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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaattgggcaacttgtgtacccttatttatttcagtatctaatgaagtttatcaatggtcatttcattggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT

Basic information

species Vitis vinifera
transcript Vv05s0062g00210.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 3
-gtgaattgggcaacttgtgtacccttatttatttcagtatctaatgaagtttatcaatggtcatttcattggctaatgaggtc-attttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT
      |||   |  || |||| || || ||  |  |   | |  | || |    |       | |||||   | |||||| |  |   ||   | |   ||||||||| || |||||||| ||||||||||| ||||||||||| |||| ||| |||||||| ||  || | || |||||||||
tccttgttgattatattatgtaaccatacttcctatatgctatgttaaattagtactccatagacttcat--accaatgagttttaccatgacatgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g05080.1 (Oryza sativa), 3'ss of exon 3
gtgaattgggcaacttgtgtacccttatttatttcagtatctaatgaagtttatcaatggtc-----atttcat-tggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT
     ||  |  ||   | | |  ||  |||| | || |        | |   | | | |||     | ||||   |||| |  |  | | | ||   | |   ||||||||| || ||||||||||||||||| || ||||| ||||| |||| ||| |||||||| ||  |  | || || ||||||
----tttatgttacccttatgcattttattatgttagcagacttcctaatgctttagtagtccatagacttcacacggctga--attttactctgacatgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
----gtgaattgggcaacttgtgtacccttatttattt---cagtatctaatgaagtttatcaatggtcatttcattggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT
    |||  |        |  ||| |     | | |||   |||| |  ||| ||||| ||  |   |   ||  |||  ||      ||||    ||  || | |||||||||||| ||||||||||| ||||||||||| ||||| || |||| ||| ||  |||| ||  |  | || |||||||||
ttgtgtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttactctaggttt-ttgttta------tcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G26580.1 (Glycine max), 3'ss of exon 3
gtgaattgggcaac--ttgtgtacccttatttatttcagtatctaatgaagtttatcaatggtcatttcattggctaatg-aggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT
 ||  |  | |||   |   ||   || |  |||||  |       |||| |  |    || |  |    | || |  || |  ||||    ||  || | ||||||||| || ||||||||||| ||||||||||| ||||| || |||| ||| ||  |||| ||  |  | || |||||||||
-tgtttgtgtcaatagtgtcgtgttctgaagtatttttggtcagtttgaaatcaagt--tgattctactctaggtttttgtatatcatgactttgattttcagAAACAACCGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgaattgggcaacttgtgtaccctta---tttatttcagtatctaatgaagtttatcaatggtcatttcattggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT
 | | ||    ||||| | |  |  ||   ||| | | | |  |  ||  ||| |   || | | |||   ||  ||  |    |  ||||||  ||||  ||| |||||||| | ||||||||| ||||| |||||||||||| |  ||| ||| || || ||||||||| |  |||||||||||
ataactttcttaacttctatttctgtagaatttgtataaattacccatctagtcttctaa-gttaattgatttttcttttcttttggttttgtcttttc--agAGACAACTGTGAGACAAATTGAGGATGCTTTCAAGGAATTCTCAGCAAGGGATGATATCGCTATCATTCTTTTAAGCCAATAT

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|110400937|gb|EC967524.1|EC967524
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|110384574|gb|EC949021.1|EC949021
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|110425951|gb|EC992347.1|EC992347
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|51052279|gb|CO819479.1|CO819479
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|26264288|gb|CA815351.1|CA815351
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGATTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|34543784|gb|CF512016.1|CF512016
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|26266198|gb|CA817261.1|CA817261
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGATTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|27583949|gb|CB006644.1|CB006644
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|110687266|gb|EE064524.1|EE064524
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
EST: gi|37188187|gb|CF607536.1|CF607536
EST:     GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA                         AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG
genomic: GGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttac ... tctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttatcaatggtcatttcattggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT
                         ggctaat  putative branch site (score: 3)
                                    tcattttgttctttct  putative PPT
     ttatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattgggcaacttgtgtacccttatttatttcagtatctaatgaagtttatcaatggtcatttcattggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg