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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04620.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 18
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
       ||  | ||  || | | ||||| || ||       || |         ||| |      |   |||    | ||    | ||        |||  |||    |||  |   || ||||||||||||||| ||||| |||||||| ||||| |  || || ||||| ||| ||||||||||||| ||||| |||
-------ttaataac--attactctatttggaatactctccaattgc--------atctgccagcaatgtaattattagtcccagagag--------ttgaaacatctgtgat-tggttaatgtagGTACTGTGGTGGATTCTAAGATCTGTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
-----------------------------gtaatattttcttacttata--------attttatttag-attat--gtcttgatggttgagct-tgat-ccgttgatcaaacaatctccact-ctagaatagcaat-acggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                             |   |||||   | ||||||        ||||| ||| | ||| |    ||    |  || | | || |   ||||  |           ||  |     |  || | ||     |    | ||     ||| |||| |||| ||||| || || |||||||| || || || |  ||||||||||||||||| ||||||||||| ||||| |||
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 19
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatagca-atacggt-tgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                                                               | ||| | ||    | |  | || | ||    | ||   | | |  ||||||||||||| ||| |||||||||| |||||||  || ||||| || || || |||||||| || ||||| |||
----------------------------------------------------------------------------gtttgtaggaaagtttgttcaatgtgcttcacaactaaaacgcttttgctagGTACTGTGGTGGATACGAAGATCTGTCATCCCACGGAATTTGATTTCTACCTCTGCAGTCACGCTGGAATACAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 17
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatagc-aatacggttg--ttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                                                     |  |  ||  |    | | || |||   | |   | |  ||       || |  |   ||| |||||||| ||||||||||| |||||||| |  ||||||||||| || || ||||| ||||| || || |||
------------------------------------------------------------------gtgctgttgccgtttataagtggcgaatttagataactaatgagagaccgttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttg--atcaaacaatctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                                      |  | ||||   ||||  | |  | | | ||||  |  |||  |         | | |    || |  |   ||| |||||||| ||||||||||| |||||||| |  ||||||||||| || || ||||| ||||| || || |||
------------------------------------------------------gtgctgttgccgtcaataagtggcgaatttagataactaatgaga-------gaccgt----tttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 19
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatag-caatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                                                        | |  |    ||  |   ||||  | |||  ||||  |  | | |  |    ||||||||||||| ||| |||||||||| |||||||  || ||||| || || || |||||||| || ||||| |||
-----------------------------------------------------------------------gtttgtagcaaagtttgttcaatgtgcttg--acaactaaaacgcttttgc--tagGTACTGTGGTGGATACGAAGATCTGTCATCCCACGGAATTTGATTTCTACCTCTGCAGTCACGCTGGAATACAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 17
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                                | |||    ||||| || |     |  | | | ||||  |  |||  |         | | |    || |  |   ||| |||||||| ||||||||||| |||||||| |  ||||||||||| || || ||||| ||||  || || |||
------------------------------------------------gtgctgttgccgttaataag----tggcgaatttagataactaatgaga-------gaccgt----tttccttgacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGGCGGCATTCAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 17
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttgatcaaacaatctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                                | |||    ||||| || |     |  | | | ||||  |  |||  |         | | |    || |  |   ||| |||||||| ||||||||||| |||||||| |  ||||||||||| || || ||||| ||||| || || |||
------------------------------------------------gtgctgttgccgttaataag----tggcgaatttagataactaatgaga-------gaccgt----tttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG

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|33407837|gb|CF213464.1|CF213464
EST:     CAACCACAATGACAAAAGCAGCACTGATAGGAGTGGGAACATCTTACCTG                         GTACTGTGGTCGATTCTAAGATCTGCCATCCCAGTGAGTTTGACTTTTATC
genomic: CAACCACAATGACAAAAGCAGCACTGATAGGAGTGGGAACATCTTACCTGgtaatatttt ... cctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG
                                           ttcctatt  CT-rich tract
          tagaata  TA-rich tract