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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaagatatcttattcttattcctggaagatatgagcttgtacttttcttgaattagccatagaatagtatgattatgtaatttgatcatatgatgtcacccagaagtttattatctaaggccatttgtaataactttttatttgggacataactgatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv14s0060g00820.t01 (Vitis vinifera), 5'ss of exon 6
GTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaagatatcttattcttattcctggaagatatgagcttgtacttttcttgaattagccatagaatagtatgattatgtaatttgatcatatgatgtcacccagaagtttattatctaaggccatttgtaataactttttatttgggacataactgatgcag
|||||| ||||| ||||||||||||||||||  |||||| ||| |  | ||||||||||||||| |     |||     |  | | ||  |     ||  ||||||| || || | ||||   | | ||    ||| ||| | || ||      |||   |    |  | ||| ||  | |                                                
GTACATATACTGCTCTTCAGCTGGTGTTTATAAGAAATCCGATCTTCTACCACATTGTGAGgtaagcttgtgat----cacacctgttttt-----atgagagcttggaccttacctgaa---ggctta----agtgtgactttgaaac-----catg-aaccatattcggaatttactcaca----------------------------------------------
















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|125303074|gb|EL317159.1|EL317159
EST:     ATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAAGACTGA
genomic: ATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGA-GACTGA
EST: gi|125199140|gb|EL214094.1|EL214094
EST:     ATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
genomic: ATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
EST: gi|125134448|gb|EL175358.1|EL175358
EST:     CACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
genomic: CACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
EST: gi|125030830|gb|EL103099.1|EL103099
EST:     GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATC
genomic: GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATC
EST: gi|124764116|gb|EH854246.1|EH854246
EST:     CTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGG
genomic: CTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGG
EST: gi|125005135|gb|EL077404.1|EL077404
EST:     CTGGNGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGC
genomic: CTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGC
EST: gi|125029870|gb|EL102139.1|EL102139
EST:     CCACATTGTGAG                         GAGGATGCAGTTGATTCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGA
genomic: CCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGA-TCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGA
EST: gi|124750536|gb|EH840666.1|EH840666
EST:     GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGA
genomic: GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGA
EST: gi|163997201|gb|ES177181.1|ES177181
EST:     GTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
genomic: GTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
EST: gi|125211534|gb|EL226488.1|EL226488
EST:     GATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
genomic: GATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
EST: gi|125309250|gb|EL323335.1|EL323335
EST:     GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGG
genomic: GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGG
EST: gi|125155403|gb|EL185550.1|EL185550
EST:     GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAAGTTGATCCGAAGAGCAGGCACAAGG
genomic: GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCA-GTTGATCCGAAGAGCAGGCACAAGG
EST: gi|124849937|gb|EH934374.1|EH934374
EST:     TTCTTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGC
genomic: TTC-TTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGC
EST: gi|116412031|gb|EG454623.1|EG454623
EST:     GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
genomic: GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAG
EST: gi|124959439|gb|EL034143.1|EL034143
EST:     GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAG                         GAGGATGCAGTTG
genomic: GTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaa ... actgatgcagGAGGATGCAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGgtatgtaaaagatatcttattcttattcctggaagatatgagcttgtacttttcttgaattagccatagaatagtatgattatgtaatttgatcatatgatgtcacccagaagtttattatctaaggccatttgtaataactttttatttgggacataactgatgcag

- - - - - - - - TCAGCT
- - - - - - - -  CAGCTG