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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatgtagatatatgtttccactgcgtggatgatatttatgctcttccatatatctttttgtatagtgactgattgatgtatttgattacttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG

Basic information

species Glycine max
transcript GLYMA13G01270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G01270.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S78_17V6.1 (Physcomitrella patens), 3'ss of exon 2
taaatgtagatatatgtttccactgcgtggatgatatttatgctcttccatatatctttttgtatagtgactgattgatgtatttg-attac--ttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG
 |||  ||||    | |  |   |   || ||| ||  |    || |||        || |||  | |  ||||| |   |   || |||    | | |||||| ||||| |||||||| || || ||||| || ||||| |||||||||||||| |||||| |||
-aaacttagaggctt-tgacgtgtatatgcatgttacctccattcgtcccagacgtgttgtgtgca-tacctgatcgcaattcctgtattgtggtggttgcagCTATTGGCTTTAATGTGGAGACTGTGCAATACAACAATATTAAATTTCAAGTTTGGGATCTAG
















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|192319248|gb|FK009132.1|FK009132
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|192313159|gb|FK003279.1|FK003279
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|26047527|gb|CA784291.1|CA784291
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|192299620|gb|FG990002.1|FG990002
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|7042626|gb|AW472520.1|AW472520
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|192308422|gb|FK000918.1|FK000918
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|298163498|gb|HO012231.1|HO012231
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTA
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTA
EST: gi|192306665|gb|FG998077.1|FG998077
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|12488647|gb|BG042170.1|BG042170
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|192326406|gb|FK017693.1|FK017693
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|10848119|gb|BF070667.1|BF070667
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|15813778|gb|BI786053.1|BI786053
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|9565450|gb|BE474959.1|BE474959
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|298165965|gb|HO008936.1|HO008936
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|208096947|gb|GD894222.1|GD894222
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCAACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGT
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCA-CCATTCCAAgttcgtactc ... cttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatatatctttttgtatagtgactgattgatgtatttgattacttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG
     tatatctttttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatgtagatatatgtttccactgcgtggatgatatttatgctcttccatatatctttttgtatagtgactgattgatgtatttgattacttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG

- aatgtag
- - - - - - - - - tccactg
- - - - - - - - - - - - - gtggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgta