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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacaaagttcatataagcaatgtcatcacactttttgtgccatgacatgtgtattaccttcttctgagttctgatagcatttgtgctattattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGTGGTGAAATTCCAATTGAG

Basic information

species Vitis vinifera
transcript Vv09s0002g06120.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G44040.1 (Glycine max), 3'ss of exon 6
---tcacaaagttcatataagcaatgtcatcacactttttgtgccatgacatgtgtattaccttcttctgagttctgatagcatttgtgctattattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGTGGTGAAATTCCAATTGAG
     | || | |  ||  ||    |  |   ||     | ||   |   | |  |        ||| |   || ||||   | ||||| |   | |  |||||||||||  ||  ||||||| |||||| |||| || || |||||||||||||||||  | |||||||||
tggaaataatgctagtagtagttgggcaacttcagaaaatttggtttatta-gcatgcctttggcttgttgtttttgatga-agttgtg-tgccaattgacagAAGCAAAATGTTGAGGAGGGGCAAGTGATTTGTTATATTGAACAGCTTGGTGGTGAGCTGCCAATTGAG
















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|110695118|gb|EE072767.1|EE072767
EST:     GGAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAAGAG                         AAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGT
genomic: GGAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAAGAGgtatccagtt ... tattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGT
EST: gi|30303221|gb|CB980015.1|CB980015
EST:     GGAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAAGAG                         AAGCAA-TAGTGAAGGANGNCCAAGTGCTTTGCTACATCGAACAGCT
genomic: GGAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAAGAGgtatccagtt ... tattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCT
EST: gi|110700778|gb|EE077729.1|EE077729
EST:     GGAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAAGAG                         AAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGT
genomic: GGAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAAGAGgtatccagtt ... tattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGT
EST: gi|110693215|gb|EE069249.1|EE069249
EST:     GAGATCTCGGACGATAAAGGG-AAGCGTGCACCTCCATCATGTAAAAGAG                         A-GCATATAGTGAAGGATGGCCAAGTGCTTTGCT
genomic: GAGATCTCGGACGATAAAGGGGAAGCGTGCACCTCCATCATGTAAA-GAGgtatccagtt ... tattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtgtattaccttcttctgagttctgatagcatttgtgctattattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGTGGTGAAATTCCAATTGAG
                        ttctgat  putative branch site (score: 3)
                                          tattattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacaaagttcatataagcaatgtcatcacactttttgtgccatgacatgtgtattaccttcttctgagttctgatagcatttgtgctattattcaacagAAGCAAATAGTGAAGGAGGGCCAAGTGCTTTGCTACATCGAACAGCTTGGTGGTGAAATTCCAATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
-cacaaag
- - - - - - - - - caatgtc
- - - - - - - - - - - - -atcacac
- - - - - - - - - - - - - - - - - - - - ccatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttg