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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaactgttttaaaaaacaattatcaaatcaaacattattttttatgtttgctcttttttaactcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG

Basic information

species Vitis vinifera
transcript Vv13s0064g00930.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G15550.1 (Glycine max), 3'ss of exon 10
-aaaaactgttttaaaaaacaattatcaaatcaaacattattttttatgtttgctcttttttaac-tcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG
     ||  | | |    | |||      |||  | || ||   ||             ||| |  | ||| |  | |  | |||||   |||   |  |||||| | || || || |||||||||||||  ||||||||||| || ||||| ||||||| ||| ||||| |||||||||||| ||||||||||| ||
tttttacattgtcagtgtataatccctttatctcatat-atcacttgcacaaaaatgaatttgatattattttctatttca-tttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG

upper sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G27300.1 (Glycine max), 3'ss of exon 11
--aaaaactgttttaaaaaa--caattatcaaatcaaacattattttttatgtttgctcttttttaactcattcttaactcaaatttttggctttcgactac-agTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG----
  ||   || |   || |||  |||  ||  |||  | ||| |  ||| |||| ||    || |||| | ||  ||| || || ||      | |   | || ||||| | || || || |||||||||||||  ||||||||||| || ||||||||||||| |||||| || |||||||||||| | ||||||||  ||    
gtaatccctataacaataaattcaacaatggaattgaccataaaattt-atgtgtgaa--ttgttaattgataattatct-aatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA

upper sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA12G36620.1 (Glycine max), 3'ss of exon 12
aaaaactgttttaaaaaacaattatcaaatcaaacattattttttatgtttgctcttt---tttaactcattcttaactcaaatttttggctttcgactac-agTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG----
      |     | | |||||    |||||  |||| |||||   |    || | |||   ||| | |  ||  | |   || ||  |   | |   | || ||||| | || || || |||||||||||||  ||||||||||| || ||||||||||||| ||| || || |||||||||||| | ||||||||  ||    
-----gtaacccatataacaa----caaattcaacaatatttggaaaccatgatatttatatttgaattgttaattatctaatttcatttatataatccactagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGTGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA

upper sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA12G36610.1 (Glycine max), 3'ss of exon 9
-aaaaactgttttaa-aaaacaattatcaaatcaaacattatttt--ttatgtttgctcttttttaactcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG----
 |  || |     || || | ||    | ||  ||| | | | ||  |  | |||     |   |   | ||| ||  || | ||  ||   ||    |  |||||| | || || || |||||||||||||  || |||||||| || ||||| || |||| ||| ||||| |||||||||||| |||| || ||  ||    
tatgaatttcaccaataagataaagcgcgaaagaaagagtgtattgatagtatttctctatacatgttttattgttttctgatatcatttattt----caccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA

upper sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
aaaaactgttttaaaaaacaattatcaaatcaaacattattttttatgtttgctcttttttaa----ctcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG
               ||  ||| ||||||| | |  |  | |  |||        ||||  ||     | | |  | |    |  || |   | |  | | |||||||| || || || || ||||| || |   | |||||||| || |||||||| || ||||||||||| |||||||| || |||||||||||||||
-------------gtaactaataatcaaataataattactatagtataaaaatcattttaaaagaattttactaatgagaagaggttatatatattta-tgcagTTTATAGCAGCAACGCAGCCAATAAACTCTCTCGCCTTTGTATTGGATGGAGTCAATTTTGGAGCATCTGATTTTGCTTACACTGCATACTCCATG

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|111283822|gb|EE296911.1|EE296911
EST:     CTCATTAGTATAAGCATTCCA                         TTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGA
genomic: CTCATTAGTATAAGCATTCCAgttatgagca ... tcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttgctcttttttaactcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG
                       tcttaac  putative branch site (score: 2)
                                          ctttc  putative PPT
                         ttaactcaaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaactgttttaaaaaacaattatcaaatcaaacattattttttatgtttgctcttttttaactcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
aaaaact
- - - - - -taaaaaa
- - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactcaa