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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG

Basic information

species Vitis vinifera
transcript Vv12s0059g02310.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G10710.1 (Glycine max), 3'ss of exon 8
gtaaataaatgatcataactaaatgccac-taaaaaactactctagccagt-actgaatttcaacacattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
                 ||||      || |   |   || | |   | || | |   |||  |   |  |||| |  |   |  | |    | | | | | ||  |  |||||    ||||| ||||||||||||||||| ||||| |||||| |||||||||| ||| | || |||||| | |||| |||||| | ||||||||| || ||| | ||||
-----------------actaggccgtaccttttattttatttttttctgttaatttttttttatctacaaatattcttagttaatgttggcttagtctgtaatctctatttat----tagGTCACATGGGTTGAGCATGTAGAAGTGGATGATAGAGGTGTTCACAATCTTTACAAGCAGCTTGTTAGCTCTGGACATGCATTTGGTGCAAAACGTTGGG

upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G38430.1 (Glycine max), 3'ss of exon 8
gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
        ||||    ||  | ||   | ||  | |   ||  ||| | ||   |||    |  | ||     |  |||  |    ||||| ||||| |  |     ||  |||| ||||| | ||||||||||||||| ||||| |||||  ||||||| |||||| |||| |||||| | |||| |||||| | |||||||||||| ||| | ||||
--------atgaagtgaatcatatcataatatcatatcccttgagcaatta---aat----aagccttg----tggttacattcggcatttgattttgttctcaatcttattgccctagGTCATATGGGTTGAGCATGTAGAAGTGGATGACAGAGGTGTCCATAATCTATACAAGCAGCTTGTTAGCTCTGGGCATGCATTTGGGGCAAAACGTTGGG

upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G46000.1 (Glycine max), 3'ss of exon 7
gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaatt-ttctgatggccttttatgcc-ttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
                | ||   | ||  |||     | | |||| | ||||    |||      |||  | ||  | | |  | |   |||||| ||||     |  | | |    |||||| ||||||||||||||||| ||||| |||||| |||||||||| ||| | || |||||| | |||| ||| || | ||||||||| || ||| | | ||
----------------acct---ttcctataaccttgtgcactaggccgtacct--ttttgttttatttttcctgttaattaatgtggcttaattattctagaatctctatgtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTTTACAAGCAGCTTGTTAGCTCCGGACATGCATTTGGTGCAAAACGTTTGG

upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G32050.1 (Glycine max), 3'ss of exon 8
gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
              ||   ||||    |  || |||  |     |  | || |||     |  |  |   | |  ||| |   | | ||| | |||  ||     ||  | |||| ||||| | |||||||||||| || ||||| |||||  ||||||| |||||| |||| |||||| | |||| ||| || | ||||||||| || ||| | ||| 
-------------tatttttaaaatggataaagaaaggaaatatg--aata-tgagacagatgatgtggttgc--atttggcatttaattgattttgttgtcaatctcat-tgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTATACAAGCAGCTTGTTAGCTCGGGGCATGCATTTGGTGCAAAACGTTGGA

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|351024273|gb|FQ423696.1|FQ423696
EST:     GAAGGCCATCTGGATGTTTAATACAAGAAATGCCTAATGGATATTCAAAG                         GTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATA
genomic: GAAGGCCATCTGGATGTTTAATACAAGAAATGCCTAATGGATATTCAAAGgtaaataaat ... tatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATA
EST: gi|110418253|gb|EC984389.1|EC984389
EST:     AAGGGCCATCTGGATGTTTAATACAAGAAATGCCTAATGGATATTCAAAG                         GTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATA
genomic: AA-GGCCATCTGGATGTTTAATACAAGAAATGCCTAATGGATATTCAAAGgtaaataaat ... tatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
                                        ccttttat  CT-rich tract
                       atttaattttctgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG