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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggagattattttcatgattttttttttttttttccgattcttttcatgaattgcaacttatgaagtatatatttgcttcaaatttttgtggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGACTCTGGGACGTTGTACCTAACGAG

Basic information

species Vitis vinifera
transcript Vv16s0050g02570.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 7
-tggagattattttcatgattttttttttttttttccgattcttttcatgaattgcaacttatga-agtat-atatttgcttcaaatttttgtggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGACTCTGGGACGTTGTACCTAACGAG
 | |     || |   ||||||     | |||| |  ||    | | |  | |   || |  | | ||| | | | |    |  |  |||  |  | |||||||| || ||| | |||||| || ||||||| ||| | ||||| ||||||||||||||||| || ||||  || || 
gttggagccatgt--gtgatttaggcatattttgttggagctatgtta-aagtgataagtggtaatagtttgacaatgtaatttatctttcatatactttcagGACCAGGAGATAGATGAACAAATTGAATTGCTTATTCTTGCAAGTGATGGACTCTGGGATGTAGTACAAAATGAC
















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|37190447|gb|CF609796.1|CF609796
EST:     TTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAG                         GATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
genomic: TTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAGgtaattcttg ... ggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
EST: gi|51050079|gb|CO818370.1|CO818370
EST:     TTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAG                         GATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
genomic: TTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAGgtaattcttg ... ggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
EST: gi|110690250|gb|EE067195.1|EE067195
EST:     TTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAG                         GATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
genomic: TTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAGgtaattcttg ... ggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
EST: gi|110425271|gb|EC991653.1|EC991653
EST:     CCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAG                         GATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA
genomic: CCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAGgtaattcttg ... ggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaattgcaacttatgaagtatatatttgcttcaaatttttgtggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGACTCTGGGACGTTGTACCTAACGAG
                                                ttttc  CT-rich tract
                     tatatatttgcttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggagattattttcatgattttttttttttttttccgattcttttcatgaattgcaacttatgaagtatatatttgcttcaaatttttgtggattttcagGATCAAGAGGTTGATGAAGAACTTGAATTACTTGTGCTTGCTAGTGATGGACTCTGGGACGTTGTACCTAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttca