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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcag

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 17
AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaacatcatga-atgtttgttagcaacttgtttgattacattaattagtagttcaagtt-----gtgtgatattttctat---gtttatgattgcag-------------------------------------
| ||  |||||| ||||||||||| ||  ||||||||||||||||||||| ||| |||| ||  |   | | ||||||||| || ||||||||||| | ||  | |       |||  || |||  |    |     | | | | |  ||||     |  ||| |     |  | ||||  ||| |    |||||| |                                          
AATTTCACATCCATGGAAAGATGAAAAGTCAAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 17
AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagt----caa----catcatgaatgtt-----tgttagcaacttg--tttgattacattaattagtagttcaag---ttgtgtgatattttctatgtttatgattgcag
| ||| |||||| ||||||||||| ||  | ||||||||||||||||||| ||| |||| ||  |   | | |||||||||  | ||||||||||| | ||  | |    |||     ||| |   ||||       | || ||  |   ||| ||| |    | |  |   | | |   |  | |||| | ||  || | | |||| ||||
AATTGCACATCCATGGAAAGATGAGAAGTCGAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgat-gcag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 19
AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtc--aacatcatgaatgtttgttagcaacttgtttgattacattaattagta-gttcaagttg-tgtgatatttt-ctatgtttatgattgcag---------------------------
|||||| ||||||||||||||||||||| |||| ||||| |||||||| | |||||||| ||||  |||||||||||||||||| ||||||||||||||||||||||  |  || |  |||    | |   |  || |||| ||    ||||  |||  || || | | | | ||||||| ||||  | || | |   |                           
AGTTGAGCATCCGTGGAAAGATGATAAACCAAAACAACACATATATGACCGTGTGTTTGATGGTGATGCCACTCAAGAAGATGTATTTGAGGATACAAGGgcaagtcttagtataacaaattaaagatcctagttt-tttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 19
AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtc--aacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttg-tgtgatattttctatgtttatgattgcag----------------------------------
    || ||||| ||||||||||||||| |||| ||||| || ||||| | |||||||| ||||  |||||||||||||||| | ||||||||||||||||||||||  |  || |  |||  | | |   |  || ||   ||| ||    ||    || || | | | | ||||||| |||  | || |     |                                  
----GAGCATCCTTGGAAAGATGATAAACCAAAACAACACATTTATGACCGTGTGTTTGATGGTGATGCCACTCAAGAAGATATATTTGAGGATACAAGGGCAAgtcttagtataacaaattatagatcatagttttttgctttagatagcatatacattgaaatggatttaatattttttatactcattaccaatgtttttcttttggaaatttgcaatgcagtacttag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 5'ss of exon 16
AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcag
 ||||||||||| |||||||| || |||  ||||||||| ||||||||||  || ||||      |||| | |||||| ||| | ||||| || |||| || |  | |     ||| |  | ||||    | ||   |     | ||  ||| |   |   | |   | | ||  | |   ||| | |  |   
TGTTGAACATCCATGGAAAGACGACAAAAGAAAGCAACACATATATGATCGCGTATTTGACATGCGTGCTAGTCAAGATGATATCTTTGAAGACACAAAGgta--ttattgatatgtaactgtgttc---atttacctttcatcctttgttattttcttgtggttactaacatcgttttccttt-taacag---

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|351015272|gb|FQ445556.1|FQ445556
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
EST: gi|351043062|gb|FQ443904.1|FQ443904
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
EST: gi|351026499|gb|FQ428511.1|FQ428511
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGAACATCCGTGGAAAGATGATAAAGCAAAGCAACATATATATGATCATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT