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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcctccttgttatccttgtaactgattactaataaatctcttagctttctttagtgattataacttattattctttttatgtctgttctttcggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCTGTTCTTGATTTCTCGTACAAGTTTGGAACCTCTTCG

Basic information

species Vitis vinifera
transcript Vv06s0061g01170.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 21
gtgaagcctccttgttatccttgtaactgattactaataaatctcttagctttctttagtgattataacttattattctttttatgtctgttctttcggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCTGTTCTTGATTTCTCGTACAAGTTTGGAACCTCTTCG
                                  || ||| |     ||     |||     || |  | ||    ||  |     |   ||  ||| ||| ||||||| |||   |||||||| ||  ||||||||||| |||| || ||||| |||||||||||||| || || |  |||||||| ||   |
---------------------------------gtactaagtgatgcagtgcagttttaatgttttttcctaccgctcaatcctcat---tttcttccgttctgtagGTCCAAATTCCACTTGAGGTTGTGAATCTTCGTGCAAGTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTG

upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 21
gtgaagcctccttgttatccttgtaactgattactaataaatctcttagctttctttagtgattataacttattatt--ctttttatgtctgttctttcggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCTGTTCTTGATTTCTCGTACAAGTTTGGAACCTCTTCG
                      || |    | | |  | |  || || | |   ||||   ||| | | || |||      ||  || |    ||||| | ||   |||||||||||||||||||| ||||| ||||| |  |||||||||||||| || |||||||| ||||| ||||||||||| | |  |  |
----------------------gtgagaattcatttgtta--ctgtttgttgcttttaaatattgttaattgttaacaagcttacattttccctcttttgattgcatagGTGCAATGCCCACTTGAGGTCATTAATCTCCACCCAAGCAGGGATGTTGCCGTTCTTGACTTCTCCTACAAGTTTGGTAACAATATG

upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 21
gtgaagcctccttgttatccttgtaactgattactaataaatctcttagctttctttagtgattataacttattattctttttatgtctgttctttcggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCTGTTCTTGATTTCTCGTACAAGTTTGGAACCTCTTCG
                      || |    | | |  | |  || || | |   || |   ||||    ||| ||   || |  | |    ||||| | ||   |||||||||||||||||||| ||||| ||||| |  |||||||||||||| || |||||||| ||||| ||||||||||| | |  |  |
----------------------gtgagaattcatttgtta--ctgtttgttgctttcaaatattaattgttaataagtttatatttttccctcttttgattgcatagGTGCAATGCCCACTTGAGGTCATTAATCTCCACCCAAGCAGGGATGTTGCCGTTCTTGACTTCTCCTACAAGTTTGGTAACGATATG

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|110685737|gb|EE062720.1|EE062720
EST:     TAAAGATGGAACTCTCATTAGTACCCGAAACTATTCCTCCACGTGCGCAG                         GTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCT
genomic: TAAAGATGGAACTCTCATTAGTACCCGAAACTATTCCTCCACGTGCGCAGgtgaagcctc ... ggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCT
EST: gi|110359386|gb|EC920788.1|EC920788
EST:     TAAAGATGGAACTCTCATTAGTACCCGAAACTATTCCTCCACGTGCGCAG                         GTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCT
genomic: TAAAGATGGAACTCTCATTAGTACCCGAAACTATTCCTCCACGTGCGCAGgtgaagcctc ... ggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCT
EST: gi|110703483|gb|EE080368.1|EE080368
EST:     CTATTCCTCCACGTGCGCAG                         GTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCT
genomic: CTATTCCTCCACGTGCGCAGgtgaagcctc ... ggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCT
EST: gi|71860409|gb|DT009464.1|DT009464
EST:     TAAAGATGGAACTCTCATTAGTACCCGAAACTATTCCTCCCCGTGCGCAG                         GTGCAATGCCCACTTGAAGTCATGAATCTTCG
genomic: TAAAGATGGAACTCTCATTAGTACCCGAAACTATTCCTCCACGTGCGCAGgtgaagcctc ... ggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttagtgattataacttattattctttttatgtctgttctttcggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCTGTTCTTGATTTCTCGTACAAGTTTGGAACCTCTTCG
          ttataac  putative branch site (score: 2)
                                      ttctttcg  putative PPT
     agtgattataacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagcctccttgttatccttgtaactgattactaataaatctcttagctttctttagtgattataacttattattctttttatgtctgttctttcggttatgtagGTGCAATGCCCACTTGAAGTCATGAATCTTCGTCCAAGCAGGGATGTAGCTGTTCTTGATTTCTCGTACAAGTTTGGAACCTCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT