | ||   || ||||| ||||||||||| |||||||||||  | || || |||||||| |||||||| || || |||||  | |||||||| || ||||||||||| || || |
--gtaacattctagctccaggttttggggtta-atttgcatctgaattctcatttgctttctcgtatttggttctgtgatgaattgagttaatataattttatagGTTAACATGGAATACGGTCTTGATCCGACGATTGGGAAAGCAATTATGCAAGCTGCTCAGGAAGTAGCTGAGGGAAAGCTCAATGATCATTTCCCCCTTG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 1
atgtatagttgatttttgtaacatcttcattacattttcatactggtctgagtaattggttgatgtaagattta--ctctcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
                       | | || || | | || ||    | | | | ||   ||  | |    ||||   ||   |||  |  ||  | || ||||| |||||||| |||||||||||||||   || ||  |||| |||||| |||| || ||||||||  |||| ||||| || ||||||||||| || || |
--------------------gtttttgcagtaaagtctctta----tgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAAGCTGCACAAGAAGTAGCAGAAGGAAAGCTCAATGATCATTTCCCTCTTG

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|71857320|gb|DT006375.1|DT006375
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|352778135|gb|FQ467188.1|FQ467188
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|352782338|gb|FQ470241.1|FQ470241
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|110713618|gb|EE089697.1|EE089697
EST:     CTGAACCAATCATTCGAGCTTTCGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGGATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|352776927|gb|FQ474234.1|FQ474234
EST:     CTGAACCAATCATTCGGGCTTTTGGCATCCTTAAAAAATATGCTGCAGAG                         GTCAACATGCAGTATGGTC
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTC
EST: gi|161712595|gb|FC062197.1|FC062197
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|352773939|gb|FQ473071.1|FQ473071
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|33402485|gb|CF208112.1|CF208112
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATACGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|352773568|gb|FQ472350.1|FQ472350
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
EST: gi|71858005|gb|DT007060.1|DT007060
EST:     CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAG                         GTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA
genomic: CTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcag ... tctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgagtaattggttgatgtaagatttactctcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
            ggttgat  putative branch site (score: 5)
                                         ttattct  putative PPT
                                        attattctattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtatagttgatttttgtaacatcttcattacattttcatactggtctgagtaattggttgatgtaagatttactctcaattgcattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - -catcttc
- - - - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttga