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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcctcgacatacatgtacgtgtatgtttccactgcgtggatggtatttgtgctcttccatatagtgactgattgatttatttgattttttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG

Basic information

species Glycine max
transcript GLYMA17G07390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07390.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S78_17V6.1 (Physcomitrella patens), 3'ss of exon 2
-ttttcctcgacat--acatgtacgtgtatgtttccactgcgtggatggtatttgtgctcttccatatagtgactgattgatttatttgattttttgat-gcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG
    |    | | |  || ||||  || ||||| || |     |      |  |||  | | | |||   |||  |    |||  | |  | |  || | ||||| ||||| |||||||| || || ||||| || ||||| |||||||||||||| |||||| |||
aaacttagaggctttgacgtgtatatgcatgttacctccattcgtcccagacgtgttgtgtgc-atacc-tgatcg--caattcctgtattgtggtggttgcagCTATTGGCTTTAATGTGGAGACTGTGCAATACAACAATATTAAATTTCAAGTTTGGGATCTAG
















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|298164029|gb|HO013674.1|HO013674
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTA
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTA
EST: gi|298181091|gb|HO022530.1|HO022530
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATT
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATT
EST: gi|15813660|gb|BI785935.1|BI785935
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|12689317|gb|BG155653.1|BG155653
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|298186094|gb|HO036727.1|HO036727
EST:     ACCGCCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|120532471|gb|EH260604.1|EH260604
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|193708401|gb|FK645423.1|FK645423
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAG
EST: gi|298194453|gb|HO041101.1|HO041101
EST:     ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAA                         CAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTA
genomic: ATCGGCTTCAGATGGGCGAAGTTGTCTCCACCATTCCAAgttcgtactc ... tttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttgtgctcttccatatagtgactgattgatttatttgattttttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG
                                          tttttt  CT-rich tract
                            attgatttatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcctcgacatacatgtacgtgtatgtttccactgcgtggatggtatttgtgctcttccatatagtgactgattgatttatttgattttttgatgcagCAATTGGGTTTAATGTCGAAACAGTGCAGTATAACAACATTAAATTTCAAGTCTGGGATTTAG

- - - - - - - catgtac
- - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - tccactg
- - - - - - - - - - - - - - - - - - - -tggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg