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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagatggtctaagtaatttttccaacagttttacctttgaattcaaacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG

Basic information

species Vitis vinifera
transcript Vv08s0105g00260.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 6
-------------gagatggtctaagtaattttt---ccaacagttttacctttgaattcaaac-atacgggac-cttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG
              | ||  |     | || |||   ||| | || | |  | ||  |  | || |||    |  || || ||  |   || |   || |  |||     ||||  || |  | || || || | ||| || || ||  | ||||||||    || |||||||| |||||||||||||||||||||||| |  |||||||||   | |
gtactcagcgaattatattattcctctgatgtttgagccatccgtgtgatgtgtggttgtagactatattacatgctgtttattgtttgtagcctgatggtgtcta--tgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGCAATGTGCACGGTGTGAACCCCAAGTTTCTGGAGGTTGGAGAGAGGATAG

upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
gagatggtctaagtaatttttccaacagttttacctttgaattcaaacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG
                |  ||   | || ||     ||   || ||  | ||||         ||   ||| |||     |  || | ||   | |  ||||  | || ||||| || || || || || ||||| |||||| |  ||||||||||||| ||||| ||||| ||||| ||||| ||||||||  || |  
---------------gtactttgtatagcttagttgttttgtt-aattacacgg---------atgcccatgaacactccta-atgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA

upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 5
-gagatggtctaagtaatttttcca-acagttttacctttgaattcaaacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG
 | | |  | |   ||| |||  ||   |||| |  | |   |    |||  |  | | |    || |   |   ||||||||   | |||| | ||| ||||||||||| || || |||||||| ||||| ||||| ||||||||||||||||||||||| |||||||| ||||| ||  ||||||||||||| ||  | |
ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaa--agggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG

upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 5
gagatggtctaagtaatttttccaacagttttacctttgaattca---aacatacgggaccttttcatattcatta---actaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG
      || |  ||  ||||    | |  |||  | | || |||    | || |   || ||   || |   |  |   ||||||||   | |||| | ||| ||||||||||| || || |||||||| ||||| ||||| ||||||||||||||||||||||| |||||||| ||||| ||  ||||||||||||| ||  | |
------gttttcgtgtttttgttgataaatttgtcatggagttcttttatcaaaaaagaactaaacaaaacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG

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|219555089|gb|FG984878.1|FG984878
EST:     TCTTTGTGAAACACATAAATAATTGGGTTGCAAGAGCATACTGCCACAAG                         GTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGC
genomic: TCTTTGTGAAACACATAAATAATTGGGTTGCAAGAGCATACTGCCACAAGgtaactgtct ... ctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGC
EST: gi|110725725|gb|EE102558.1|EE102558
EST:     TCTTTGTGAAACACATAAATAATTGGGTTGCAAGAGCATACTGCCACAAG                         GTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGC
genomic: TCTTTGTGAAACACATAAATAATTGGGTTGCAAGAGCATACTGCCACAAGgtaactgtct ... ctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG
                                            tctctatcc  CT-rich tract
             ttttcatattcattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagatggtctaagtaatttttccaacagttttacctttgaattcaaacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - tccaaca
- - - - - - - - - - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatctg