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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccattgttatttccatcataagaatgaaatgccaatttgtgttaattgaatattttttttgtatgtttgtttatgtgttgttttttttttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCCACAATGTAAACATCCTTTTGAATTTCTCAACATTCATCGCTCACTAGAT

Basic information

species Vitis vinifera
transcript Vv06s0009g03430.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G05050.1 (Glycine max), 3'ss of exon 2
atccattgtt--atttccatcataagaatgaaatgccaatttgtgttaattgaatattttttttgtatgtttgtttatgtgttgttttttttttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCCACAATGTAAACATCCTTTTGAATTTCTCAACATTCATCGCTCACTAGAT
  | | | ||  |||  |  | |  |  ||| ||    |||  | ||| ||     |||| |   | | |||||||||| ||| ||  ||  ||||    ||||| ||||||||||||| |||||| |||||  || |||||   || ||||| || ||||||||||| ||||| || |||||  | ||||||||||| |||
cactactattgaattgactgctttggcttgagattattattattattatttttgcgttttctacatctttttgtttatg-gtt-ttaattgattttgtgtagTGTAACATGCATCCTTCATTGGGCTACATACCGTGAGAAAGTTACCTGCCCTCAGTGTAAACATCCATTTGAGTTCCTCAATGTCCATCGCTCACTTGAT

upper sequence: Vv06s0009g03430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G35790.1 (Glycine max), 3'ss of exon 2
atccattgttatttccatcataagaatgaaatgccaatttgtgttaattgaatattttttttgtatgtttgtttatgtgttgttttttttttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCCACAATGTAAACATCCTTTTGAATTTCTCAACATTCATCGCTCACTAGAT
 |  |||||   ||    |||  ||    | |   | ||| | ||  |   || | |||| |  || ||| | | | || | ||  ||  ||||    ||||| ||||||||||||| |||||| |||||  || |||||   || ||||| || ||||||||||| ||||| || |||||  | ||||||||||| |||
ttgaattgtctgttttggcatgtgatattattattattttttttttttgagatgtgttttctacatctttttgtttatggttttacttgattttgtgtagTGTAACATGCATCCTTCATTGGGCTACATACCGTGAGAAAGTTACCTGCCCTCAGTGTAAACATCCATTTGAGTTCCTCAATGTCCATCGCTCACTTGAT

upper sequence: Vv06s0009g03430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G19430.2 (Arabidopsis thaliana), 3'ss of exon 2
atccattgttatttccatcataagaatgaaatgccaatttgtgttaattgaatattttttt--tgtatgtttgtttatgtgttgttttttttttttcaac-agTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCCACAATGTAAACATCCTTTTGAATTTCTCAACATTCATCGCTCACTAGAT
|||   | |||| | |    |  |  |  | |||| |   ||| ||| ||| | | ||| |  | |  ||||    | | ||  ||  ||| | |  |   |||||||||||||| ||||||||||| |  |  |   |||  || ||||||||||||||||| ||||| ||||| |||||||   | || ||  |||| |||
atcaccttttatcttctgtgtttgctttta-tgcctac--gtggtaactgactttctttctactttgggttttaagaggagtaattcatttctatctatttagTGTGACATGCATACTTCGTTGGGCGAGTTGCAAAGAGAGTCCCACATGCCCACAATGTAAGCATCCATTTGATTTTCTCAGTGTCCACCGAGCACTTGAT

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|26267617|gb|CA818680.1|CA818680
EST:     TTCAGGAAACTGCTATGGTAAAAGGTTGCGAGCACGCATACTG                         TGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCC
genomic: TTCAGGAAACTGCTATGGTAAAAGGTTGCGAGCACGCATACTGgtgtgttatc ... ttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCC
EST: gi|30297350|gb|CB974144.1|CB974144
EST:     ATAGTGCTTCAGGAAACTGCTATGGTAAAAGGTTGCGAGCACGCATACTG                         TGTGACATGCATCCTTCGTTGGGCCACATACAGTCAGAAACCAACATGCCC
genomic: ATAGTGCTTCAGGAAACTGCTATGGTAAAAGGTTGCGAGCACGCATACTGgtgtgttatc ... ttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgaatattttttttgtatgtttgtttatgtgttgttttttttttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCCACAATGTAAACATCCTTTTGAATTTCTCAACATTCATCGCTCACTAGAT
 tgttaat  putative branch site (score: 3)
                                tgttgttttttttttt  putative PPT
     aatattttttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccattgttatttccatcataagaatgaaatgccaatttgtgttaattgaatattttttttgtatgtttgtttatgtgttgttttttttttttcaacagTGTGACATGCATCCTTCGTTGGGCCACATATAGTCAGAAACCAACATGCCCACAATGTAAACATCCTTTTGAATTTCTCAACATTCATCGCTCACTAGAT

- - - - - - - - - -ataagaa
- - - - - - - - - - - - - - aaatgcc
- - - - - - - - - - - - - - - - - - - - - - -aattgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt