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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttatgaatggatccaagaaactctacctttctctatatgttgtatatttttatttttaatctttcatttttctgattaccttttttcctgcatgacagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG

Basic information

species Vitis vinifera
transcript Vv18s0001g05270.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g05270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G01920.1 (Glycine max), 3'ss of exon 4
acttatgaatggatccaagaaactctacctttctctatatgttgtatatttttatttttaatctttcatttttctgattaccttttttcctgcatga-cagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG
   ||| | |   ||  | |   |     |       | |||  |     |||    ||| | ||  |   || |  | |  |   |   |   ||| |||||||||||||| || ||||  |||||||||||||| ||||| || || || |||||||| || ||||||||| | |||| |
-tctataatttcttcttaaattatggttttaaggacttttgtattgctcatttcaccttatttttggagcattttattcatttaactctttatttgatcagATTGAAAAGCCATTGCAGAGGCATGGAGGCAGGCTCGAGCACAATGAGACTTATTGTGGTTCCTGTTATGGTTCTGAAGTG

upper sequence: Vv18s0001g05270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G34600.1 (Glycine max), 3'ss of exon 4
acttatgaatggatccaagaaactctacctttctctatatgt-tgtatatttttatttttaatctttcatttttctgattaccttttttcctgcatga-cagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG
|  ||| | |   ||  |  || | |   |||    |  | | | |   || ||    ||| | ||  |   || |  |||  |   |   |   ||| |||||||||||||| || || |  || ||||||||||||||||| || || || |||||||| || ||||||||||| |||| |
atctataatttcttctta--aattatggttttaagaaattatgtattccttgttcaccttatttttggagcattttatttatttaactctttatttgatcagATTGAAAAGCCCTTGCAAAGGCACGGAGGCAGGCTTGAGCACAATGAGACTTATTGTGGTTCCTGTTATGGTGCTGAAGAG

upper sequence: Vv18s0001g05270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ21748 (Selaginella moellendorffii), 3'ss of exon 4
acttatgaatggatccaagaaactctacctttctctatatgttgtatatttttatttttaatctttcatttttctgattaccttttttcctgcatgacagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG
                                              ||  || ||||      |    ||||   ||        ||   |   ||  ||||||| || ||  | || |||||||| || ||||| ||||||||||||||||| ||||| || |||| |||||| ||    
---------------------------------------------gtaaattgatttc---cttcgagttttctcgaccttaacattcgattgttgctagATTGATAAACCACTCCAAAAACATGGTGGAAGGCTAGAGCATAACGAAACGTACTGTGGTTCCTGTTTTGGTGCCGAGCAA

upper sequence: Vv18s0001g05270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ06790 (Selaginella moellendorffii), 3'ss of exon 4
acttatgaatggatccaagaaactctacctttctctatatgttgtatatttttatttttaatctttcatttttctgattaccttttttcctgcatgacagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG
                                                   | | |  |   |||   ||||   || |      ||   |   ||  ||||||| || ||  | || |||||||| || ||||| ||||||||||||||||| ||||| || |||| |||||| ||    
--------------------------------------------------gtaaatgatttccttcagttttctcgactttaacattcgattgttgctagATTGATAAACCACTCCAAAAACATGGTGGAAGGCTAGAGCATAACGAAACGTACTGTGGTTCCTGTTTTGGTGCCGAGCAA

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|71859145|gb|DT008200.1|DT008200
EST:     CCCATGGCAGTGTTATAGAAGCAAGGCAGGATGGGATTGGTTCTCCTAAG                         ATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACG
genomic: CCCATGGCAGTGTTATAGAAGCAAGGCAGGATGGGATTGGTTCTCCTAAGgttagtaata ... tgcatgacagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttttatttttaatctttcatttttctgattaccttttttcctgcatgacagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG
                          ttctgat  putative branch site (score: 3)
                tctttcatttttctga  CT-rich tract
     tttatttttaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttatgaatggatccaagaaactctacctttctctatatgttgtatatttttatttttaatctttcatttttctgattaccttttttcctgcatgacagATTGAAAAGCCTTTACAGAAACATGGAGGCAGGCTTGAGCATAACGAAACGTATTGTGGGTCATGTTATGGTGCAGAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -tgaatgg
- - - - - - - ccaagaa
- - - - - - - - - - - ctctacc