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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagtgcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA

Basic information

species Vitis vinifera
transcript Vv05s0051g00340.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 5
gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagtgcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA
                            ||| || ||||   || || ||     ||  | ||  |    |  | ||   | |  |   | ||||  | | |   | ||  ||    || |  | || |||| || ||||||||||||||||| || || |||||||||||  | || ||||||||||||||||| |||||||| ||||| |||||||| ||| | 
----------------------------gta-atacttgtgattcattgc-----agatctcattatg--tgtttgacttgtttcttaatcttaatctgttactaagttcttatg--ttcatatataaagGTGGGCACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 5
gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagtgcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA
   |   | ||   ||  | | | || |  || ||  |   |||  |  | ||||    | |||  || |  |    | |      |   |||| ||  ||||             |||  ||| |||||||||| || |||||||| ||||| || || |||||||||||  | || ||||| ||||||||||| ||||||||||||||||| ||||| ||| | 
--gtaactgctgatctgcaatgagttagaaagctgtgtcatgttttttcctctctt---ctcagttctctcta----agacactccatgctttatatattcatt------------attctcttttatagGTTGGTACTATATCAGCTAATGGGGAAAGGGAAATTGGTGAGCTCATTGCAAAAGCTATGGAGAAGGTTGGCAAAGAGGGAGTCATCACTATTACG

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 4
gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagt-gcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA
                                     |  |  ||  ||| | |||||  |       | ||  |    |   | |   |   | |  | |  | | |||      |       | || |||| || ||||||||||||||||| || || |||||||||||  | || || |||||||||||||| |||||||||||||| || ||||| ||| | 
------------------------------------gtatatctg-cagcaccctagttactttattttgttctt----atcctgtccatccctcaccttt--ttttattctctctatcctgtatgtaaagGTGGGTACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagtgcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctat-------agGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA
                                                                     |  ||    ||||   ||||||| |  ||  | |    ||  || || |     |||||       |||| || ||||||||||||||||| || || |||||||||||  | || || |||||||||||||| |||||||||||||| || ||||| ||| | 
--------------------------------------------------------------------gtatatctgcaaggctctagtttt-atgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG

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|161718112|gb|FC066924.1|FC066924
EST:     ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAG                         GTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
genomic: ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAGgtttgtttac ... acttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
EST: gi|110686767|gb|EE064783.1|EE064783
EST:     ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAG                         GTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
genomic: ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAGgtttgtttac ... acttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
EST: gi|30300026|gb|CB976820.1|CB976820
EST:     ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAG                         GTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
genomic: ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAGgtttgtttac ... acttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
EST: gi|110691710|gb|EE070124.1|EE070124
EST:     ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAG                         GTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
genomic: ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAGgtttgtttac ... acttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
EST: gi|110690897|gb|EE068383.1|EE068383
EST:     ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAG                         GTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATTGCA
genomic: ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAGgtttgtttac ... acttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
EST: gi|110731644|gb|EE106246.1|EE106246
EST:     GCTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAG                         GTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA
genomic: ACTTGAAAAGCAGAGCTAAGATGATCAGCACATCTGAAGAAATAGCACAGgtttgtttac ... acttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA
                                        aattaac  putative branch site (score: 2)
                                              cttctat  CT-rich tract
       tattagtttttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagtgcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctatagGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG