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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaatattatagatgcttcaaatttttcataaaataatccaactccaaggtctttgtaattatttttctctattacag

Basic information

species Glycine max
transcript GLYMA04G01470.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 15
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 15
GACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaata-----ttatagatgcttcaaatttttcataaaataatccaactccaaggtctttgtaattatttttctctat-tacag----------------
||| ||||||||  |||||||  |||| ||||| |    ||| ||||||||||| ||||||||||| |||||||| ||||| || ||| || | ||| ||||||  |  |     |||   |   || ||  | ||| |  |   |  || ||   |  ||    | |  |||||| |  || ||                   
GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagcaaacaattaagtacaattaaatatgttcttggaggca--cagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtag

upper sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 15
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 14
GACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaatattatagatgcttcaaatttttcataaaataatccaactccaaggtctttgt--aattatttttctcta---ttacag
 |||||||| || || |||||  |||| || || ||||| || ||||| ||||| |||||||||||||| ||||| ||||||||||| ||||||||    ||| |||| |||   | ||    | |||  |   ||    |||  |        || |  |  ||||| |||    |    ||  ||
AACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCACTAACACAATACCAGAGCAGTTGTTGGAGAGGgtactgaacatt---ggtgtagaatattagtgtcaagcatatcttatctttctttcctcatttaattaatttggcatggggttgtag

upper sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 15
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 15
GACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaatattatagatgcttcaaatttttcataaaataatccaactccaaggtctttgtaattatttttctcta-ttacag----
 ||||||||||| ||||||||  | || ||||||||||||||||||||||||||||||||||||||||| || || || || ||||||||| ||||| |||||||||  | | ||||        | ||    |    | | |  ||||   |   |   |  | | |||||| || ||   |    
AACAGAATATGCTGTTAATGTTGTCAAGCACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACCAATACAATTCCTGAGCAATTGCTGGAAAATgtaatgaccaatttagaacagctgcacttcatgttttctgaccttactc-gggacttccattgtaacttttctatacttgttggcag

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|208313873|gb|GE113055.1|GE113055
EST:     TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGAT                         GTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
genomic: TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaata ... tctattacagGTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
EST: gi|207783747|gb|GD758883.1|GD758883
EST:     TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGAT                         GTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
genomic: TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaata ... tctattacagGTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
EST: gi|10236799|gb|BE805687.1|BE805687
EST:     TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGAT                         GTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
genomic: TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaata ... tctattacagGTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
EST: gi|151393638|gb|EV263513.1|EV263513
EST:     TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGAT                         GTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC
genomic: TGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaata ... tctattacagGTTATTGTGACTGTGGATGCTTCAGATGCAGATGAATTCTCAGAGGTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaatattatagatgcttcaaatttttcataaaataatccaactccaaggtctttgtaattatttttctctattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA