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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataattttttttcggcccctttactgttaagcatgcaggtaaaccttaacatgttgatccaccaacacttta...

Basic information

species Vitis vinifera
transcript Vv05s0062g00210.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g57854.1 (Oryza sativa), 5'ss of exon 4
AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataattttttttcggcccctttactgttaagcatgcaggtaaaccttaacatgttgatccaccaacacttta--
||||||| || |||||||| ||||||||||| ||||||||||| |||| ||| |||||||| ||  || | || ||||||||||||||| | |   |   ||| ||||  |   |||| || |        |||   | |   |||    |          ||   | ||    || |    |  
AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatcttgattg-tat-acatccagctatttcttcttctgtttgttaagatgatcaatgatcatcttatcacttatccaggtcttataaaatgagaat

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g57854.2 (Oryza sativa), 5'ss of exon 1
-----------------AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataattttttttcggcccctttactgttaagcatgcaggtaaaccttaacatgttgatccaccaacacttta--
                 ||||||| || |||||||| ||||||||||| ||||||||||| |||| ||| |||||||| ||  || | || ||||||||||||||| | |   |   ||| ||||  |   |||| || |        |||   | |   |||    |          ||   | ||    || |    |  
ACCATGACATGTTACAGAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatcttgattg-tat-acatccagctatttcttcttctgtttgttaagatgatcaatgatcatcttatcacttatccaggtcttataaaatgagaat

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g05080.1 (Oryza sativa), 5'ss of exon 4
AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataattttttt--tcggcccctttactgttaagcatgcaggtaaaccttaa-catgttgatccaccaacacttta
||||||| || ||||||||||||||||| || ||||| ||||| |||| ||| |||||||| ||  |  | || || ||||||||||||   |   |   ||| ||||    | |||| |||  |       |  | || |||     ||| |   |  |||  ||  ||  |    ||       
AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATATgtaagtagcttgattg-tat-acatcaggttatttctttgtttatataatgaagtgataactgatcagcttgtcactaagtatcctggcctcagaaagtcac-

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G09570.1 (Glycine max), 5'ss of exon 4
AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataatttt--ttttcggcccctttactgttaagca-tgcaggtaaaccttaacatgttgatccaccaacacttta
|||||||||| ||||||||||| ||||||||||| ||||| || |||| ||| ||  |||| ||  |  | || |||||||||||||||   | |||||     | | | |||   | |   | | |  | |||   ||||||  | | |         ||    |  |  | ||      ||   
AAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATATgtaagt-catatttcatggctataataaatgggtctggctgttgtgcacttgcatgttaattaatactatctgcaattgttttcctacttcatatggcctg--

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G02620.1 (Arabidopsis thaliana), 5'ss of exon 4
AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataattttttttcggcccctttactgttaagcatgcaggtaaaccttaacatgttgatccaccaacacttta-
| |||||||| | ||||||||| ||||| |||||||||||| |  ||| ||| || || ||||||||| |  ||||||||||||||||||| |  |||   ||    |||| |  |  | || |  |  ||| |||| || |  || |        || |  |  | ||| |   |  | | | 
AGACAACTGTGAGACAAATTGAGGATGCTTTCAAGGAATTCTCAGCAAGGGATGATATCGCTATCATTCTTTTAAGCCAATATgtaagtgtcttcttccaaatccagtttacttgtaatgttact-catcttaactgctatgtctgtactgtcttgtttaagtcgtaatcaaaggattcatgac

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:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCAGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|110384574|gb|EC949021.1|EC949021
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCAGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|110425951|gb|EC992347.1|EC992347
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTCGTAGATAGCTACAACAAGCCGGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|51052279|gb|CO819479.1|CO819479
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCAGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|26264288|gb|CA815351.1|CA815351
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|34543784|gb|CF512016.1|CF512016
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCAGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|26266198|gb|CA817261.1|CA817261
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|27583949|gb|CB006644.1|CB006644
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|110687266|gb|EE064524.1|EE064524
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|37188187|gb|CF607536.1|CF607536
EST:     AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTCGTAGATAGCTACAACAAGCCGGTACCA
genomic: AGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA
EST: gi|110419762|gb|EC986011.1|EC986011
EST:     GGAAGACATTGCTATCATTTTAATAAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTCGTAGATAGCTACAACAAGCCGGTACCA
genomic: GGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgttt ... tgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATATgtaagtgtttctttcactatgacatttaataattttttttcggcccctttactgttaagcatgcaggtaaaccttaacatgttgatccaccaacacttta

- - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggtaaa