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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctttcacagatgtgccttaacatatgtattgcataataagaaccgacaaacaataatttattttttgcatttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG

Basic information

species Vitis vinifera
transcript Vv08s0105g00590.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 10
gtattctttcacagatgtgccttaacatatgtattgcataataagaaccgacaaacaataatttattttttgcatttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG
||||   |||| |    | | ||         | || ||  |        |  | || | |    | ||| |   ||  | | |||| || || || ||||||||||||||||| |||||||| |||||||||||  |||| ||||||
gtatatcttcatacgattacttttcttgtaacagtgtatgctt----ttcatgatcattgacc-gtctttcgtgatt--ttctagCTAGGGATTGCTATTGTAAATGACTTTAAGAGTGTTGAGGGAGATAGAGCTCTGGGGCTTCAG

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattctttcacagatgtgccttaacatatgtattgcataataagaaccgacaaacaat-aatttattttttgcattt----catgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG-------------------------------------
||| |||||     |      |||   |   | || | | ||  |     | |  |  |   || || || | | |||     |   ||| | || || |||||||| || ||||| |||||||||||||||||||||||||| |||||||||                                     
gtactcttttggcaa-accttttatgttgcttttttcgttatctgttgtaatatgctcttgcttcatgttgtacctttgtgataatgcagTTAGGAATAGCCATTGTTAACGACTTCAAAAGTGTTGAAGGAGATAGAGCATTAGGACTTCAGTCTCTCCCAGTAGCTTTTGGCACCGAAACTGCAAAAT
















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|30252103|gb|CB968742.1|CB968742
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|161705814|gb|FC057091.1|FC057091
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|349830671|gb|FQ416969.1|FQ416969
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTTAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|351033623|gb|FQ447782.1|FQ447782
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCCTCGCCATTGTAAATG
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATG
EST: gi|351041270|gb|FQ447397.1|FQ447397
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACCGCATAGCTGGG                         CTGGGCATCGCC
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCC
EST: gi|351034199|gb|FQ463133.1|FQ463133
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|351025946|gb|FQ427958.1|FQ427958
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|351031189|gb|FQ445016.1|FQ445016
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|349833147|gb|FQ416525.1|FQ416525
EST:     CTCTGAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCTCCATTGTAAATGACTTTAAAAGT
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGT
EST: gi|110698374|gb|EE075807.1|EE075807
EST:     CTCTTAATCCTGATATAATTGGTCCCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAG-GTTGAAAGAGATAGA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGA
EST: gi|351018561|gb|FQ424668.1|FQ424668
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
EST: gi|349829107|gb|FQ419639.1|FQ419639
EST:     CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGG                         CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA
genomic: CTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtattctttc ... ttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattgcataataagaaccgacaaacaataatttattttttgcatttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG
                      aaacaataatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctttcacagatgtgccttaacatatgtattgcataataagaaccgacaaacaataatttattttttgcatttcatgccagCTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA