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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgtggcaccatattcttattttttctcagtacatatatctgtagtgaaatgactcttgtactcttgtggctgaccttattttttattatcttggtagGTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCTGGAGATCCCATACGTTGCATTGTTGCTTGTTTAAGCG

Basic information

species Vitis vinifera
transcript Vv06s0009g01460.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G21060.3 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------aagtgtggcaccatattcttattttttctcagta-----------catatatctgtagtgaaatgact---cttgtactcttgtggctga-----ccttattttttat-----tatcttggtagGTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCTGGAGATCCCATACGTTGCATTGTTGCTTGTTTAAGCG
                                  | | |   | || ||| |  |  |   |    |             || |  ||| |||  ||   |     | |||  | |    |||       ||     | |      | | ||  |||||||||||||| || |||||||| ||||| ||||| |||||| |||| |||||||||||  | | | | ||||| | | |||| ||||
gtaggtgaaacacagcttgtgtatagagtataacactattatatcacattttagtactcatttgaaaatgaaactagttgtaaacatgtggtggtattgttggctctatacagtaggtagtgaaaagcttttgcgcctgacatatgtttatttatagGTTGGTGCTGGTCTTCCTGTCATCGCATCCTTGAACCGCATAATTTCGTCTGGAGATCCTGTTCATAGGATTGTCGGTAGTTTGAGCG
















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|110688641|gb|EE067425.1|EE067425
EST:     ATTATGACAAACTGGTTGCTCACCCACGTCGCATTCGGTATGAGTCAACT                         GTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCT
genomic: ATTATGACAAACTGGTTGCTCACCCACGTCGCATTCGGTATGAGTCAACTgtaagtgtgt ... atcttggtagGTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCT
EST: gi|110409000|gb|EC974653.1|EC974653
EST:     ATTATGACAAACTGGTTGCTCACCCACGTCGCATTCGGTATGAGTCAACT                         GTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCT
genomic: ATTATGACAAACTGGTTGCTCACCCACGTCGCATTCGGTATGAGTCAACTgtaagtgtgt ... atcttggtagGTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgaaatgactcttgtactcttgtggctgaccttattttttattatcttggtagGTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCTGGAGATCCCATACGTTGCATTGTTGCTTGTTTAAGCG
                         ggctgac  putative branch site (score: 3)
                                    ttttttattatctt  putative PPT
                                 ttattttttattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgtggcaccatattcttattttttctcagtacatatatctgtagtgaaatgactcttgtactcttgtggctgaccttattttttattatcttggtagGTTGGTGCTGGCCTCCCTGTCATAGCATCTTTGAATCGCATACTTTCATCTGGAGATCCCATACGTTGCATTGTTGCTTGTTTAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - -gcaccat
- - - - - - - - - - - - - - - - - - - - - - - - gaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggctga