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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgattagtatttccacttaaaggatgacgttgacagattcaacagcttttgctgaacattcttgtattggtttgcag

Basic information

species Glycine max
transcript GLYMA12G30520.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 26
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 26
GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgattagtatttc-----cacttaaaggatgacgttgacagattcaacagcttttgctgaacattcttgtattggtttgcag
| ||||||||||||||| ||||| ||||||||||| || ||| |||| || |  || || || || || || |||||||||||||  ||   |   ||     |||  |    |   || | |||||||   |  | |||||      |       ||  | | |||
GCAAGAATTGAAACAGACCCAGCGGACAGAACCCAACTACGATTGACAGTAGGCTCGGGAGATCCTACCCTTACATTTGAgtatgatatatctgcctcttaatcacaaacccaacctcgatcacagatttt-cttcatttgcaattgttgaccccttttatctacag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 26
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 5'ss of exon 26
GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgattagtatttccacttaaaggatgacgttgacagattcaacagcttttgctgaacattcttgtattggtttgcag-------------
| |||||| |||||||| ||||| |||||||||||  |||||||||| || |   | || || || || || |||||||||||||  ||   |   ||     | |     |   |   | ||        ||||  |     || ||| ||| |||  |               
GCAAGAATAGAAACAGACCCAGCGGACAGAACCCAATTGCGAATGACAGTAGGCACGGGAGATCCTACCCTTACATTTGAgtatgatatctctgcctcttagcacaaacccaacctcgaacat---gtgtttttttttttttttttttgcatttgttgacctcttttatccacag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 26
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 26
GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtg--attagtatttccacttaaaggatgacgttgac-agattcaacagcttttgctgaacattcttgtattggtttgcag--
 | ||||||||||||||||| ||||||||||| || || || ||||| ||| | ||||||||||| ||||||||||| ||||||||    | |  |||   ||||  |   |   ||   | |||  |      ||| || |||  ||||   |||    |  |   
ATGAGAATTGAAACAGATCCGGCAGACAGAACACAACTACGGATGACAGTTTCCTCAGGGGACCCTACACTAACATTCGAgtatgtattgtcatcattgaaacttttacttttgtgtactctagaaacttgcagtttagcagaatgttctgagattctcataaacag

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|192307606|gb|FG999645.1|FG999645
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
EST: gi|192307607|gb|FG999646.1|FG999646
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
EST: gi|21286017|gb|BQ473888.1|BQ473888
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
EST: gi|10231964|gb|BE800852.1|BE800852
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATT
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATT
EST: gi|151404341|gb|EV274151.1|EV274151
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGG-ACCCAACACTAACATTTGA                         GATGAAG-AGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
EST: gi|151400490|gb|EV270304.1|EV270304
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
EST: gi|51334703|gb|CO978569.1|CO978569
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
EST: gi|298170085|gb|HO018709.1|HO018709
EST:     ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA                         GATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC
genomic: ACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgatt ... tggtttgcagGATGAAGGAGTTCATCAAGGACCAATTAGTCAGCATTCCCGCCATAGCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGAgtatgtgattagtatttccacttaaaggatgacgttgacagattcaacagcttttgctgaacattcttgtattggtttgcag

- - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - AGCTGC