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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG

Basic information

species Vitis vinifera
transcript Vv09s0002g03930.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 9
-----------------gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
                   || |    | ||   |  ||    | |   | ||||||  | | | | |     | |    |||  || | |      || |  || ||||||         | |||| ||||||||||| || || ||||| ||||| ||||| |||||||| ||||||||||| ||||| || |||
gtataataagaaatggacaaaatgccatgttatctgtatctgttctttttcttggttctttgtttggaaagatagatagatgtggttatgtgggtcgtaatccaagttttgttacttttgat-agGTGGGAGCACAAACAGAGACCGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCTACCAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 8
gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttct--tttctacccactattttaatttttgtgttgcacatt----cagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
||||| |    |   |       |||||| | | || ||| |  | |    |  |  |   | ||||     |       |  |   |||||  ||| | ||         ||||| ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||| |||
gtaatgtgaagtccacg-ggtcgcaatgt-gttatttgttcaatgttcttttcatcgattcaatgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 3
--------------gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
                |  |     ||||  |        |    |  |   |  || ||| ||||  || ||| || ||   |  ||      ||  | |  | | |||||||     ||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| |||||||| |||
gtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactg-----taagtcatatctggtgttgcctga-cagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 9
--------------------gtaatttttttttttcttaaatacaatgtagctgttggttgatagat--ggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
                     || ||   |   || || || ||    ||| ||    ||| |  ||   | || || |    | |        |||   |  ||  ||    |||  ||| |  |  |||| |||||||| || ||||| || || || |||||||||||||| || ||||||||||| ||||| ||||||
gtaaaccccaatgttaaaccctagttgcctcaatttttcaaaac--cttagttgcctcttggtgtatttaggatgcttagcagaataaaaaaaactag--aacatgatatgccttgctttgtat-tgtagGTAGGAGCACAGACAGAAACTGAGCTCAAGGAAAAGAAATTGAGGGTTGAGGATGCCCTGAATGCTACAAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
                                               | || | | |   |   ||  ||||     |||   ||||| || | |||   |  |  |||| || ||||||||||| |||||| | ||||||||||| || |||||||| |||||  | ||||| || |||
-----------------------------------------------gtaagttt-attttgcagtatttttagcagcacatctttaacttctctgta--aattgaagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
                                          ||  |  | ||      | | | || ||  |  | ||   ||  || |||| |||   |  |  |||| || ||||||||||| |||||||| ||||||||||| || |||||||| |||||  | |||||||| |||
-----------------------------------------gtaagtttatttt-----gcagtatttttagcagcacatcgtt--aacttttctgta--aattgaagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAG

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|110363342|gb|EC926920.1|EC926920
EST:     AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAG                         GTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAACTGAGAGTGGAG
genomic: AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAGgtaatttttt ... gcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAG
EST: gi|71866122|gb|DT015177.1|DT015177
EST:     AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAG                         GTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAACTGAGAGTGGAG
genomic: AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAGgtaatttttt ... gcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAG
EST: gi|37188483|gb|CF607832.1|CF607832
EST:     AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAG                         GTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAACTGAGAGTGGAG
genomic: AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAGgtaatttttt ... gcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAG
EST: gi|77586832|gb|DV222559.1|DV222559
EST:     AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAG                         GTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAACTGAGAGTGGAG
genomic: AGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAGgtaatttttt ... gcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG
                             ttttaat  putative branch site (score: 3)
                           tattttaatttttgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttcttttctacccactattttaatttttgtgttgcacattcagGTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG